Table 1

List of the names of 59 test protein families together with their CDD accession names, lengths, number of protein pairs, Pearson correlation coefficients between LHM (AHM) and normalized Blast bitscore. The families are ordered with respect to decreasing quality of LHM correlation. The supplementary table is available at [27].
Family name
 CDD acc
 Length
 #Obs
 AHM
 LHM
Xylose_isom
 pfam00259
 381
 28
 -0.99
 -0.98
MHC_I
 pfam00129
 175
 28
 -0.95
 -0.96
PTPc
 smart00194
 248
 25
 -0.92
 -0.96
IPT
 smart00429
 97
 21
 -0.90
 -0.94
ZnMc_1
 smart00235
 137
 34
 -0.83
 -0.94
RNAse_Pc
 cd00163
 99
 25
 -0.82
 -0.94
gpdh_C
 pfam02800
 153
 39
 -0.72
 -0.93
Aamy_C
 smart00632
 81
 31
 -0.94
 -0.90
peroxidase
 pfam00141
 240
 48
 -0.90
 -0.90
copper-bind
 pfam00127
 81
 87
 -0.84
 -0.89
CBM_20
 pfam00686
 94
 15
 -0.91
 -0.89
RnaseA
 pfam00074
 98
 44
 -0.48
 -0.87
IGv
 cd00099
 105
 133
 -0.78
 -0.86
ADH_zinc_N
 pfam00107
 337
 64
 -0.93
 -0.86
ldh_C
 pfam02866
 143
 29
 -0.93
 -0.86
RIP
 pfam00161
 232
 28
 -0.87
 -0.85
Peptidase_C1
 pfam00112
 200
 55
 -0.82
 -0.85
ZnMc_2
 cd00203
 134
 23
 -0.87
 -0.85
PROF
 cd00148
 120
 15
 -0.90
 -0.85
plant_peroxidase
 cd00314
 236
 76
 -0.90
 -0.83
alpha-amylase_C
 pfam02806
 78
 39
 -0.93
 -0.82
sodcu
 pfam00080
 139
 15
 -0.98
 -0.81
fer2_1
 cd00207
 78
 38
 -0.86
 -0.80
Pept_C1
 smart00645
 202
 90
 -0.86
 -0.79
ferritin
 pfam00210
 152
 19
 -0.94
 -0.79
ldh
 pfam00056
 135
 44
 -0.82
 -0.78
SH2
 pfam00017
 86
 21
 -0.48
 -0.78
flavodoxin
 pfam00258
 143
 26
 -0.88
 -0.78
EFh
 cd00051
 57
 59
 -0.75
 -0.77
rhv_1
 cd00205
 195
 71
 -0.86
 -0.76
LYZ1_1
 smart00263
 116
 67
 -0.66
 -0.75
aldo_ket_red
 pfam00248
 277
 28
 -0.93
 -0.73
COesterase
 pfam00135
 485
 28
 -0.80
 -0.72
TIG
 pfam01833
 89
 39
 -0.90
 -0.72
fer2_2
 pfam00111
 69
 73
 -0.77
 -0.70
beta-lactamase
 pfam00144
 264
 45
 -0.90
 -0.70
rhv_2
 pfam00073
 216
 95
 -0.86
 -0.70
GLECT
 cd00070
 124
 28
 -0.80
 -0.67
globin
 pfam00042
 133
 96
 -0.74
 -0.66
GST_C
 pfam00043
 107
 77
 -0.77
 -0.63
LYZ1_2
 cd00119
 109
 24
 -0.43
 -0.61
PA2c
 smart00085
 102
 210
 -0.29
 -0.57
lipocalin
 pfam00061
 131
 55
 -0.62
 -0.56
phoslip
 pfam00068
 102
 102
 -0.21
 -0.54
proteasome
 pfam00227
 189
 56
 -0.80
 -0.51
UBCc
 smart00212
 141
 45
 -0.79
 -0.50
Sm
 smart00651
 63
 30
 -0.54
 -0.49
Tryp_SPc
 smart00020
 208
 561
 -0.55
 -0.46
CLECT_1
 smart00034
 90
 35
 -0.59
 -0.44
crystall
 pfam00030
 81
 10
 -0.76
 -0.41
CLECT_2
 cd00037
 93
 263
 -0.45
 -0.36
RHO
 smart00174
 173
 10
 -0.52
 -0.36
IGc1
 cd00098
 88
 85
 -0.65
 -0.32
Tryp_SPc
 cd00190
 211
 378
 -0.55
 -0.31
MHC_II_beta
 pfam00969
 86
 32
 -0.52
 -0.26
ADK
 pfam00406
 174
 28
 -0.37
 -0.19
Rho
 cd00157
 172
 66
 -0.20
 -0.16
Phycobilisome
 pfam00502
 148
 15
 -0.85
 -0.10
ADF
 smart00102
 116
 10
 -0.85
 0.34

Panchenko and Madej BMC Evolutionary Biology 2005 5:10   doi:10.1186/1471-2148-5-10