RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8912
(538 letters)
>gnl|CDD|221713 pfam12689, Acid_PPase, Acid Phosphatase. This family contains
phosphatase enzymes and other proteins of the HAD
superfamily. It includes MDP-1 which is a eukaryotic
magnesium-dependent acid phosphatase.
Length = 164
Score = 183 bits (468), Expect = 1e-55
Identities = 67/143 (46%), Positives = 86/143 (60%), Gaps = 8/143 (5%)
Query: 15 FPKMVVFDLDYTLWPLHVHDLV-APFKKIGQ-KVMDAKGTLIKYYRGVPEILRYLKENKC 72
PK++VFDLDYTLWP V PFKK V+D +G + Y VP IL+ LKE
Sbjct: 2 LPKLIVFDLDYTLWPFWCDTHVGPPFKKDKNGTVVDRRGEELSLYPDVPSILQELKEKGI 61
Query: 73 LVAAASRTSEILHAKQILNLINLN------QYFSNKEIYPGQKTTHFESLKKATGIEYKD 126
+A ASRT A+++L L+++N YF EIYPG KTTHF+ + K +G+ Y D
Sbjct: 62 TIAVASRTDAPDWARELLKLLHINDGPPAIDYFDYLEIYPGSKTTHFKKIHKKSGVPYSD 121
Query: 127 MVFFDDEERNSHDVSPLGVTCIH 149
M+FFDDE RN VS LGVT +
Sbjct: 122 MLFFDDESRNIDVVSRLGVTFVL 144
Score = 157 bits (400), Expect = 1e-45
Identities = 55/132 (41%), Positives = 78/132 (59%), Gaps = 6/132 (4%)
Query: 412 DKVLDAGGAIIKYYRDVPAILKYLKQNNCLVAAASRTTEMLRAHQLVDLFNWN------Q 465
V+D G + Y DVP+IL+ LK+ +A ASRT A +L+ L + N
Sbjct: 33 GTVVDRRGEELSLYPDVPSILQELKEKGITIAVASRTDAPDWARELLKLLHINDGPPAID 92
Query: 466 HFDHKEIFPGQKTTHFANLKKATGIEYKDMVFFDDEERNSHDVSPLGVTCIHVKDGMSHS 525
+FD+ EI+PG KTTHF + K +G+ Y DM+FFDDE RN VS LGVT + V DG++
Sbjct: 93 YFDYLEIYPGSKTTHFKKIHKKSGVPYSDMLFFDDESRNIDVVSRLGVTFVLVPDGLTRE 152
Query: 526 VLHKGLKQWASK 537
+GL++W +
Sbjct: 153 EFERGLRKWRKR 164
Score = 124 bits (314), Expect = 2e-33
Identities = 51/119 (42%), Positives = 67/119 (56%), Gaps = 7/119 (5%)
Query: 297 KHLKKDRVEDAKGTLLNLYRDIPEIVKYLKDHNIKLALASRTVHIRNAYSLLHLL----- 351
K K V D +G L+LY D+P I++ LK+ I +A+ASRT A LL LL
Sbjct: 28 KKDKNGTVVDRRGEELSLYPDVPSILQELKEKGITIAVASRTDAPDWARELLKLLHINDG 87
Query: 352 -GLSDFFDYKEIFPAEKKIKHFANLKKDSKIKYKDMVFFDDEERNARSISKLGVIGIQV 409
D+FDY EI+P K HF + K S + Y DM+FFDDE RN +S+LGV + V
Sbjct: 88 PPAIDYFDYLEIYPG-SKTTHFKKIHKKSGVPYSDMLFFDDESRNIDVVSRLGVTFVLV 145
Score = 68.8 bits (169), Expect = 1e-13
Identities = 28/76 (36%), Positives = 40/76 (52%), Gaps = 6/76 (7%)
Query: 232 VLDSNGMVIKYYQDVPRILEYLREHNILVAAVSTTVRILHVQNILEMIGV------ARYF 285
V+D G + Y DVP IL+ L+E I +A S T + +L+++ + YF
Sbjct: 35 VVDRRGEELSLYPDVPSILQELKEKGITIAVASRTDAPDWARELLKLLHINDGPPAIDYF 94
Query: 286 DHKEIYPRQKTKHLKK 301
D+ EIYP KT H KK
Sbjct: 95 DYLEIYPGSKTTHFKK 110
Score = 54.1 bits (131), Expect = 1e-08
Identities = 23/66 (34%), Positives = 31/66 (46%), Gaps = 15/66 (22%)
Query: 172 YFDDEQ-------EHVNDISKLGVTATRKDSKIKYKDMVFFDDEERNARSISKLGVIGIQ 224
YFD + H K+ K S + Y DM+FFDDE RN +S+LGV +
Sbjct: 93 YFDYLEIYPGSKTTH---FKKI-----HKKSGVPYSDMLFFDDESRNIDVVSRLGVTFVL 144
Query: 225 VMHSMT 230
V +T
Sbjct: 145 VPDGLT 150
>gnl|CDD|233529 TIGR01685, MDP-1, magnesium-dependent phosphatase-1. This model
represents two closely related clades of sequences from
eukaryotes and archaea. The mouse enzyme has been
characterized as a phosphatase and has been positively
identified as a member of the haloacid dehalogenase
(HAD) superfamily by site-directed mutagenesis of the
active site residues.
Length = 174
Score = 70.6 bits (173), Expect = 3e-14
Identities = 41/159 (25%), Positives = 69/159 (43%), Gaps = 22/159 (13%)
Query: 15 FPKMVVFDLDYTLWPLH-VHDLVAPFKKIGQK---VMDAKGTLIKYYRGVPEILRYLKEN 70
P+++VFDLD TLW + + L PFK + Q ++D GT + + V ++L+ LK+
Sbjct: 1 LPRVIVFDLDGTLWDHYMISLLGGPFKPVKQNNSIIIDKSGTEVTLIKEVRDVLQTLKDA 60
Query: 71 KCLVAAASRTSEILHAKQILNL---------INLNQYFSNKEI--YPGQKTTHFESLKK- 118
+A AS A +IL + ++ F ++ P + L+K
Sbjct: 61 GTYLATASWNDVPEWAYEILGTFEITYAGKTVPMHSLFDDRIEIYKPNKAKQLEMILQKV 120
Query: 119 -ATG---IEYKDMVFFDDEERNSHDVSPLGVT--CIHSW 151
++ ++FFDD N +V GVT S
Sbjct: 121 NKVDPSVLKPAQILFFDDRTDNVREVWGYGVTSCYCPSG 159
Score = 67.9 bits (166), Expect = 2e-13
Identities = 28/119 (23%), Positives = 46/119 (38%), Gaps = 15/119 (12%)
Query: 301 KDRVEDAKGTLLNLYRDIPEIVKYLKDHNIKLALASRTVHIRNAYSLLHLL--------- 351
+ D GT + L +++ ++++ LKD LA AS AY +L
Sbjct: 33 NSIIIDKSGTEVTLIKEVRDVLQTLKDAGTYLATASWNDVPEWAYEILGTFEITYAGKTV 92
Query: 352 GLSDFFDYKEIFPAEKKIKHFANLKKD------SKIKYKDMVFFDDEERNARSISKLGV 404
+ FD + K K + + S +K ++FFDD N R + GV
Sbjct: 93 PMHSLFDDRIEIYKPNKAKQLEMILQKVNKVDPSVLKPAQILFFDDRTDNVREVWGYGV 151
Score = 50.6 bits (121), Expect = 3e-07
Identities = 29/139 (20%), Positives = 52/139 (37%), Gaps = 16/139 (11%)
Query: 414 VLDAGGAIIKYYRDVPAILKYLKQNNCLVAAASRTTEMLRAHQLVDLFN---------WN 464
++D G + ++V +L+ LK +A AS A++++ F +
Sbjct: 36 IIDKSGTEVTLIKEVRDVLQTLKDAGTYLATASWNDVPEWAYEILGTFEITYAGKTVPMH 95
Query: 465 QHFDHKEIFP-GQKTTHFANL------KKATGIEYKDMVFFDDEERNSHDVSPLGVTCIH 517
FD + K + + ++ ++FFDD N +V GVT +
Sbjct: 96 SLFDDRIEIYKPNKAKQLEMILQKVNKVDPSVLKPAQILFFDDRTDNVREVWGYGVTSCY 155
Query: 518 VKDGMSHSVLHKGLKQWAS 536
GM K L+ W S
Sbjct: 156 CPSGMDKGTFKKILEMWRS 174
Score = 33.7 bits (77), Expect = 0.12
Identities = 10/26 (38%), Positives = 14/26 (53%)
Query: 195 SKIKYKDMVFFDDEERNARSISKLGV 220
S +K ++FFDD N R + GV
Sbjct: 126 SVLKPAQILFFDDRTDNVREVWGYGV 151
Score = 28.3 bits (63), Expect = 7.8
Identities = 12/78 (15%), Positives = 30/78 (38%), Gaps = 10/78 (12%)
Query: 232 VLDSNGMVIKYYQDVPRILEYLREHNILVAAVSTT---------VRILHVQNILEMIGVA 282
++D +G + ++V +L+ L++ +A S + + + + +
Sbjct: 36 IIDKSGTEVTLIKEVRDVLQTLKDAGTYLATASWNDVPEWAYEILGTFEITYAGKTVPMH 95
Query: 283 RYFDHKEIYPR-QKTKHL 299
FD + + K K L
Sbjct: 96 SLFDDRIEIYKPNKAKQL 113
>gnl|CDD|233526 TIGR01681, HAD-SF-IIIC, HAD-superfamily phosphatase, subfamily
IIIC. This model represents the IIIC subfamily of the
Haloacid Dehalogenase (HAD) superfamily of aspartate
nucleophile hydrolases. Subfamily III (also including
IIIA - TIGR01662 and IIIB - pfam03767) contains
sequences which do not contain either of the insert
domains (between the 1st and 2nd conserved catalytic
motifs, subfamily I - TIGR01493, TIGR01509, TIGR01549,
TIGR01488, TIGR01494, TIGR01658, TIGR01544 and
TIGR01545, or between the 2nd and 3rd, subfamily II -
TIGR01460 and TIGR01484). Subfamily IIIC contains five
relatively distantly related clades: a family of viral
proteins (TIGR01684), a family of eukaryotic proteins
called MDP-1 and a family of archaeal proteins most
closely related to MDP-1 (TIGR01685), a family of
bacteria including the Streptomyces FkbH protein
(TIGR01686), and a small clade including the Pasteurella
BcbF and EcbF proteins. The overall lack of species
overlap among these clades may indicate a conserved
function, but the degree of divergence between the
clades and the differences in archetecture outside of
the domain in some clades warns against such a
conclusion. No member of this subfamily is characterized
with respect to function, however the MDP-1 protein is a
characterized phosphatase. All of the characterized
enzymes within subfamily III are phosphatases, and all
of the active site residues characteristic of
HAD-superfamily phosphatases are present in subfamily
IIIC.
Length = 128
Score = 49.3 bits (118), Expect = 3e-07
Identities = 36/135 (26%), Positives = 58/135 (42%), Gaps = 20/135 (14%)
Query: 17 KMVVFDLDYTLWPLHVHDLVAPFKKIGQKVMDAKGTLIKYYRGVPEILRYLKENKCLVAA 76
K++VFDLD TLW +G+ + IK + + L+ LK+N L+A
Sbjct: 1 KVIVFDLDNTLWTGE-------NIVVGEDPIIDLEVTIKE---IRDKLQTLKKNGFLLAL 50
Query: 77 ASRTS------EILHAKQILNLIN-LNQYFSNKEI--YPGQKTTHFESLKKATG-IEYKD 126
AS E+L + +I L +YF I + + E K G ++ K
Sbjct: 51 ASYNDDPHVAYELLKIFEDFGIIFPLAEYFDPLTIGYWLPKSPRLVEIALKLNGVLKPKS 110
Query: 127 MVFFDDEERNSHDVS 141
++F DD N+ +V
Sbjct: 111 ILFVDDRPDNNEEVD 125
Score = 47.0 bits (112), Expect = 1e-06
Identities = 28/108 (25%), Positives = 43/108 (39%), Gaps = 9/108 (8%)
Query: 305 EDAKGTLLNLYRDIPEIVKYLKDHNIKLALASRTVHIRNAYSLL-------HLLGLSDFF 357
ED L ++I + ++ LK + LALAS AY LL + L+++F
Sbjct: 21 EDPIIDLEVTIKEIRDKLQTLKKNGFLLALASYNDDPHVAYELLKIFEDFGIIFPLAEYF 80
Query: 358 DYKEIFPAEKKIKHFAN--LKKDSKIKYKDMVFFDDEERNARSISKLG 403
D I K LK + +K K ++F DD N +
Sbjct: 81 DPLTIGYWLPKSPRLVEIALKLNGVLKPKSILFVDDRPDNNEEVDYYL 128
Score = 34.7 bits (80), Expect = 0.029
Identities = 23/104 (22%), Positives = 43/104 (41%), Gaps = 10/104 (9%)
Query: 416 DAGGAIIKYYRDVPAILKYLKQNNCLVAAASRTT------EMLRAHQLVDLFNW-NQHFD 468
D + +++ L+ LK+N L+A AS E+L+ + + ++FD
Sbjct: 22 DPIIDLEVTIKEIRDKLQTLKKNGFLLALASYNDDPHVAYELLKIFEDFGIIFPLAEYFD 81
Query: 469 HKEIFP-GQKTTHFAN--LKKATGIEYKDMVFFDDEERNSHDVS 509
I K+ LK ++ K ++F DD N+ +V
Sbjct: 82 PLTIGYWLPKSPRLVEIALKLNGVLKPKSILFVDDRPDNNEEVD 125
>gnl|CDD|227329 COG4996, COG4996, Predicted phosphatase [General function
prediction only].
Length = 164
Score = 46.4 bits (110), Expect = 5e-06
Identities = 33/125 (26%), Positives = 57/125 (45%), Gaps = 14/125 (11%)
Query: 285 FDHKEIY----PRQKTKHLKKDRVEDAKGTLLNLYRDIPEIVKYLKDHNIKLALASRTVH 340
+DH I P ++ +ED+KG ++L+ D+ E +K+ ++ L LAS
Sbjct: 12 WDHHNISSLEPPFRRVSSNT---IEDSKGREVHLFPDVKETLKWARNSGYILGLASWNFE 68
Query: 341 IRNAYSLLHLLGLSDFFDYKEIFPAEKKIKHFA------NLKKDSKIKYKDMVFFDDEER 394
+ A L L L +F Y I P K + N +++ KIK ++V+ DD
Sbjct: 69 DK-AIKALRALDLLQYFHYIVIEPHPYKFLMLSQLLREINTERNQKIKPSEIVYLDDRRI 127
Query: 395 NARSI 399
+ +I
Sbjct: 128 HFGNI 132
Score = 42.9 bits (101), Expect = 8e-05
Identities = 37/146 (25%), Positives = 66/146 (45%), Gaps = 12/146 (8%)
Query: 17 KMVVFDLDYTLWPLH-VHDLVAPFKKIGQ-KVMDAKGTLIKYYRGVPEILRYLKENKCLV 74
+ +VFD D TLW H + L PF+++ + D+KG + + V E L++ + + ++
Sbjct: 1 RAIVFDADKTLWDHHNISSLEPPFRRVSSNTIEDSKGREVHLFPDVKETLKWARNSGYIL 60
Query: 75 AAASRTSEILHAKQILNLINLNQYFSNKEIYPGQK-----TTHFESLKKATGIEYK--DM 127
AS E A + L ++L QYF I P + + + K ++
Sbjct: 61 GLASWNFE-DKAIKALRALDLLQYFHYIVIEPHPYKFLMLSQLLREINTERNQKIKPSEI 119
Query: 128 VFFDDEERNSHDV-SPLG-VTCIHSW 151
V+ DD + ++ LG V C+ W
Sbjct: 120 VYLDDRRIHFGNIWEYLGNVKCLEMW 145
>gnl|CDD|216069 pfam00702, Hydrolase, haloacid dehalogenase-like hydrolase. This
family is structurally different from the alpha/beta
hydrolase family (pfam00561). This family includes
L-2-haloacid dehalogenase, epoxide hydrolases and
phosphatases. The structure of the family consists of
two domains. One is an inserted four helix bundle, which
is the least well conserved region of the alignment,
between residues 16 and 96 of Pseudomonas sp.
(S)-2-haloacid dehalogenase 1. The rest of the fold is
composed of the core alpha/beta domain. Those members
with the characteristic DxD triad at the N-terminus are
probably phosphatidylglycerolphosphate (PGP)
phosphatases involved in cardiolipin biosynthesis in the
mitochondria.
Length = 187
Score = 46.1 bits (109), Expect = 8e-06
Identities = 29/181 (16%), Positives = 60/181 (33%), Gaps = 7/181 (3%)
Query: 229 MTNVLDSNGMVIKYYQDVPRILEYLREHNILVAAVSTTVRILH--VQNILEMIGVARYFD 286
+ L V+ + + L ++ A + T V+ +L
Sbjct: 8 LDGTLTDGEPVVPEAEALLEAAAALGVAIVIAAGENLTKEGREELVRRLLLRALAGEELL 67
Query: 287 HKEIYPRQKTKHLKKDRVEDAKGTLLNLYRDIPEIVKYLKDHNIKLALASRTVHIRNAYS 346
+ + + V LY E +K LK+ IKLA+ + + A +
Sbjct: 68 EELLRAGATVVAVLDLVVLGLIALTDPLYPGAREALKELKEAGIKLAILTGD-NRLTANA 126
Query: 347 LLHLLGLSDFFDYKEIFPAEKKIKH----FANLKKDSKIKYKDMVFFDDEERNARSISKL 402
+ LLGL D +++ K F ++ +K ++++ D + +
Sbjct: 127 IARLLGLFDALVSADLYGLVGVGKPDPKIFELALEELGVKPEEVLMVGDGVNDIPAAKAA 186
Query: 403 G 403
G
Sbjct: 187 G 187
>gnl|CDD|223943 COG1011, COG1011, Predicted hydrolase (HAD superfamily) [General
function prediction only].
Length = 229
Score = 43.4 bits (102), Expect = 1e-04
Identities = 34/183 (18%), Positives = 63/183 (34%), Gaps = 15/183 (8%)
Query: 267 VRILHVQNILEMIGVARYFDHKEIYPRQKTKHLKKD--RVEDAKGTLLNLYRDIPEIVKY 324
+ L + + + + + +D VE+ L L D PE ++
Sbjct: 48 IEKLEARFLRGEYTGEYGLTLERLLELLERLLGDEDAELVEELLAALAKLLPDYPEALEA 107
Query: 325 LKD--HNIKLALASRTVHIRNAYSLLHLLGLSDFFDYKEIFPAEKKIK----HFANLKKD 378
LK+ KL + + + L LGL D+FD I K F +
Sbjct: 108 LKELGKKYKLGILTNGAR-PHQERKLRQLGLLDYFDAVFISEDVGVAKPDPEIFEYALEK 166
Query: 379 SKIKYKDMVFFDDEERN-ARSISKLGVIGIQVHR-----DKVLDAGGAIIKYYRDVPAIL 432
+ ++ +F D N LG+ + ++R L+A I ++ +L
Sbjct: 167 LGVPPEEALFVGDSLENDILGARALGMKTVWINRGGKPLPDALEAPDYEISSLAELLDLL 226
Query: 433 KYL 435
+ L
Sbjct: 227 ERL 229
>gnl|CDD|222115 pfam13419, HAD_2, Haloacid dehalogenase-like hydrolase.
Length = 176
Score = 39.6 bits (93), Expect = 0.001
Identities = 28/135 (20%), Positives = 55/135 (40%), Gaps = 13/135 (9%)
Query: 281 VARYFDHKEIYPRQKTKHLKKDRVEDAKGTLLNLYRDIPEIVKYLKDHNIKLALASRTVH 340
+A I P + + L + +E L + D+ E+++ LK +KL + S
Sbjct: 49 LADLLREHPIDPDEILEALLEYNLESR----LEPFPDVVELLRRLKAKGVKLVILS-NGS 103
Query: 341 IRNAYSLLHLLGLSDFFDYKEIFPAE--KKIKH----FANLKKDSKIKYKDMVFFDDEER 394
LL LGL D FD +F ++ K + + + + ++++F DD
Sbjct: 104 REAVERLLEKLGLLDLFD--AVFTSDDVGARKPDPEAYERVLERLGLPPEEILFIDDSPE 161
Query: 395 NARSISKLGVIGIQV 409
+ + G+ + V
Sbjct: 162 DLEAARAAGIKTVHV 176
Score = 29.2 bits (66), Expect = 4.1
Identities = 11/45 (24%), Positives = 21/45 (46%), Gaps = 1/45 (2%)
Query: 243 YQDVPRILEYLREHNILVAAVSTTVRILHVQNILEMIGVARYFDH 287
+ DV +L L+ + + +S V+ +LE +G+ FD
Sbjct: 79 FPDVVELLRRLKAKGVKLVILS-NGSREAVERLLEKLGLLDLFDA 122
>gnl|CDD|233443 TIGR01509, HAD-SF-IA-v3, haloacid dehalogenase superfamily,
subfamily IA, variant 3 with third motif having DD or
ED. This model represents part of one structural
subfamily of the Haloacid Dehalogenase (HAD) superfamily
of aspartate-nucleophile hydrolases. The superfamily is
defined by the presence of three short catalytic motifs.
The subfamilies are defined based on the location and
the observed or predicted fold of a so-called "capping
domain", or the absence of such a domain. Subfamily I
consists of sequences in which the capping domain is
found in between the first and second catalytic motifs.
Subfamily II consists of sequences in which the capping
domain is found between the second and third motifs.
Subfamily III sequences have no capping domain in either
of these positions.The Subfamily IA and IB capping
domains are predicted by PSI-PRED to consist of an alpha
helical bundle. Subfamily I encompasses such a wide
region of sequence space (the sequences are highly
divergent) that representing it with a single model is
impossible, resulting in an overly broad description
which allows in many unrelated sequences. Subfamily IA
and IB are separated based on an aparrent phylogenetic
bifurcation. Subfamily IA is still too broad to model,
but cannot be further subdivided into large chunks based
on phylogenetic trees. Of the three motifs defining the
HAD superfamily, the third has three variant forms : (1)
hhhhsDxxx(x)D, (2) hhhhssxxx(x)D and (3) hhhhDDxxx(x)s
where _s_ refers to a small amino acid and _h_ to a
hydrophobic one. All three of these variants are found
in subfamily IA. Individual models were made based on
seeds exhibiting only one of the variants each. Variant
3 (this model) is found in the enzymes
beta-phosphoglucomutase (TIGR01990) and
deoxyglucose-6-phosphatase, while many other enzymes of
subfamily IA exhibit this variant as well as variant 1
(TIGR01549). These three variant models were created
withthe knowledge that there will be overlap among them
- this is by design and serves the purpose of
eliminating the overlap with models of more distantly
relatedHAD subfamilies caused by an overly broad single
model [Unknown function, Enzymes of unknown
specificity].
Length = 177
Score = 39.7 bits (93), Expect = 0.001
Identities = 29/155 (18%), Positives = 48/155 (30%), Gaps = 13/155 (8%)
Query: 264 STTVRILHVQNILEMIGVARYFDHKEIYPRQKTK----HLKKDRVEDAK-GTLLNLYRDI 318
L V + + R + K Y R + L K +A L +
Sbjct: 27 PLVPDELGVSEVGSLELALRRW--KAKYGRTMSAEDAQLLYKQLFYEALEKEGLKPLPGV 84
Query: 319 PEIVKYLKDHNIKLALASRTVHIRNAYSLLHLLGLSDFFDYKEIFPAEKKIK----HFAN 374
+++ L+ KLAL + + L LGL FD K +
Sbjct: 85 RALLEALRARGKKLALLTNSPRADAKLVLE--LGLRALFDVVIDSSDVGLGKPDPDIYLQ 142
Query: 375 LKKDSKIKYKDMVFFDDEERNARSISKLGVIGIQV 409
K +K + +F DD + G+ + V
Sbjct: 143 ALKKLGLKPSECLFVDDSPAGIDAAKAAGMHTVLV 177
Score = 30.8 bits (70), Expect = 0.92
Identities = 17/92 (18%), Positives = 30/92 (32%), Gaps = 11/92 (11%)
Query: 420 AIIKYYRDVPAILKYLKQNNCLVAAASRTTEMLRAHQLVDLFN-WNQHFDHKEIFPGQKT 478
+K V A+L+ L+ +A + + RA + L FD I
Sbjct: 76 EGLKPLPGVRALLEALRARGKKLALLTNS---PRADAKLVLELGLRALFDV-VIDSSDVG 131
Query: 479 TH------FANLKKATGIEYKDMVFFDDEERN 504
+ K G++ + +F DD
Sbjct: 132 LGKPDPDIYLQALKKLGLKPSECLFVDDSPAG 163
>gnl|CDD|213672 TIGR01990, bPGM, beta-phosphoglucomutase. This model represents
the beta-phosphoglucomutase enzyme which catalyzes the
interconverison of beta-D-glucose-1-phosphate and
beta-D-glucose-6-phosphate. The 6-phosphate is capable
of non-enzymatic anomerization (alpha <-> beta) while
the 1-phosphate is not. A separate enzyme is responsible
for the isomerization of the alpha anomers.
Beta-D-glucose-1-phosphate results from the
phosphorylysis of maltose (2.4.1.8), trehalose
(2.4.1.64) or trehalose-6-phosphate (2.4.1.216).
Alternatively, these reactions can be run in the
synthetic direction to create the disaccharides. All
sequenced genomes which contain a member of this family
also appear to contain at least one putative maltose or
trehalose phosphorylase. Three species, Lactococcus,
Enterococcus and Neisseria appear to contain a pair of
paralogous beta-PGM's. Beta-phosphoglucomutase is a
member of the haloacid dehalogenase superfamily of
hydrolase enzymes. These enzymes are characterized by a
series of three catalytic motifs positioned within an
alpha-beta (Rossman) fold. beta-PGM contains an inserted
alpha helical domain in between the first and second
conserved motifs and thus is a member of subfamily IA of
the superfamily. The third catalytic motif comes in
three variants, the third of which, containing a
conserved DD or ED, is the only one found here as well
as in several other related enzymes (TIGR01509). The
enzyme from L. lactis has been extensively characterized
including a remarkable crystal structure which traps the
pentacoordinate transition state [Energy metabolism,
Biosynthesis and degradation of polysaccharides].
Length = 185
Score = 34.6 bits (80), Expect = 0.057
Identities = 18/42 (42%), Positives = 27/42 (64%), Gaps = 3/42 (7%)
Query: 318 IPEIVKYLKDHNIKLALASRTVHIRNAYSLLHLLGLSDFFDY 359
I ++ LK +NIK+ALAS + +NA ++L L L D+FD
Sbjct: 92 IKSLLADLKKNNIKIALASAS---KNAPTILEKLELIDYFDA 130
>gnl|CDD|119389 cd01427, HAD_like, Haloacid dehalogenase-like hydrolases. The
haloacid dehalogenase-like (HAD) superfamily includes
L-2-haloacid dehalogenase, epoxide hydrolase,
phosphoserine phosphatase, phosphomannomutase,
phosphoglycolate phosphatase, P-type ATPase, and many
others, all of which use a nucleophilic aspartate in
their phosphoryl transfer reaction. All members possess
a highly conserved alpha/beta core domain, and many also
possess a small cap domain, the fold and function of
which is variable. Members of this superfamily are
sometimes referred to as belonging to the DDDD
superfamily of phosphohydrolases.
Length = 139
Score = 33.5 bits (77), Expect = 0.098
Identities = 33/137 (24%), Positives = 48/137 (35%), Gaps = 41/137 (29%)
Query: 309 GTLLN------------LYRDIPEIVKYLKDHNIKLALAS----RTVHIRNAYSLLHLLG 352
GTLL+ LY + E +K LK+ IKLALA+ R V LL LG
Sbjct: 8 GTLLDSEPGIAEIEELELYPGVKEALKELKEKGIKLALATNKSRREVL-----ELLEELG 62
Query: 353 LSDFFDY-------KEIFPAEKKIKH-------------FANLKKDSKIKYKDMVFFDDE 392
L D+FD +P E K + ++++ D
Sbjct: 63 LDDYFDPVITSNGAAIYYPKEGLFLGGGPFDIGKPNPDKLLAALKLLGVDPEEVLMVGDS 122
Query: 393 ERNARSISKLGVIGIQV 409
+ G +G+ V
Sbjct: 123 LNDIEMAKAAGGLGVAV 139
Score = 32.3 bits (74), Expect = 0.22
Identities = 21/82 (25%), Positives = 35/82 (42%), Gaps = 17/82 (20%)
Query: 19 VVFDLDYTLWPLHVHDLVAPFKKIGQKVMDAKGTLIKYYRGVPEILRYLKENKCLVAAAS 78
V+FDLD TL + + ++ Y GV E L+ LKE +A A+
Sbjct: 2 VLFDLDGTLL-DSEPGIAEIEE-------------LELYPGVKEALKELKEKGIKLALAT 47
Query: 79 -RTSEILHAKQILNLINLNQYF 99
++ + +L + L+ YF
Sbjct: 48 NKSRREVLE--LLEELGLDDYF 67
>gnl|CDD|223710 COG0637, COG0637, Predicted phosphatase/phosphohexomutase [General
function prediction only].
Length = 221
Score = 34.3 bits (79), Expect = 0.10
Identities = 31/112 (27%), Positives = 50/112 (44%), Gaps = 5/112 (4%)
Query: 249 ILEYLREHNILVAAVSTTVRILHVQNILEMIGVARYFDHKE-IYPRQKTKHLKKDRVEDA 307
LE L+E+ I ++ +R LH I +I + R E + + L +
Sbjct: 24 WLEALKEYGIEISD--EEIRELHGGGIARIIDLLRKLAAGEDPADLAELERLLYEAEALE 81
Query: 308 KGTLLNLYRDIPEIVKYLKDHNIKLALASRTVHIRNAYSLLHLLGLSDFFDY 359
L + + E+++ LK I LA+AS + R A +L LGL D+FD
Sbjct: 82 LEGLKPIP-GVVELLEQLKARGIPLAVASSS-PRRAAERVLARLGLLDYFDV 131
Score = 30.5 bits (69), Expect = 1.7
Identities = 14/48 (29%), Positives = 24/48 (50%), Gaps = 1/48 (2%)
Query: 240 IKYYQDVPRILEYLREHNILVAAVSTTVRILHVQNILEMIGVARYFDH 287
+K V +LE L+ I +A S++ R + +L +G+ YFD
Sbjct: 85 LKPIPGVVELLEQLKARGIPLAVASSSPR-RAAERVLARLGLLDYFDV 131
>gnl|CDD|181872 PRK09456, PRK09456, ?-D-glucose-1-phosphatase; Provisional.
Length = 199
Score = 32.3 bits (74), Expect = 0.38
Identities = 15/34 (44%), Positives = 17/34 (50%)
Query: 487 ATGIEYKDMVFFDDEERNSHDVSPLGVTCIHVKD 520
A G D VFFDD N + LG+T I V D
Sbjct: 153 AEGFSAADAVFFDDNADNIEAANALGITSILVTD 186
Score = 29.2 bits (66), Expect = 4.4
Identities = 11/31 (35%), Positives = 16/31 (51%)
Query: 385 DMVFFDDEERNARSISKLGVIGIQVHRDKVL 415
D VFFDD N + + LG+ I V + +
Sbjct: 160 DAVFFDDNADNIEAANALGITSILVTDKQTI 190
>gnl|CDD|200170 TIGR02252, DREG-2, REG-2-like, HAD superfamily (subfamily IA)
hydrolase. This family of proteins includes
uncharacterized sequences from eukaryotes, cyanobacteria
and Leptospira as well as the DREG-2 protein from
Drosophila melanogaster which has been identified as a
rhythmically (diurnally) regulated gene. This family is
a member of the Haloacid Dehalogenase (HAD) superfamily
of aspartate-nucleophile hydrolases. The superfamily is
defined by the presence of three short catalytic motifs.
The subfamilies are defined based on the location and
the observed or predicted fold of a so-called 'capping
domain', or the absence of such a domain. This family is
a member of subfamily 1A in which the cap domain
consists of a predicted alpha helical bundle found in
between the first and second catalytic motifs. A
distinctive feature of this family is a conserved tandem
pair of tryptophan residues in the cap domain. The most
divergent sequences included within the scope of this
model are from plants and have "FW" at this position
instead. Most likely, these sequences, like the vast
majority of HAD sequences, represent phosphatase
enzymes.
Length = 203
Score = 31.5 bits (72), Expect = 0.72
Identities = 14/45 (31%), Positives = 25/45 (55%), Gaps = 2/45 (4%)
Query: 243 YQDVPRILEYLREHNILVAAVSTTVRILHVQNILEMIGVARYFDH 287
Y D ++L+ LRE +++ +S L + +LE +G+ YFD
Sbjct: 107 YPDAIKLLKDLRERGLILGVISNFDSRL--RGLLEALGLLEYFDF 149
Score = 29.6 bits (67), Expect = 3.5
Identities = 13/45 (28%), Positives = 23/45 (51%), Gaps = 2/45 (4%)
Query: 314 LYRDIPEIVKYLKDHNIKLALASRTVHIRNAYSLLHLLGLSDFFD 358
+Y D +++K L++ + L + S LL LGL ++FD
Sbjct: 106 VYPDAIKLLKDLRERGLILGVISNFDSR--LRGLLEALGLLEYFD 148
>gnl|CDD|130521 TIGR01454, AHBA_synth_RP, 3-amino-5-hydroxybenoic acid synthesis
related protein. The enzymes in this equivalog are all
located in the operons for the biosynthesis of
3-amino-5-hydroxybenoic acid (AHBA), which is a
precursor of several antibiotics including ansatrienin ,
naphthomycin , rifamycin and mitomycin. The role that
this enzyme plays in this biosynthesis has not been
elucidated. This enzyme is a member of the Haloacid
dehalogenase superfamily (pfam00702) of
aspartate-nucleophile hydrolases. This enzyme is closely
related to phosphoglycolate phosphatase (TIGR01449), but
it is unclear what purpose a PGPase or PGPase-like
activity would serve in these biosyntheses. This model
is limited to the Gram positive Actinobacteria. The most
closely related enzyme below the noise cutoff is IndB
which is involved in the biosynthesis of Indigoidine in
Pectobacterium (Erwinia) chrysanthemi, a gamma
proteobacter. This enzyme is similarly related to PGP.
In this case, too it is unclear what role would be be
played by a PGPase activity.
Length = 205
Score = 31.4 bits (71), Expect = 0.81
Identities = 18/68 (26%), Positives = 30/68 (44%), Gaps = 9/68 (13%)
Query: 292 PRQKTKHLKKDRVEDAKGTLLNLYRDIPEIVKYLKDHNIKLALASRTVHIRNAYSLLHLL 351
P + + VE ++ +PE++ L+ + A+A+ R A SLL L
Sbjct: 62 PFVRESYRLAGEVE--------VFPGVPELLAELRADGVGTAIATGKSGPR-ARSLLEAL 112
Query: 352 GLSDFFDY 359
GL FD+
Sbjct: 113 GLLPLFDH 120
Score = 29.1 bits (65), Expect = 4.6
Identities = 13/48 (27%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 240 IKYYQDVPRILEYLREHNILVAAVSTTVRILHVQNILEMIGVARYFDH 287
++ + VP +L LR + A++T +++LE +G+ FDH
Sbjct: 74 VEVFPGVPELLAELRADG-VGTAIATGKSGPRARSLLEALGLLPLFDH 120
>gnl|CDD|237905 PRK15083, PRK15083, PTS system mannitol-specific transporter
subunit IICBA; Provisional.
Length = 639
Score = 31.9 bits (73), Expect = 0.94
Identities = 26/82 (31%), Positives = 38/82 (46%), Gaps = 21/82 (25%)
Query: 189 TATRKDSKIK-------YKDMVFFDDEERNARSISKLGVIGI--------QVMHSMTNVL 233
T KD +K Y + V F +EE I++L VIGI QV+ S+TN L
Sbjct: 557 TVEAKDRVLKTGVVFCQYPEGVRFGEEED---DIARL-VIGIAARNNEHIQVITSLTNAL 612
Query: 234 DSNGMV--IKYYQDVPRILEYL 253
D ++ + + V +LE L
Sbjct: 613 DDESVIERLAHTTSVDEVLELL 634
>gnl|CDD|213673 TIGR02009, PGMB-YQAB-SF, beta-phosphoglucomutase family hydrolase.
This subfamily model groups together three clades: the
characterized beta-phosphoglucomutases (including those
from E.coli, B.subtilus and L.lactis, TIGR01990), a
clade of putative bPGM's from mycobacteria and a clade
including the uncharacterized E.coli and H.influenzae
yqaB genes which may prove to be beta-mutases of a
related 1-phosphosugar. All of these are members of the
larger Haloacid dehalogenase (HAD) subfamily IA and
include the "variant 3" glu-asp version of the third
conserved HAD domain (TIGR01509).
Length = 185
Score = 31.2 bits (71), Expect = 0.95
Identities = 15/36 (41%), Positives = 19/36 (52%), Gaps = 3/36 (8%)
Query: 323 KYLKDHNIKLALASRTVHIRNAYSLLHLLGLSDFFD 358
K LK I + L S +NA +L LGL D+FD
Sbjct: 98 KRLKAKGIAVGLGS---SSKNAPRILAKLGLRDYFD 130
>gnl|CDD|181563 PRK08841, PRK08841, aspartate kinase; Validated.
Length = 392
Score = 31.6 bits (72), Expect = 1.0
Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 7/70 (10%)
Query: 205 FDDEERNARSISKLGVIGIQV---MHSMTNVLDSNGMVIKYYQDVPRILEYLREHNILVA 261
FDD+ RN+ S+S L ++G++ + N+L NG+ ++ P+ + + A
Sbjct: 308 FDDKIRNSESVSLLTLVGLEANGMVEHACNLLAQNGIDVRQCSTEPQSSMLV----LDPA 363
Query: 262 AVSTTVRILH 271
V ILH
Sbjct: 364 NVDRAANILH 373
>gnl|CDD|235068 PRK02769, PRK02769, histidine decarboxylase; Provisional.
Length = 380
Score = 31.6 bits (72), Expect = 1.1
Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 8/79 (10%)
Query: 214 SISKLGVIGIQVMHSMTNVLDSNGMVIKYYQDVPRILEYLREHNILVAAVSTTVR----- 268
S+SK+ + +++ + L NG I Y + +I E + I+ A + TT+
Sbjct: 122 SVSKIARL-LRIKSRVITSLP-NGE-IDYDDLISKIKENKNQPPIIFANIGTTMTGAIDN 178
Query: 269 ILHVQNILEMIGVARYFDH 287
I +Q IL+ IG+ Y+ H
Sbjct: 179 IKEIQEILKKIGIDDYYIH 197
>gnl|CDD|213990 cd07435, PHP_PolIIIA_POLC, Polymerase and Histidinol Phosphatase
domain of alpha-subunit of bacterial polymerase III at
PolC gene. DNA polymerase III alphas (PolIIIAs) that
contain a PHP domain have been classified into four
basic groups based on phylogenetic and domain structural
analyses: polC, dnaE1, dnaE2, and dnaE3. The PolC group
is distinct from the other three and is clustered
together. The PHP (also called histidinol
phosphatase-2/HIS2) domain is associated with several
types of DNA polymerases, such as PolIIIA and family X
DNA polymerases, stand alone histidinol phosphate
phosphatases (HisPPases), and a number of
uncharacterized protein families. DNA polymerase III
holoenzyme is one of the five eubacterial DNA
polymerases that are responsible for the replication of
the DNA duplex. The alpha subunit of DNA polymerase III
core enzyme catalyzes the reaction for polymerizing both
DNA strands. PolC PHP is located in different location
compare to dnaE1, 2, and 3. The PHP domain has four
conserved sequence motifs and and contains an invariant
histidine that is involved in metal ion coordination.The
PHP domain of PolC is structurally homologous to other
members of the PHP family that have a distorted
(beta/alpha)7 barrel fold with a trinuclear metal site
on the C-terminal side of the barrel. PHP domains found
in dnaEs of thermophilic origin exhibit 3'-5'
exonuclease activity. In contrast, PolC PHP lacks
detectable nuclease activity.
Length = 268
Score = 31.3 bits (72), Expect = 1.2
Identities = 28/110 (25%), Positives = 47/110 (42%), Gaps = 15/110 (13%)
Query: 240 IKYYQDVPRI----LEYLREHNILVAA-----VSTTVRILHVQNILEMIGVARYFDHKEI 290
KY+ VPRI LE RE ++ +A + LE I A ++D+ EI
Sbjct: 95 TKYFYRVPRIPKSELEKYREGLLIGSACENGELFEAALNKKSDEELEEI--ASFYDYIEI 152
Query: 291 YPRQKTKHLKKDRVEDAKGTLLNLYRDIPEIVKYLKDHNIKLALASRTVH 340
P + L + + ++ L + + I ++ K L K +A+ VH
Sbjct: 153 QPLDNYQFLIEKGLIKSEEELKEINKRIIKLGKKLN----KPVVATGDVH 198
>gnl|CDD|223634 COG0560, SerB, Phosphoserine phosphatase [Amino acid transport and
metabolism].
Length = 212
Score = 30.7 bits (70), Expect = 1.2
Identities = 15/68 (22%), Positives = 24/68 (35%), Gaps = 1/68 (1%)
Query: 270 LHVQNILEMIGVARYFDHKEIYPRQKT-KHLKKDRVEDAKGTLLNLYRDIPEIVKYLKDH 328
V I E + + R K L + +E+ + L L E+V LK
Sbjct: 33 EEVLAITERAMRGELDFEESLRLRVALLKGLPVEVLEEVREEFLRLTPGAEELVAALKAA 92
Query: 329 NIKLALAS 336
K+ + S
Sbjct: 93 GAKVVIIS 100
>gnl|CDD|223635 COG0561, Cof, Predicted hydrolases of the HAD superfamily [General
function prediction only].
Length = 264
Score = 30.8 bits (70), Expect = 1.5
Identities = 16/54 (29%), Positives = 27/54 (50%), Gaps = 7/54 (12%)
Query: 309 GTLLNLYRDIP----EIVKYLKDHNIKLALAS-RTVHIRNAYSLLHLLGLSDFF 357
GTLL+ + I E + L++ +K+ LA+ R + + S+L LGL
Sbjct: 12 GTLLDSNKTISPETKEALARLREKGVKVVLATGR--PLPDVLSILEELGLDGPL 63
>gnl|CDD|219777 pfam08282, Hydrolase_3, haloacid dehalogenase-like hydrolase. This
family contains haloacid dehalogenase-like hydrolase
enzymes.
Length = 254
Score = 30.7 bits (70), Expect = 1.7
Identities = 19/54 (35%), Positives = 27/54 (50%), Gaps = 7/54 (12%)
Query: 309 GTLLNLYRDIP----EIVKYLKDHNIKLALAS-RTVHIRNAYSLLHLLGLSDFF 357
GTLLN + I E +K L++ IK+ +A+ R R A +L LGL
Sbjct: 7 GTLLNSDKKISERTKEAIKKLQEKGIKVVIATGR--PYRGALPVLEELGLDLPV 58
>gnl|CDD|218602 pfam05478, Prominin, Prominin. The prominins are an emerging
family of proteins that among the multispan membrane
proteins display a novel topology. Mouse prominin and
human prominin (mouse)-like 1 (PROML1) are predicted to
contain five membrane spanning domains, with an
N-terminal domain exposed to the extracellular space
followed by four, alternating small cytoplasmic and
large extracellular, loops and a cytoplasmic C-terminal
domain. The exact function of prominin is unknown
although in humans defects in PROM1, the gene coding for
prominin, cause retinal degeneration.
Length = 807
Score = 31.1 bits (71), Expect = 1.9
Identities = 14/87 (16%), Positives = 30/87 (34%), Gaps = 10/87 (11%)
Query: 339 VHIRNAY-------SLLHLLGLSDFFDYKEIFPAEKKIKHFANLKKDSKIKYKDMVFFDD 391
+ I Y L +L L++ +D E+ ++ + K+ +
Sbjct: 531 LTISEVYRDCEQNEPLYTVLQLNNSYDLNELLDIKQYTPEIDQELESLKVNLSTITLLTP 590
Query: 392 EERNARSISKLGVIGIQ-VHRDKVLDA 417
E R R++ L G+ ++ L
Sbjct: 591 EAR--RNLEDLASSGLDDINFSNFLKQ 615
>gnl|CDD|215413 PLN02770, PLN02770, haloacid dehalogenase-like hydrolase family
protein.
Length = 248
Score = 30.2 bits (68), Expect = 2.3
Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 13/76 (17%)
Query: 283 RYFDHKEIYPRQKTKHLKKDRVEDAKGTLLNLYRDIPEIVKYLKDHNIKLALASRTVHIR 342
++ D KE R+ L ++++ G LY+ + K+++D +K A +
Sbjct: 90 KFTDDKEALFRK----LASEQLKPLNG----LYK----LKKWIEDRGLKRAAVTNAPR-E 136
Query: 343 NAYSLLHLLGLSDFFD 358
NA ++ LLGLSDFF
Sbjct: 137 NAELMISLLGLSDFFQ 152
>gnl|CDD|217328 pfam03031, NIF, NLI interacting factor-like phosphatase. This
family contains a number of NLI interacting factor
isoforms and also an N-terminal regions of RNA
polymerase II CTC phosphatase and FCP1 serine
phosphatase. This region has been identified as the
minimal phosphatase domain.
Length = 153
Score = 29.5 bits (67), Expect = 2.3
Identities = 28/122 (22%), Positives = 51/122 (41%), Gaps = 11/122 (9%)
Query: 17 KMVVFDLDYTLWPLHVHDLVAPFKKIGQKVMDAKGTLIKYYRGVPEILRYLKENKCLVA- 75
K +V DLD TL VH P + G +K G+ E L+ L + +V
Sbjct: 1 KTLVLDLDETL----VHSSFEPDLPFDFVLNFNHGVYVKKRPGLDEFLQELSKYYEIVIF 56
Query: 76 -AASRTSEILHAKQILNLINLNQYFSNKEIYPGQKTTHFESLKKATGIEYKDMVFFDDEE 134
A+S+ +A +L+ ++ + + +Y T + + L G + +V D+
Sbjct: 57 TASSKE----YADPVLDKLDPKKKYFKHRLYRESCTFYVKDLSL-LGRDLSRVVIVDNSP 111
Query: 135 RN 136
R+
Sbjct: 112 RS 113
>gnl|CDD|237311 PRK13226, PRK13226, phosphoglycolate phosphatase; Provisional.
Length = 229
Score = 30.2 bits (68), Expect = 2.3
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 9 DPSVKKFPKMVVFDLDYTL 27
+ + +FP+ V+FDLD TL
Sbjct: 5 EVAAVRFPRAVLFDLDGTL 23
>gnl|CDD|130495 TIGR01428, HAD_type_II, 2-haloalkanoic acid dehalogenase, type II.
Catalyzes the hydrolytic dehalogenation of small
L-2-haloalkanoic acids to yield the corresponding
D-2-hydroxyalkanoic acids. Belongs to the Haloacid
Dehalogenase (HAD) superfamily of aspartate-nucleophile
hydrolases (pfam00702), class (subfamily) I. Note that
the Type I HAD enzymes have not yet been fully
characterized, but clearly utilize a substantially
different catalytic mechanism and are thus unlikely to
be related.
Length = 198
Score = 29.6 bits (67), Expect = 2.8
Identities = 18/60 (30%), Positives = 25/60 (41%), Gaps = 7/60 (11%)
Query: 305 EDAKGTLLNLYR------DIPEIVKYLKDHNIKLALASRTVHIRNAYSLLHLLGLSDFFD 358
E A L Y D+P ++ LK+ +LA+ S SL+ GL D FD
Sbjct: 78 ESAADRLAEAYLRLPPHPDVPAGLRALKERGYRLAILSNGSPAMLK-SLVKHAGLDDPFD 136
>gnl|CDD|236710 PRK10534, PRK10534, L-threonine aldolase; Provisional.
Length = 333
Score = 30.1 bits (68), Expect = 2.8
Identities = 18/67 (26%), Positives = 29/67 (43%), Gaps = 4/67 (5%)
Query: 206 DDEERNARSISKLGVIGIQVMHSMTNVLDSNGMVIKYYQDVPRILEYLREHNILVAAVST 265
+D + A +L G VM TN+L V + + EY+RE N+L+ A
Sbjct: 251 EDHDNAAWLAEQLREAGADVMRQDTNML----FVRVGEEQAAALGEYMRERNVLINASPI 306
Query: 266 TVRILHV 272
+ H+
Sbjct: 307 VRLVTHL 313
>gnl|CDD|221451 pfam12167, DUF3596, Domain of unknown function (DUF3596). This
presumed domain is functionally uncharacterized.This
domain family is found in bacteria and viruses, and is
approximately 90 amino acids in length. The family is
found in association with pfam00589.
Length = 88
Score = 28.0 bits (63), Expect = 3.0
Identities = 12/24 (50%), Positives = 13/24 (54%)
Query: 357 FDYKEIFPAEKKIKHFANLKKDSK 380
FDY E FP KK FA L + K
Sbjct: 54 FDYAEYFPDSKKAAKFAALDAEIK 77
>gnl|CDD|233530 TIGR01686, FkbH, FkbH-like domain. This model describes a domain
of a family of proteins of unknown overall function. One
of these, however, is a modular polyketide synthase 4800
amino acids in length from Streptomyces avermilitis in
which this domain is the C-terminal segment. By
contrast, the FkbH protein from Streptomyces
hygroscopicus aparently contains only this domain. The
remaining members of the family all contain an
additional N-terminal domain of between 200 and 275
amino acids which show less than 20% identity to one
another. It seems likely then that these proteins are
involved in disparate functions, probably the
biosynthesis of different natural products. For
instance, the FkbH gene is found in a gene cluster
believed to be responsible for the biosynthesis of
unususal "PKS extender units" in the ascomycin pathway.
This domain is composed of two parts, the first of which
is a member of subfamily IIIC (TIGR01681) of the
haloacid dehalogenase (HAD) superfamily of
aspartate-nucleophile hydrolases. All of the
characterized enzymes within subfamily III are
phosphatases, and all of the active site residues
characteristic of HAD-superfamily phosphatases are
present in this domain. The C-terminal portion of this
domain is unique to this family (by BLAST).
Length = 320
Score = 29.4 bits (66), Expect = 5.2
Identities = 24/90 (26%), Positives = 39/90 (43%), Gaps = 16/90 (17%)
Query: 311 LLNLYRDIPEIVKYLKDHNIKLALASRTVHIRNAYSLL----HLLGLSDFFDYKEIF--P 364
L L++ + E +K LK LALAS+ +A + + ++ FD + I P
Sbjct: 29 LSPLHKTLQEKIKTLKKQGFLLALASKNDE-DDAKKVFERRKDFILQAEDFDARSINWGP 87
Query: 365 AEKKIKHFA---NLKKDSKIKYKDMVFFDD 391
+ ++ A NL DS +F DD
Sbjct: 88 KSESLRKIAKKLNLGTDS------FLFIDD 111
>gnl|CDD|136007 PRK06698, PRK06698, bifunctional
5'-methylthioadenosine/S-adenosylhomocysteine
nucleosidase/phosphatase; Validated.
Length = 459
Score = 29.2 bits (65), Expect = 6.2
Identities = 15/31 (48%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 425 YRDVPAILKYLKQNNCLVAAASR-TTEMLRA 454
Y +V I Y+K+NNC + AS TE LRA
Sbjct: 332 YPNVKEIFTYIKENNCSIYIASNGLTEYLRA 362
>gnl|CDD|226984 COG4637, COG4637, Predicted ATPase [General function prediction
only].
Length = 373
Score = 29.0 bits (65), Expect = 6.2
Identities = 8/57 (14%), Positives = 18/57 (31%), Gaps = 3/57 (5%)
Query: 234 DSNGMVIKYYQDVPRILEYLREHNILVAAVSTTVRILHVQNILEM---IGVARYFDH 287
NG I + R+ E E + + I + + ++ R++
Sbjct: 128 FRNGPGIAIRGEGGRLFEQTDEELTFETQLLESNDIGAIPELGQLRRAKAQWRFYHL 184
>gnl|CDD|240421 PTZ00445, PTZ00445, p36-lilke protein; Provisional.
Length = 219
Score = 28.5 bits (64), Expect = 6.8
Identities = 9/35 (25%), Positives = 17/35 (48%)
Query: 192 RKDSKIKYKDMVFFDDEERNARSISKLGVIGIQVM 226
D + +++F DD+ N ++ K G I + V
Sbjct: 171 CSDFNVNPDEILFIDDDMNNCKNALKEGYIALHVT 205
>gnl|CDD|237336 PRK13288, PRK13288, pyrophosphatase PpaX; Provisional.
Length = 214
Score = 28.5 bits (64), Expect = 7.8
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 3/49 (6%)
Query: 311 LLNLYRDIPEIVKYLKDHNIKLALASRTVHIRNAYSL-LHLLGLSDFFD 358
L+ Y + E +K LK KL + T +R+ + L L GL +FFD
Sbjct: 80 LVTEYETVYETLKTLKKQGYKLGIV--TTKMRDTVEMGLKLTGLDEFFD 126
>gnl|CDD|188955 cd09556, SAM_VTS1_fungal, SAM domain of VTS1 RNA-binding proteins.
SAM (sterile alpha motif) domain of VTS1 subfamily
proteins is RNA binding domain located in the C-terminal
region. SAM interacts with stem-loop structures of mRNA.
Proteins of this subfamily participate in regulation of
transcript stability and degradation, and also may be
involved in vacuolar protein transport regulation. VTS1
protein of S.cerevisiae induces mRNA degradation via the
major deadenylation-dependent mRNA decay pathway; VTS1
recruits CCR4/POP2/NOT deadenylase complex to target
mRNA. The recruitment is the initial step resulting in
poly(A) tail removal transcripts. Potentially SAM domain
may be responsible not only for RNA binding but also for
deadenylase binding.
Length = 69
Score = 26.5 bits (59), Expect = 8.0
Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 8/50 (16%)
Query: 148 IHSWLMMSSGRLKEAT----GIDYKDMIYFDDEQEHVNDISKLGVTATRK 193
I +WL S RL + T + +K++I DDE +S LG A RK
Sbjct: 9 IPAWL--RSLRLHKYTDNLKDLSWKELIELDDEDLEDKGVSALG--ARRK 54
>gnl|CDD|133450 cd05211, NAD_bind_Glu_Leu_Phe_Val, NAD(P) binding domain of
glutamate dehydrogenase, leucine dehydrogenase,
phenylalanine dehydrogenase, and valine dehydrogenase.
Amino acid dehydrogenase (DH) is a widely distributed
family of enzymes that catalyzes the oxidative
deamination of an amino acid to its keto acid and
ammonia with concomitant reduction of NAD(P)+. This
subfamily includes glutamate, leucine, phenylalanine,
and valine DHs. Glutamate DH is a multi-domain enzyme
that catalyzes the reaction from glutamate to
2-oxyoglutarate and ammonia in the presence of NAD or
NADP. It is present in all organisms. Enzymes involved
in ammonia assimilation are typically NADP+-dependent,
while those involved in glutamate catabolism are
generally NAD+-dependent. As in other NAD+-dependent
DHs, monomers in this family have 2 domains separated by
a deep cleft. Here the c-terminal domain contains a
modified NAD-binding Rossmann fold with 7 rather than
the usual 6 beta strands and one strand anti-parrallel
to the others. Amino acid DH-like NAD(P)-binding domains
are members of the Rossmann fold superfamily and include
glutamate, leucine, and phenylalanine DHs, methylene
tetrahydrofolate DH, methylene-tetrahydromethanopterin
DH, methylene-tetrahydropholate DH/cyclohydrolase,
Shikimate DH-like proteins, malate oxidoreductases, and
glutamyl tRNA reductase. Amino acid DHs catalyze the
deamination of amino acids to keto acids with NAD(P)+ as
a cofactor. The NAD(P)-binding Rossmann fold superfamily
includes a wide variety of protein families including
NAD(P)- binding domains of alcohol DHs,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DH, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 217
Score = 28.3 bits (63), Expect = 8.2
Identities = 15/57 (26%), Positives = 23/57 (40%), Gaps = 8/57 (14%)
Query: 406 GIQVHRDKVLDAGGAIIKYYRDVPAILKYLKQNNCLVAAASRTTEMLRAHQLVDLFN 462
GI V D V +AGG I+ Y+ V QN ++ + + D+ N
Sbjct: 143 GIVVAPDIVANAGGVIVSYFEWV--------QNLQRLSWDAEEVRSKLEQVMTDIHN 191
>gnl|CDD|223620 COG0546, Gph, Predicted phosphatases [General function prediction
only].
Length = 220
Score = 28.2 bits (63), Expect = 8.4
Identities = 26/133 (19%), Positives = 54/133 (40%), Gaps = 12/133 (9%)
Query: 314 LYRDIPEIVKYLKDHNIKLALASRTVHIRNAYSLLHLLGLSDFFD----YKEIFPAEKKI 369
L+ + E++ LK KL + + R LL LGL+D+FD ++ P +
Sbjct: 90 LFPGVKELLAALKSAGYKLGIVTNKPE-RELDILLKALGLADYFDVIVGGDDVPPPKPDP 148
Query: 370 KHFANLKKDSKIKYKDMVFFDDEERNARSISKLGVIGIQV-----HRDKVLDAGGAIIKY 424
+ L + + ++ + D + + GV + V R+++ AG ++
Sbjct: 149 EPLLLLLEKLGLDPEEALMVGDSLNDILAAKAAGVPAVGVTWGYNSREELAQAGADVV-- 206
Query: 425 YRDVPAILKYLKQ 437
+ +L L +
Sbjct: 207 IDSLAELLALLAE 219
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.321 0.136 0.398
Gapped
Lambda K H
0.267 0.0774 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 28,088,651
Number of extensions: 2826605
Number of successful extensions: 2923
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2891
Number of HSP's successfully gapped: 100
Length of query: 538
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 436
Effective length of database: 6,413,494
Effective search space: 2796283384
Effective search space used: 2796283384
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 61 (27.2 bits)