RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7890
(196 letters)
>gnl|CDD|215285 PLN02521, PLN02521, galactokinase.
Length = 497
Score = 101 bits (253), Expect = 3e-25
Identities = 40/77 (51%), Positives = 51/77 (66%), Gaps = 1/77 (1%)
Query: 59 KSSHEIYLEAYRVERFLSVCRSDISEEQKLQQLGTLMNQSHTSLATKYECSHEALDSLVT 118
++ H +Y EA RV F S +SEE+KL++LG LMN+SH S + YECS L+ LV
Sbjct: 364 RAVH-VYSEAKRVHAFRDTVSSSLSEEEKLKKLGDLMNESHYSCSVLYECSCPELEELVK 422
Query: 119 CFREAGAYGARLTGAGW 135
R+ GA GARLTGAGW
Sbjct: 423 VCRDNGALGARLTGAGW 439
>gnl|CDD|235163 PRK03817, PRK03817, galactokinase; Provisional.
Length = 351
Score = 60.4 bits (147), Expect = 4e-11
Identities = 27/52 (51%), Positives = 33/52 (63%)
Query: 84 EEQKLQQLGTLMNQSHTSLATKYECSHEALDSLVTCFREAGAYGARLTGAGW 135
+E ++ LG L+ +SH LA YE S E LD V E GAYGARLTGAG+
Sbjct: 253 KEGDIETLGELLTESHWDLADNYEVSCEELDFFVEFALELGAYGARLTGAGF 304
>gnl|CDD|223231 COG0153, GalK, Galactokinase [Carbohydrate transport and
metabolism].
Length = 390
Score = 60.4 bits (147), Expect = 4e-11
Identities = 30/73 (41%), Positives = 37/73 (50%), Gaps = 6/73 (8%)
Query: 64 IYLEAYRVERFLSVCRSDISEEQKLQQLGTLMNQSHTSLATKYECSHEALDSLV-TCFRE 122
+ E RV RS L + G LMN+SH SL YE + LD+LV
Sbjct: 276 VVTENQRVLEAAKALRSG-----DLTEFGELMNESHESLRDDYEVTCPELDTLVEIALAA 330
Query: 123 AGAYGARLTGAGW 135
GAYGAR+TGAG+
Sbjct: 331 GGAYGARMTGAGF 343
>gnl|CDD|232841 TIGR00131, gal_kin, galactokinase. Galactokinase is a member of
the GHMP kinases (Galactokinase, Homoserine kinase,
Mevalonate kinase, Phosphomevalonate kinase) and shares
with them an amino-terminal domain probably related to
ATP binding.The galactokinases found by This model are
divided into two sets. Prokaryotic forms are generally
shorter. The eukaryotic forms are longer because of
additional central regions and in some cases are known
to be bifunctional, with regulatory activities that are
independent of galactokinase activity [Energy
metabolism, Sugars].
Length = 386
Score = 54.4 bits (131), Expect = 5e-09
Identities = 30/91 (32%), Positives = 45/91 (49%), Gaps = 12/91 (13%)
Query: 57 ESKSSHEIYLEAYRVERFLSVCRSDISEEQKLQQLGTLMNQSHTSLATKYECSHEALDSL 116
E ++ H + E RV + + ++ +Q G LMN+SH S YEC+ +D L
Sbjct: 267 EERAKH-VVSENLRVLKAVKAM-----KDNDFKQFGALMNESHASCDDDYECTCPEIDEL 320
Query: 117 VTCFREA-GAYGARLTGAGW--CISQDAHLV 144
V G+ G+R+TGAG+ C HLV
Sbjct: 321 VCSAALVNGSGGSRMTGAGFGGCT---VHLV 348
>gnl|CDD|235407 PRK05322, PRK05322, galactokinase; Provisional.
Length = 387
Score = 54.5 bits (132), Expect = 5e-09
Identities = 23/52 (44%), Positives = 32/52 (61%), Gaps = 1/52 (1%)
Query: 84 EEQKLQQLGTLMNQSHTSLATKYECSHEALDSLV-TCFREAGAYGARLTGAG 134
+ L++ G LMN SH SL YE + LD+LV +++ G GAR+TGAG
Sbjct: 289 KAGDLEKFGRLMNASHVSLRDDYEVTGLELDTLVEAAWKQEGVLGARMTGAG 340
>gnl|CDD|233017 TIGR00549, mevalon_kin, mevalonate kinase. This model represents
mevalonate kinase, the third step in the mevalonate
pathway of isopentanyl pyrophosphate (IPP) biosynthesis.
IPP is a common intermediate for a number of pathways
including cholesterol biosynthesis. This model covers
enzymes from eukaryotes, archaea and bacteria. The
related enzyme from the same pathway, phosphmevalonate
kinase, serves as an outgroup for this clade. Paracoccus
exhibits two genes within the
phosphomevalonate/mevalonate kinase family, one of which
falls between trusted and noise cutoffs of this model.
The degree of divergence is high, but if the trees
created from this model are correct, the proper names of
these genes have been swapped [Central intermediary
metabolism, Other].
Length = 274
Score = 46.9 bits (112), Expect = 2e-06
Identities = 24/56 (42%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 80 SDISEEQKLQQLGTLMNQSHTSLATKYECSHEALDSLVTCFREAGAYGARLTGAGW 135
E+ ++ LG LMN + L SH LD LV R+AGA GA+LTGAG
Sbjct: 213 KAALEDGDVESLGELMNINQGLLKA-LGVSHPKLDQLVEIARKAGALGAKLTGAGG 267
>gnl|CDD|224493 COG1577, ERG12, Mevalonate kinase [Lipid metabolism].
Length = 307
Score = 46.1 bits (110), Expect = 3e-06
Identities = 23/56 (41%), Positives = 28/56 (50%), Gaps = 3/56 (5%)
Query: 84 EEQKLQQLGTLMNQSHTSLATKYECSHEALDSLVTCFREAGAYGARLTGAGW--CI 137
+ ++LG LMN + L S LD LV R GA GA+LTGAG CI
Sbjct: 221 QTGDFEELGELMNINQ-GLLKALGVSTPELDELVEAARSLGALGAKLTGAGGGGCI 275
>gnl|CDD|240351 PTZ00298, PTZ00298, mevalonate kinase; Provisional.
Length = 328
Score = 45.6 bits (108), Expect = 5e-06
Identities = 20/47 (42%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 88 LQQLGTLMNQSHTSLATKYECSHEALDSLVTCFREAGAYGARLTGAG 134
L ++G LMN +H L K S LDS+V R GA GA+++G G
Sbjct: 239 LFRVGELMNANHD-LCQKLTVSCRELDSIVQTCRTYGALGAKMSGTG 284
>gnl|CDD|179677 PRK03926, PRK03926, mevalonate kinase; Provisional.
Length = 302
Score = 43.9 bits (104), Expect = 1e-05
Identities = 20/60 (33%), Positives = 28/60 (46%), Gaps = 1/60 (1%)
Query: 75 LSVCRSDISEEQKLQQLGTLMNQSHTSLATKYECSHEALDSLVTCFREAGAYGARLTGAG 134
+S ++ LG LMN + L S + L L+ R AGA GA++TGAG
Sbjct: 200 ISEKGEELILSGDYVSLGELMNINQ-GLLDALGVSTKELSELIYAARTAGALGAKITGAG 258
>gnl|CDD|219894 pfam08544, GHMP_kinases_C, GHMP kinases C terminal. This family
includes homoserine kinases, galactokinases and
mevalonate kinases.
Length = 86
Score = 40.6 bits (95), Expect = 3e-05
Identities = 20/54 (37%), Positives = 28/54 (51%), Gaps = 2/54 (3%)
Query: 84 EEQKLQQLGTLMNQSHTSLATK--YECSHEALDSLVTCFREAGAYGARLTGAGW 135
E L+ LG L+N++ SL LD L+ RE GA GA+L+G+G
Sbjct: 6 REGDLELLGELLNENALSLEPLLYLGILSPELDELLEELRELGALGAKLSGSGG 59
>gnl|CDD|179063 PRK00555, PRK00555, galactokinase; Provisional.
Length = 363
Score = 40.2 bits (94), Expect = 3e-04
Identities = 17/44 (38%), Positives = 25/44 (56%)
Query: 92 GTLMNQSHTSLATKYECSHEALDSLVTCFREAGAYGARLTGAGW 135
G L+ SH S+ +E + E +D + AGA GAR+TG G+
Sbjct: 273 GQLLTASHASMRDDFEITTERIDLIADSAVRAGALGARMTGGGF 316
>gnl|CDD|215466 PLN02865, PLN02865, galactokinase.
Length = 423
Score = 39.8 bits (93), Expect = 4e-04
Identities = 20/49 (40%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 88 LQQLGTLMNQSHTSLATKYECSHEALDSLVTCFREA-GAYGARLTGAGW 135
L++ G L++ S S YEC E L L +A G YGAR +GAG+
Sbjct: 322 LEEFGKLISASGLSSIENYECGCEPLIQLYEILLKAPGVYGARFSGAGF 370
>gnl|CDD|179937 PRK05101, PRK05101, galactokinase; Provisional.
Length = 382
Score = 35.7 bits (83), Expect = 0.010
Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 8/56 (14%)
Query: 88 LQQLGTLMNQSHTSLATKYECSHEALDSLVTCFREA----GAYGARLTGAGW--CI 137
L+++G LM +SH S+ +E + +D+LV + G G R+TG G+ CI
Sbjct: 287 LKRMGELMAESHASMRDDFEITVPQIDTLVEIVKAVIGDQG--GVRMTGGGFGGCI 340
>gnl|CDD|225325 COG2605, COG2605, Predicted kinase related to galactokinase and
mevalonate kinase [General function prediction only].
Length = 333
Score = 34.7 bits (80), Expect = 0.022
Identities = 21/76 (27%), Positives = 41/76 (53%), Gaps = 13/76 (17%)
Query: 62 HEIYLEAYRVERFLSVCRSDISEEQKLQQLGTLMN---QSHTSLATKYECSHEALDSLVT 118
HE+ AY + ++ R+DI E G +++ ++ L+++ S++A+D +
Sbjct: 224 HEMKALAYEM--KDALVRNDIPE------FGQILDRGWEAKKKLSSR--ISNDAIDRIYE 273
Query: 119 CFREAGAYGARLTGAG 134
+ GAYG +L+GAG
Sbjct: 274 LALKNGAYGGKLSGAG 289
>gnl|CDD|240347 PTZ00290, PTZ00290, galactokinase; Provisional.
Length = 468
Score = 32.9 bits (75), Expect = 0.095
Identities = 18/77 (23%), Positives = 35/77 (45%), Gaps = 5/77 (6%)
Query: 66 LEAYRVERFLSVCRSD--ISEEQKLQQLGTLMNQSHTSLATKYECSHEALDSL-VTCFRE 122
+E R F+ + + +S E++ ++ G ++N H + + + LD + E
Sbjct: 338 MEQIRTLEFIKLNDPELPLSREERFRKAGEILNAGHQGMRDLMKITTPELDFIHELINEE 397
Query: 123 AGAYGARLTGAGW--CI 137
G G R+ G G+ CI
Sbjct: 398 KGVAGGRMMGGGFGGCI 414
>gnl|CDD|171704 PRK12751, cpxP, periplasmic stress adaptor protein CpxP; Reviewed.
Length = 162
Score = 29.0 bits (64), Expect = 1.0
Identities = 17/42 (40%), Positives = 21/42 (50%), Gaps = 2/42 (4%)
Query: 85 EQKLQQLGTLMNQSHTSLATKYECSHEALDSLVTC--FREAG 124
EQ+ QQ+ LM QSH S EA+ L+T F EA
Sbjct: 59 EQQRQQMRDLMRQSHQSQPRLDLEDREAMHKLITADKFDEAA 100
>gnl|CDD|236813 PRK10993, PRK10993, outer membrane protease; Reviewed.
Length = 314
Score = 27.7 bits (62), Expect = 4.2
Identities = 18/64 (28%), Positives = 24/64 (37%), Gaps = 12/64 (18%)
Query: 129 RLTGAGW--CISQDAHLVNIMAWVQSQPRWC---ISQDAHL-------VNIMAWVQSQPR 176
L +GW S H+V+ SQP W D L +N+ W+ P
Sbjct: 86 SLGASGWTTLASGGGHMVDYDWLDSSQPGWTDRSHHPDTDLNYANEFDLNLKGWLLQNPN 145
Query: 177 YRLS 180
YRL
Sbjct: 146 YRLG 149
>gnl|CDD|237145 PRK12583, PRK12583, acyl-CoA synthetase; Provisional.
Length = 558
Score = 27.8 bits (62), Expect = 4.2
Identities = 24/108 (22%), Positives = 35/108 (32%), Gaps = 28/108 (25%)
Query: 97 QSHTSLATKYECSHEALDSLVTCF--REAGAY---GARLTGAGWCISQDAHLVNIMA--- 148
Q + +A D+ V F REA R T + D ++A
Sbjct: 8 QGGGDKPLLTQTIGDAFDATVARFPDREALVVRHQALRYTWRQLADAVDRLARGLLALGV 67
Query: 149 --------WVQSQPRWCISQ------DAHLVNIMAWVQSQPRYRLSQV 182
W + W ++Q A LVNI P YR S++
Sbjct: 68 QPGDRVGIWAPNCAEWLLTQFATARIGAILVNI------NPAYRASEL 109
>gnl|CDD|190325 pfam02488, EMA, Merozoite Antigen. This family represents the
immunodominant surface antigen of Theileria parasites
including equi merozoite antigen-1 (EMA-1) and equi
merozoite antigen-2 (EMA-2). The protein shows variation
at a putative glycosylation site, a potential mechanism
for host immune response evasion.
Length = 251
Score = 27.0 bits (60), Expect = 6.6
Identities = 19/66 (28%), Positives = 28/66 (42%), Gaps = 15/66 (22%)
Query: 2 LDTVKFSFEVETKLSSVVVNALDFGSGVKFSFEVETKLSSVVVNALDFGSGGWWFESKSS 61
LD KF +T L + + FGSG K++F+ K+S V D G
Sbjct: 115 LDASKF---ADTALFT----SAAFGSGKKYTFKAPFKVSKVTFGKKDVG--------DGD 159
Query: 62 HEIYLE 67
+ YL+
Sbjct: 160 NAKYLD 165
>gnl|CDD|224431 COG1514, LigT, 2'-5' RNA ligase [Translation, ribosomal structure
and biogenesis].
Length = 180
Score = 26.5 bits (59), Expect = 6.7
Identities = 14/74 (18%), Positives = 25/74 (33%), Gaps = 11/74 (14%)
Query: 4 TVKFSFEVETKLSSVVVNALDFGSGVKFSFEVETKLSSVVVNALDFGSGG----WWFESK 59
T+KF EV+ + ++ AL + L F + W +
Sbjct: 41 TLKFLGEVDEDKADELIEALA---RIAAPEPFPITLDGAGS----FPNPRRPRVIWVGVE 93
Query: 60 SSHEIYLEAYRVER 73
+ E+ A +ER
Sbjct: 94 ETEELRALAEELER 107
>gnl|CDD|168796 PRK07066, PRK07066, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 321
Score = 27.1 bits (60), Expect = 7.3
Identities = 10/35 (28%), Positives = 21/35 (60%)
Query: 115 SLVTCFREAGAYGARLTGAGWCISQDAHLVNIMAW 149
+++T + A G+ + G+GW AH ++++AW
Sbjct: 2 AVITDIKTFAAIGSGVIGSGWVARALAHGLDVVAW 36
>gnl|CDD|153085 cd01676, RNR_II_monomer, Class II ribonucleotide reductase,
monomeric form. Ribonucleotide reductase (RNR)
catalyzes the reductive synthesis of
deoxyribonucleotides from their corresponding
ribonucleotides. It provides the precursors necessary
for DNA synthesis. RNRs are separated into three classes
based on their metallocofactor usage. Class I RNRs,
found in eukaryotes, bacteria, and bacteriophage, use a
diiron-tyrosyl radical. Class II RNRs, found in
bacteria, bacteriophage, algae and archaea, use coenzyme
B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found
in anaerobic bacteria, bacteriophage, and archaea, use
an FeS cluster and S-adenosylmethionine to generate a
glycyl radical. Many organisms have more than one class
of RNR present in their genomes. All three RNRs have a
ten-stranded alpha-beta barrel domain that is
structurally similar to the domain of PFL (pyruvate
formate lyase). Class II RNRs are found in bacteria that
can live under both aerobic and anaerobic conditions.
Many, but not all members of this class, are found to be
homodimers. This particular subfamily is found to be
active as a monomer. Adenosylcobalamin interacts
directly with an active site cysteine to form the
reactive cysteine radical.
Length = 658
Score = 27.1 bits (60), Expect = 7.8
Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 4/56 (7%)
Query: 63 EIYLEAYR----VERFLSVCRSDISEEQKLQQLGTLMNQSHTSLATKYECSHEALD 114
EI LE+Y VE F D+ + Q+ L ++ T L +E ++E +
Sbjct: 357 EISLESYELCNLVEVFPLKHEGDLEDLQETLYLAGRYAKTVTLLPLHWEITNEIIL 412
>gnl|CDD|222645 pfam14280, DUF4365, Domain of unknown function (DUF4365). This
family of proteins is functionally uncharacterized.
This family of proteins is found in bacteria,
eukaryotes and viruses. Proteins in this family are
typically between 182 and 530 amino acids in length.
There is a single completely conserved residue D that
may be functionally important.
Length = 139
Score = 26.2 bits (58), Expect = 7.9
Identities = 6/31 (19%), Positives = 11/31 (35%)
Query: 51 SGGWWFESKSSHEIYLEAYRVERFLSVCRSD 81
GG+ F + H Y + + L +
Sbjct: 63 GGGFSFRLEREHLNYWLNHPLPVILVLVDPS 93
>gnl|CDD|200528 cd11267, Sema_6B, The Sema domain, a protein interacting module, of
semaphorin 6B (Sema6B). Sema6B functions as repellents
for axon growth; this repulsive activity is mediated by
its receptor Plexin A4. Sema6B is expressed in CA3, and
repels mossy fibers in a Plexin A4 dependent manner. In
human, it was shown that peroxisome
proliferator-activated receptors (PPARs) and
9-cis-retinoic acid receptor (RXR) regulate human
semaphorin 6B (Sema6B) gene expression. Sema6B is a
member of the class 6 semaphorin family of proteins,
which are membrane associated semaphorins. Semaphorins
are regulatory molecules in the development of the
nervous system and in axonal guidance. They also play
important roles in other biological processes, such as
angiogenesis, immune regulation, respiration systems and
cancer. The Sema domain is located at the N-terminus and
contains four disulfide bonds formed by eight conserved
cysteine residues. It serves as a receptor-recognition
and -binding module.
Length = 466
Score = 26.7 bits (59), Expect = 8.4
Identities = 20/67 (29%), Positives = 35/67 (52%), Gaps = 6/67 (8%)
Query: 44 VNALDFGSGGWWFESKSSHEI-YLEAYRVERFLSVCRSDISEEQKLQQLGTLMNQSHTSL 102
V+A+++GS ++F + + E YLE V R VC++D+ Q++ L Q + L
Sbjct: 176 VHAVEWGSHVYFFFREIAMEFNYLEKVVVSRVARVCKNDMGGSQRV-----LEKQWTSFL 230
Query: 103 ATKYECS 109
+ CS
Sbjct: 231 KARLNCS 237
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
0.320 0.131 0.403
Gapped
Lambda K H
0.267 0.0597 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,326,300
Number of extensions: 802644
Number of successful extensions: 650
Number of sequences better than 10.0: 1
Number of HSP's gapped: 642
Number of HSP's successfully gapped: 30
Length of query: 196
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 104
Effective length of database: 6,857,034
Effective search space: 713131536
Effective search space used: 713131536
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 (21.9 bits)
S2: 56 (25.6 bits)