RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1102
(138 letters)
>gnl|CDD|152787 pfam12352, V-SNARE_C, Snare region anchored in the vesicle
membrane C-terminus. Within the SNARE proteins
interactions in the C-terminal half of the SNARE helix
are critical to the driving of membrane fusion; whereas
interactions in the N-terminal half of the SNARE domain
are important for promoting priming or docking of the
vesicle pfam05008.
Length = 66
Score = 48.4 bits (116), Expect = 1e-08
Identities = 20/44 (45%), Positives = 27/44 (61%)
Query: 53 EEIERTGKHLETGYRIAIETEKIATDVLKDLESQRETLQRTRTR 96
E + R L+ +RIA ET I +L+DL SQRETL+R R +
Sbjct: 1 ERLLREHDRLKNSHRIADETISIGQAILEDLHSQRETLKRARNK 44
>gnl|CDD|197699 smart00397, t_SNARE, Helical region found in SNAREs. All
alpha-helical motifs that form twisted and parallel
four-helix bundles in target soluble
N-ethylmaleimide-sensitive factor (NSF) attachment
protein (SNAP) receptor proteins. This motif found in
"Q-SNAREs".
Length = 66
Score = 33.7 bits (78), Expect = 0.004
Identities = 13/55 (23%), Positives = 23/55 (41%), Gaps = 7/55 (12%)
Query: 42 EEQSQRLLDTSEEIERTGKHLETGYRIAIETEKIATDVLKDLESQRETLQRTRTR 96
++ R + EE+E+ + E ++I D+ +LE Q E L R
Sbjct: 1 QQALAREEERDEELEQLE-------KSIQELKQIFLDMGTELEEQGEQLDRIEDN 48
>gnl|CDD|217862 pfam04051, TRAPP, Transport protein particle (TRAPP) component.
TRAPP plays a key role in the targeting and/or fusion of
ER-to-Golgi transport vesicles with their acceptor
compartment. TRAPP is a large multimeric protein that
contains at least 10 subunits. This family contains many
TRAPP family proteins. The Bet3 subunit is one of the
better characterized TRAPP proteins and has a dimeric
structure with hydrophobic channels. The channel
entrances are located on a putative membrane-interacting
surface that is distinctively flat, wide and decorated
with positively charged residues. Bet3 is proposed to
localise TRAPP to the Golgi.
Length = 148
Score = 30.6 bits (70), Expect = 0.14
Identities = 18/86 (20%), Positives = 29/86 (33%), Gaps = 20/86 (23%)
Query: 46 QRLLDTSEEIERTGKHLET-GYRIAIETEKIATDVLKDLESQRETLQRTRTRHSHTDFIN 104
LL E++ LE GY I ++ +L S+R T D +
Sbjct: 11 SYLLRDVEDVN---ARLEKMGYNIGQ---RLIERLLARSGSKRCT-----------DLLE 53
Query: 105 LACGSMICQTVWTWWGGAPPQSLNWN 130
+ IC+ +W G L +
Sbjct: 54 VL--KFICKDLWKMLFGKQADVLETS 77
>gnl|CDD|224202 COG1283, NptA, Na+/phosphate symporter [Inorganic ion transport and
metabolism].
Length = 533
Score = 30.3 bits (69), Expect = 0.25
Identities = 21/108 (19%), Positives = 37/108 (34%), Gaps = 36/108 (33%)
Query: 37 STNINEEQSQR---LLDTSEEIERTGKHLETG-------------------------YRI 68
++EE+S+R ++D + +E G +E + +
Sbjct: 391 KEGLSEEESRRWAEIIDAAINLEHIGDIIERLLELADKKIANGRAFSEDGLEELDALFAL 450
Query: 69 AIETEKIATDVL--KDLESQRET------LQRTRTRHSHTDFINLACG 108
+E ++A VL DLE R ++R R S L G
Sbjct: 451 TLENLRLAISVLVTGDLELARRLVERKKRVRRLERRSSKRHLDRLRDG 498
>gnl|CDD|181305 PRK08226, PRK08226, short chain dehydrogenase; Provisional.
Length = 263
Score = 29.4 bits (66), Expect = 0.52
Identities = 18/67 (26%), Positives = 29/67 (43%), Gaps = 8/67 (11%)
Query: 48 LLDTSEEIERTGKHL-ETGYRIAIETEKIATDVLKDLESQRETLQRTRTRHSHTDFINLA 106
LLD S EIE+ L G+R + DV +D S ++R + + D L
Sbjct: 35 LLDISPEIEKLADELCGRGHRCT----AVVADV-RDPASVAAAIKRAKEKEGRIDI--LV 87
Query: 107 CGSMICQ 113
+ +C+
Sbjct: 88 NNAGVCR 94
>gnl|CDD|236454 PRK09288, purT, phosphoribosylglycinamide formyltransferase 2;
Validated.
Length = 395
Score = 28.9 bits (66), Expect = 0.89
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 71 ETEKIATDVLKDLESQ 86
E E IATD L +LE +
Sbjct: 82 EIEAIATDALVELEKE 97
>gnl|CDD|169452 PRK08463, PRK08463, acetyl-CoA carboxylase subunit A; Validated.
Length = 478
Score = 28.2 bits (63), Expect = 1.3
Identities = 20/62 (32%), Positives = 28/62 (45%), Gaps = 13/62 (20%)
Query: 23 FLLSEYHVEYFSENSTNINEEQSQRLLDTSEEIERTGKHLETGYRIAIETEKIATDVLKD 82
FLL +Y+ YF E +T I E +EEI TG + + +IA + D
Sbjct: 276 FLLDDYNRFYFMEMNTRIQVEHG-----VTEEI--------TGIDLIVRQIRIAAGEILD 322
Query: 83 LE 84
LE
Sbjct: 323 LE 324
>gnl|CDD|184143 PRK13561, PRK13561, putative diguanylate cyclase; Provisional.
Length = 651
Score = 27.8 bits (62), Expect = 2.0
Identities = 12/27 (44%), Positives = 14/27 (51%), Gaps = 2/27 (7%)
Query: 68 IAIETEKIATDVLKDLESQRETLQRTR 94
I ET + VLK E+QRE L T
Sbjct: 264 ITCETLRDTAGVLK--EAQREILLLTL 288
>gnl|CDD|145192 pfam01893, UPF0058, Uncharacterized protein family UPF0058. This
archaebacterial protein has no known function.
Length = 88
Score = 26.1 bits (58), Expect = 3.0
Identities = 10/35 (28%), Positives = 17/35 (48%)
Query: 23 FLLSEYHVEYFSENSTNINEEQSQRLLDTSEEIER 57
FLL E SE+ + S+RL + +E+ +
Sbjct: 54 FLLGNAIAEAMSEDEFSSPRRVSKRLKELAEKALK 88
>gnl|CDD|112053 pfam03222, Trp_Tyr_perm, Tryptophan/tyrosine permease family.
Length = 393
Score = 27.2 bits (61), Expect = 3.0
Identities = 9/28 (32%), Positives = 17/28 (60%), Gaps = 4/28 (14%)
Query: 3 LSVPT----GGFLGTELALLISWCFLLS 26
L++P GF+ + L L++SW +L+
Sbjct: 22 LALPVATAGAGFIPSLLLLILSWFLMLA 49
>gnl|CDD|129810 TIGR00727, ISP4_OPT, small oligopeptide transporter, OPT family.
This model represents a family of transporters of small
oligopeptides, demonstrated experimentally in three
different species of yeast. A set of related proteins
from the plant Arabidopsis thaliana forms an outgroup to
the yeast set by neighbor joining analysis but is
remarkably well conserved and is predicted here to have
equivalent function [Transport and binding proteins,
Amino acids, peptides and amines].
Length = 681
Score = 27.1 bits (60), Expect = 3.3
Identities = 9/31 (29%), Positives = 15/31 (48%)
Query: 102 FINLACGSMICQTVWTWWGGAPPQSLNWNLL 132
++ AC + VW W P+ L+W +L
Sbjct: 581 WLIGACIGIFFWLVWKKWPKFYPRYLDWPML 611
>gnl|CDD|219286 pfam07072, DUF1342, Protein of unknown function (DUF1342). This
family consists of several hypothetical bacterial
proteins of around 250 residues in length. Members of
this family are often known as YacF after the
Escherichia coli protein. The function of this family
is unknown.
Length = 211
Score = 26.7 bits (60), Expect = 3.4
Identities = 10/18 (55%), Positives = 15/18 (83%)
Query: 77 TDVLKDLESQRETLQRTR 94
+++LKDLE QR+TL + R
Sbjct: 43 SELLKDLERQRQTLLKWR 60
>gnl|CDD|220464 pfam09903, DUF2130, Uncharacterized protein conserved in bacteria
(DUF2130). This domain, found in various hypothetical
prokaryotic proteins, has no known function.
Length = 267
Score = 26.8 bits (60), Expect = 3.5
Identities = 13/67 (19%), Positives = 24/67 (35%), Gaps = 16/67 (23%)
Query: 27 EYHVEYFSENSTNINEEQSQRLLDTSEEIERTGKHLETGYRIAIETE--------KIATD 78
E V+ F ++++E + I++ K LE + + KIA
Sbjct: 201 EAIVKNFELAQKDLDKE--------IKAIDKAWKKLEKQIEAVLGSTNNLRGANNKIAGL 252
Query: 79 VLKDLES 85
+K L
Sbjct: 253 TIKKLTR 259
>gnl|CDD|178606 PLN03043, PLN03043, Probable pectinesterase/pectinesterase
inhibitor; Provisional.
Length = 538
Score = 27.1 bits (60), Expect = 3.9
Identities = 19/65 (29%), Positives = 26/65 (40%)
Query: 57 RTGKHLETGYRIAIETEKIATDVLKDLESQRETLQRTRTRHSHTDFINLACGSMICQTVW 116
RT + TG I T + A D+ D S L R +S T ++ G +I W
Sbjct: 409 RTDPNQNTGISIINCTIEAAPDLAMDPNSTMNFLGRPWKPYSRTVYMQSYIGDLIQPVGW 468
Query: 117 TWWGG 121
W G
Sbjct: 469 LEWNG 473
>gnl|CDD|235389 PRK05287, PRK05287, hypothetical protein; Provisional.
Length = 250
Score = 26.7 bits (60), Expect = 4.3
Identities = 9/15 (60%), Positives = 13/15 (86%)
Query: 77 TDVLKDLESQRETLQ 91
+D+LK+LE QR+ LQ
Sbjct: 61 SDLLKELERQRQKLQ 75
>gnl|CDD|151872 pfam11433, DUF3198, Protein of unknown function (DUF3198). Some
members in this family of proteins are annotated as
membrane proteins however this cannot be confirmed.
Currently, this archaeal family has no known function.
Length = 51
Score = 24.9 bits (54), Expect = 4.3
Identities = 12/35 (34%), Positives = 15/35 (42%)
Query: 40 INEEQSQRLLDTSEEIERTGKHLETGYRIAIETEK 74
IN E + E+ER K L Y I +E K
Sbjct: 11 INSESKSVFVRNLTELERLAKRLGKSYEIQLEEAK 45
>gnl|CDD|131688 TIGR02640, gas_vesic_GvpN, gas vesicle protein GvpN. Members of
this family are the GvpN protein associated with the
production of gas vesicles produced in some prokaryotes
to give cells buoyancy. This family belongs to a larger
family of ATPases (pfam07728) [Cellular processes,
Other].
Length = 262
Score = 26.7 bits (59), Expect = 4.8
Identities = 9/54 (16%), Positives = 24/54 (44%)
Query: 38 TNINEEQSQRLLDTSEEIERTGKHLETGYRIAIETEKIATDVLKDLESQRETLQ 91
T++ E+ + ++ E +G + +G R ++ ++AT ++ E
Sbjct: 198 TDVAEDSAATIVRLVREFRASGDEITSGLRASLMIAEVATQQDIPVDVDDEDFV 251
>gnl|CDD|99865 cd06112, citrate_synt_like_1_1, Citrate synthase (CS) catalyzes the
condensation of acetyl coenzyme A (AcCoA) and
oxalacetate (OAA) to form citrate and coenzyme A (CoA),
the first step in the oxidative citric acid cycle (TCA
or Krebs cycle). Peroxisomal CS is involved in the
glyoxylate cycle. This group also includes CS proteins
which functions as a 2-methylcitrate synthase (2MCS).
2MCS catalyzes the condensation of propionyl-CoA (PrCoA)
and OAA to form 2-methylcitrate and CoA during
propionate metabolism. This group contains proteins
which functions exclusively as either a CS or a 2MCS, as
well as those with relaxed specificity which have dual
functions as both a CS and a 2MCS. The overall CS
reaction is thought to proceed through three partial
reactions and involves both closed and open
conformational forms of the enzyme: a) the carbanion or
equivalent is generated from AcCoA by base abstraction
of a proton, b) the nucleophilic attack of this
carbanion on OAA to generate citryl-CoA, and c) the
hydrolysis of citryl-CoA to produce citrate and CoA.
There are two types of CSs: type I CS and type II CSs.
Type I CSs are found in eukarya, gram-positive bacteria,
archaea, and in some gram-negative bacteria and are
homodimers with both subunits participating in the
active site. Type II CSs are unique to gram-negative
bacteria and are homohexamers of identical subunits
(approximated as a trimer of dimers). Some type II CSs
are strongly and specifically inhibited by NADH through
an allosteric mechanism.
Length = 373
Score = 26.6 bits (59), Expect = 4.8
Identities = 9/33 (27%), Positives = 17/33 (51%)
Query: 48 LLDTSEEIERTGKHLETGYRIAIETEKIATDVL 80
L +E++ L Y IA+E E++ ++L
Sbjct: 271 LQKLAEDLFAKMGELSKLYEIALEVERLCEELL 303
>gnl|CDD|172635 PRK14146, PRK14146, heat shock protein GrpE; Provisional.
Length = 215
Score = 26.2 bits (57), Expect = 5.7
Identities = 16/67 (23%), Positives = 33/67 (49%)
Query: 39 NINEEQSQRLLDTSEEIERTGKHLETGYRIAIETEKIATDVLKDLESQRETLQRTRTRHS 98
N+N E+SQ + + ++E G ET + ++ K + LKD ++ + R S
Sbjct: 32 NMNSEESQTITEETQEQAVEGAETETSLQKELDNAKKEIESLKDSWARERAEFQNFKRRS 91
Query: 99 HTDFINL 105
+F+++
Sbjct: 92 AQEFVSI 98
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily
archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and C-terminal
domains of this protein are well conserved, but the
central hinge region is skewed in composition and highly
divergent [Cellular processes, Cell division, DNA
metabolism, Chromosome-associated proteins].
Length = 1164
Score = 26.6 bits (59), Expect = 6.4
Identities = 10/43 (23%), Positives = 20/43 (46%)
Query: 53 EEIERTGKHLETGYRIAIETEKIATDVLKDLESQRETLQRTRT 95
+ +E + LE +AI+ + L +L+ +R L+ R
Sbjct: 961 QRVEEEIRALEPVNMLAIQEYEEVLKRLDELKEKRAKLEEERK 1003
>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional.
Length = 880
Score = 26.5 bits (59), Expect = 6.5
Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 4/47 (8%)
Query: 46 QRLLDTSEEIERTGKHLETGYRIAIETEKIATDVLKDLESQRETLQR 92
L + EEIE E A ET A +VL++ E +RE L+
Sbjct: 213 SELAELDEEIE----RYEEQREQARETRDEADEVLEEHEERREELET 255
>gnl|CDD|129194 TIGR00086, smpB, SsrA-binding protein. This model describes the
SsrA-binding protein, also called tmRNA binding
protein, small protein B, and SmpB. The small, stable
RNA SsrA (also called tmRNA or 10Sa RNA) recognizes
stalled ribosomes such as occur during translation from
message that lacks a stop codon. It becomes charged
with Ala like a tRNA, then acts as mRNA to resume
translation started with the defective mRNA. The short
C-terminal peptide tag added by the SsrA system marks
the abortively translated protein for degradation. SmpB
binds SsrA after its aminoacylation but before the
coupling of the Ala to the nascent polypeptide chain
and is an essential part of the SsrA peptide tagging
system. SmpB has been associated with the survival of
bacterial pathogens in conditions of stress. It is
universal in the first 100 sequenced bacterial genomes
[Protein synthesis, Other].
Length = 144
Score = 25.7 bits (57), Expect = 6.7
Identities = 12/47 (25%), Positives = 23/47 (48%), Gaps = 1/47 (2%)
Query: 23 FLLSEYHVEYFSENSTNINEEQSQRLLDTSEEIER-TGKHLETGYRI 68
+L + + Y N N + + ++LL +EI++ GK E G +
Sbjct: 52 WLKNMHIAPYKFGNYFNHDPRRPRKLLLHKKEIDKLQGKVKEKGLTL 98
>gnl|CDD|226948 COG4582, COG4582, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 244
Score = 25.9 bits (57), Expect = 7.1
Identities = 8/21 (38%), Positives = 16/21 (76%)
Query: 71 ETEKIATDVLKDLESQRETLQ 91
E ++ T++LK+L+ Q++ LQ
Sbjct: 52 ERGEVRTELLKELDRQQQKLQ 72
>gnl|CDD|234141 TIGR03185, DNA_S_dndD, DNA sulfur modification protein DndD. This
model describes the DndB protein encoded by an operon
associated with a sulfur-containing modification to DNA.
The operon is sporadically distributed in bacteria, much
like some restriction enzyme operons. DndD is described
as a putative ATPase. The small number of examples known
so far include species from among the Firmicutes,
Actinomycetes, Proteobacteria, and Cyanobacteria [DNA
metabolism, Restriction/modification].
Length = 650
Score = 26.2 bits (58), Expect = 7.8
Identities = 17/62 (27%), Positives = 31/62 (50%), Gaps = 6/62 (9%)
Query: 41 NEEQSQRLLDTSEEI-ERTGKHLETGYRIAIETEKIATDVLKDLESQRETLQRTRTRHSH 99
EEQSQ+ T EE+ ER + LE+ ++A+ E +K++ ++ + + T S
Sbjct: 311 KEEQSQQNQLTQEELEERDKELLESLPKLALPAE-----HVKEIAAELAEIDKPATTDSE 365
Query: 100 TD 101
Sbjct: 366 IP 367
>gnl|CDD|129733 TIGR00647, MG103, conserved hypothetical protein. [Hypothetical
proteins, Conserved].
Length = 279
Score = 26.0 bits (57), Expect = 7.9
Identities = 12/38 (31%), Positives = 18/38 (47%), Gaps = 5/38 (13%)
Query: 26 SEYHVEYFSENSTNINEEQSQRLLDTSEEIERTGKHLE 63
S +H++ S NEEQ +L E + T K L+
Sbjct: 119 SNFHLQISS-----NNEEQIDQLCKLFNEFKLTSKTLQ 151
>gnl|CDD|214599 smart00283, MA, Methyl-accepting chemotaxis-like domains
(chemotaxis sensory transducer). Thought to undergo
reversible methylation in response to attractants or
repellants during bacterial chemotaxis.
Length = 262
Score = 25.7 bits (57), Expect = 7.9
Identities = 16/68 (23%), Positives = 25/68 (36%)
Query: 29 HVEYFSENSTNINEEQSQRLLDTSEEIERTGKHLETGYRIAIETEKIATDVLKDLESQRE 88
V E EEQ++ L + +E +E +E A E A + E RE
Sbjct: 1 DVSEAVEEIAAGAEEQAEELEELAERMEELSASIEEVAANADEIAATAQSAAEAAEEGRE 60
Query: 89 TLQRTRTR 96
++ T
Sbjct: 61 AVEDAITA 68
>gnl|CDD|219797 pfam08326, ACC_central, Acetyl-CoA carboxylase, central region.
The region featured in this family is found in various
eukaryotic acetyl-CoA carboxylases, N-terminal to the
catalytic domain (pfam01039). This enzyme (EC:6.4.1.2)
is involved in the synthesis of long-chain fatty acids,
as it catalyzes the rate-limiting step in this process.
Length = 707
Score = 26.1 bits (58), Expect = 8.5
Identities = 13/55 (23%), Positives = 16/55 (29%), Gaps = 8/55 (14%)
Query: 17 LLISWCFLLSEYHVEYFSENSTNINEEQSQRLL---DTSEEIERTG-----KHLE 63
+ SW F L H + + S L ERTG LE
Sbjct: 354 PIASWEFQLPSSHSSRLNGIPSESTRAASDSDLSAVVEKRSEERTGVMVALDDLE 408
>gnl|CDD|151320 pfam10871, DUF2748, Protein of unknown function (DUF2748). This
is a bacterial family of proteins with unknown
function.
Length = 452
Score = 25.7 bits (56), Expect = 9.2
Identities = 13/47 (27%), Positives = 20/47 (42%)
Query: 33 FSENSTNINEEQSQRLLDTSEEIERTGKHLETGYRIAIETEKIATDV 79
FSE + NIN S L+ I T + Y+ E +K+ +
Sbjct: 49 FSEPALNINIAISNEELNDPHLIHETKALFQNIYKKIAEDDKVIHKI 95
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
0.317 0.132 0.409
Gapped
Lambda K H
0.267 0.0788 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,822,714
Number of extensions: 577698
Number of successful extensions: 704
Number of sequences better than 10.0: 1
Number of HSP's gapped: 704
Number of HSP's successfully gapped: 38
Length of query: 138
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 51
Effective length of database: 7,078,804
Effective search space: 361019004
Effective search space used: 361019004
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (24.5 bits)