RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16527
(562 letters)
>gnl|CDD|218009 pfam04290, DctQ, Tripartite ATP-independent periplasmic
transporters, DctQ component. The function of the
members of this family is unknown, but DctQ homologues
are invariably found in the tripartite ATP-independent
periplasmic transporters.
Length = 133
Score = 41.1 bits (97), Expect = 2e-04
Identities = 13/81 (16%), Positives = 28/81 (34%), Gaps = 10/81 (12%)
Query: 110 ERRKLLCAVLFHAVALTCVIWSLYVLIERTVDEI----YTGILEWPFWIKLIVVVIGFTG 165
R + + +L +AL + + V T L P W + + +GF
Sbjct: 59 PRVRRVLDLLAALLALAFAAVLAWAGWDLVVASAGSGETTPALGIPLWWVYLALPVGF-- 116
Query: 166 GVVFMYIQCKAYLHICQRWKA 186
+ ++ A L + + +
Sbjct: 117 --ALLALR--ALLRLLRLLRG 133
>gnl|CDD|212048 cd11478, SLC5sbd_u2, Uncharacterized bacterial solute carrier 5
subfamily; putative solute-binding domain. SLC5 (also
called the sodium/glucose cotransporter family or solute
sodium symporter family) is a family of proteins that
co-transports Na+ with sugars, amino acids, inorganic
ions or vitamins. Prokaryotic members of this family
include Vibrio parahaemolyticus glucose/galactose
(vSGLT), and Escherichia coli proline (PutP) and
pantothenate (PutF) cotransporters. One member of the
SLC5 family, human SGLT3, has been characterized as a
glucose sensor and not a transporter. This subfamily
belongs to the solute carrier 5 (SLC5) transporter
family.
Length = 495
Score = 37.3 bits (87), Expect = 0.018
Identities = 13/73 (17%), Positives = 32/73 (43%), Gaps = 23/73 (31%)
Query: 109 MERR-----KLLCAVLFHAVALTCV----IWSLYVLIERTVDEIYTGILEWPFWIKLIVV 159
++ R + L A+ F A+ + +++L ++++ +L WPFW +++
Sbjct: 105 LKLRFNESTRTLNAISF-AIMTILMSGINLYALALVLQ--------VLLGWPFWASILL- 154
Query: 160 VIGFTGGVVFMYI 172
+ +V Y
Sbjct: 155 ----SAAIVLAYT 163
>gnl|CDD|225632 COG3090, DctM, TRAP-type C4-dicarboxylate transport system, small
permease component [Carbohydrate transport and
metabolism].
Length = 177
Score = 36.2 bits (84), Expect = 0.021
Identities = 12/86 (13%), Positives = 30/86 (34%), Gaps = 10/86 (11%)
Query: 96 LSVRSWEHLEMTGM-----ERRKLLCAVLFHAVALTC---VIWSLYVLIERTVDEIYTGI 147
VR H+ + + R + + ++ + L +IW + L + +
Sbjct: 66 YGVREGGHIGVDVLVNLLPPRARKILRIIADLLILVFFLLLIWGGWKLAAINWSQ-GSPA 124
Query: 148 LEWPFWIKLIVVVIGFTGGVVFMYIQ 173
L P + + IG + +++
Sbjct: 125 LGIPMGWVYLALPIGG-VLMALRFLE 149
>gnl|CDD|148085 pfam06265, DUF1027, Protein of unknown function (DUF1027). This
family consists of several hypothetical bacterial
proteins of unknown function.
Length = 86
Score = 33.3 bits (77), Expect = 0.052
Identities = 13/32 (40%), Positives = 18/32 (56%), Gaps = 7/32 (21%)
Query: 285 LKGVRNLHIFFNEENRICVQKDEKQSRLVDYL 316
LKG F++++N+ KD K S L DYL
Sbjct: 48 LKG------FYDDDNKK-ATKDTKISTLQDYL 72
>gnl|CDD|218889 pfam06088, TLP-20, Nucleopolyhedrovirus telokin-like protein-20
(TLP20). This family consists of several
Nucleopolyhedrovirus telokin-like protein-20 (TLP20)
sequences. The function of this family is unknown but
TLP20 is known to shares some antigenic similarities to
the smooth muscle protein telokin although the amino
acid sequence shows no homologies to telokin.
Length = 162
Score = 32.3 bits (74), Expect = 0.33
Identities = 22/89 (24%), Positives = 30/89 (33%), Gaps = 13/89 (14%)
Query: 399 ESPVLNLQIKKAEIVIKFGGSPNENVANNTNDTAAVENDRGDNAVNININPEEAKAGSS- 457
+S +L+ A I G + V N V N R N + NI P K G
Sbjct: 50 DSQLLDALHNNAHSTITCG---DYTVVYN-----LVSNSRRINVILFNIKPTVLKKGGCI 101
Query: 458 -KLTELPNPDLKKKT--NESQADDEGSED 483
K+ N ++DE ED
Sbjct: 102 FKIV-YWNSKKFVSAPVPHHSSEDENDED 129
>gnl|CDD|237726 PRK14488, PRK14488, cbb3-type cytochrome c oxidase subunit I;
Provisional.
Length = 473
Score = 31.8 bits (73), Expect = 1.0
Identities = 22/80 (27%), Positives = 36/80 (45%), Gaps = 18/80 (22%)
Query: 121 HAVALTCV----IWSLYVLIER--TVDEIY-TGILEWPFWIKLIVVVIGFTGGVVFMYIQ 173
H+ AL V I +LY LI R + +Y ++ W FW+ I +V+ M++
Sbjct: 346 HSGALGWVGMISIGALYHLIPRLWGRERMYSLKLVNWHFWLATIGIVLYIAS----MWVA 401
Query: 174 CKAYLHICQ--RWKAYNSEG 191
I Q W+A + +G
Sbjct: 402 -----GIMQGLMWRAVDEDG 416
>gnl|CDD|212051 cd11482, SLC-NCS1sbd_NRT1-like, nucleobase-cation-symport-1 (NCS1)
transporter NRT1-like; solute-binding domain. This
fungal NCS1 subfamily includes various Saccharomyces
cerevisiae transporters: nicotinamide riboside
transporter 1 (Nrt1p, also called Thi71p), Dal4p
(allantoin permease), Fui1p (uridine permease), Fur4p
(uracil permease), and Thi7p (thiamine transporter).
NCS1s are essential components of salvage pathways for
nucleobases and related metabolites. NCS1s belong to a
superfamily which also contains the solute carrier 5
family sodium/glucose transporters, and solute carrier 6
family neurotransmitter transporters.
Length = 478
Score = 31.7 bits (73), Expect = 1.2
Identities = 16/71 (22%), Positives = 28/71 (39%), Gaps = 18/71 (25%)
Query: 100 SWEHLEMT-----GMERRKLLCAVLFHAVALTCVIWSLYVLIERTVDEIYTGILEWPFWI 154
S+ ++ T G+ +LL LF + L L++ E+ L F +
Sbjct: 129 SFLNIPNTLPASAGITTAQLLGFFLFWLIQLPF----LFIPPEK---------LRHLFTV 175
Query: 155 KLIVVVIGFTG 165
K ++V I G
Sbjct: 176 KAVIVPIAAFG 186
>gnl|CDD|225817 COG3278, CcoN, Cbb3-type cytochrome oxidase, subunit 1
[Posttranslational modification, protein turnover,
chaperones].
Length = 482
Score = 30.4 bits (69), Expect = 2.4
Identities = 22/80 (27%), Positives = 36/80 (45%), Gaps = 18/80 (22%)
Query: 121 HAVALTCV----IWSLYVLIERT--VDEIY-TGILEWPFWIKLIVVVIGFTGGVVFMYIQ 173
HA AL V I S+Y ++ R + +Y ++ FW+ I +V+ M+I
Sbjct: 352 HAGALGWVGFITIGSIYHMVPRLFGRERMYSLRLVNAHFWLATIGIVLYI----AAMWIA 407
Query: 174 CKAYLHICQ--RWKAYNSEG 191
I Q W+AY+ +G
Sbjct: 408 -----GITQGLMWRAYDEDG 422
>gnl|CDD|128983 smart00744, RINGv, The RING-variant domain is a C4HC3 zinc-finger
like motif found in a number of cellular and viral
proteins. Some of these proteins have been shown both
in vivo and in vitro to have ubiquitin E3 ligase
activity. The RING-variant domain is reminiscent of
both the RING and the PHD domains and may represent an
evolutionary intermediate. To describe this domain the
term PHD/LAP domain has been used in the past. Extended
description: The RING-variant (RINGv) domain contains a
C4HC3 zinc-finger-like motif similar to the PHD domain,
while some of the spacing between the Cys/His residues
follow a pattern somewhat closer to that found in the
RING domain. The RINGv domain, similar to the RING, PHD
and LIM domains, is thought to bind two zinc ions
co-ordinated by the highly conserved Cys and His
residues. RING variant domain: C-x (2) -C-x(10-45)-C-x
(1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to
a PHD: C-x(1-2) -C-x
(7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C
Classical RING domain: C-x (2) -C-x
(9-39)-C-x(1-3)-H-x(2-3)-C-x(2)-C-x(4-48) -C-x(2)-C.
Length = 49
Score = 27.3 bits (61), Expect = 2.5
Identities = 12/22 (54%), Positives = 12/22 (54%), Gaps = 1/22 (4%)
Query: 35 ICRICHCEVTPEASPDVSPAYC 56
ICRICH E P VSP C
Sbjct: 1 ICRICHDEGDEG-DPLVSPCRC 21
>gnl|CDD|221171 pfam11700, ATG22, Vacuole effluxer Atg22 like. Autophagy is a
major survival survival mechanism in which eukaryotes
recycle cellular nutrients during stress conditions.
Atg22, Avt3 and Avt4 are partially redundant vacuolar
effluxes, which mediate the efflux of leucine and other
amino acids resulting from autophagy. This family also
includes other transporter proteins.
Length = 475
Score = 30.3 bits (69), Expect = 2.8
Identities = 11/61 (18%), Positives = 24/61 (39%), Gaps = 4/61 (6%)
Query: 113 KLLCAVLFHAVALTCVIWSLYVLIERTVDEIYTGILEWPFWIKLIVVVIGFTGGVVFMYI 172
L A + + + SL +L +TV + T L + ++ + G ++ Y+
Sbjct: 283 LFLVAWFLLSDGIA-TVLSLAILFAKTVLGMSTAAL---TVLSILAQIAAVLGAFLWPYL 338
Query: 173 Q 173
Sbjct: 339 S 339
>gnl|CDD|235268 PRK04282, PRK04282, exosome complex RNA-binding protein Rrp42;
Provisional.
Length = 271
Score = 30.2 bits (69), Expect = 2.8
Identities = 9/41 (21%), Positives = 19/41 (46%), Gaps = 10/41 (24%)
Query: 268 VDPSWDEDMMSNTKSIDLKGVRNLHIFFNEENRIC-VQKDE 307
VDP+ +E+ + + + + I +E+ I +QK
Sbjct: 207 VDPTLEEESVMDAR---------ITITTDEDGNIVAIQKSG 238
>gnl|CDD|236412 PRK09204, secY, preprotein translocase subunit SecY; Reviewed.
Length = 426
Score = 29.7 bits (68), Expect = 4.3
Identities = 11/36 (30%), Positives = 18/36 (50%)
Query: 136 IERTVDEIYTGILEWPFWIKLIVVVIGFTGGVVFMY 171
I +T + TG L ++ LIV+ + VVF+
Sbjct: 199 IGQTFELARTGSLSILVFLLLIVLFLAVIAFVVFVE 234
>gnl|CDD|222701 pfam14349, SprA_N, Motility related/secretion protein. This domain
is found repeated three times in the N-terminal half of
the gliding motility-related SprA proteins. The role of
this domain in motility is uncertain. It is also found
in proteins required for secretion.
Length = 413
Score = 29.8 bits (67), Expect = 4.6
Identities = 30/139 (21%), Positives = 50/139 (35%), Gaps = 23/139 (16%)
Query: 322 SNPETTTSNVISRPEHDNINGGGTTWHIQIEKT------SAGPDITKAIDNRTFEEVTQA 375
S+ V P ++++ G T Q + S P ++A+ ++ + T
Sbjct: 182 SSLYVLPPGVGREPGNNSLFGINTNL--QFGEQSLTLVVSQLPSDSRAVSSKGGFKNTNF 239
Query: 376 ELDARPYRNTN-----EDYKVTCNNDDSESPVLNLQIKKAEIVIKFGGSPNENVANNTND 430
ELDAR Y+ D++ +N P + I + E+ P N
Sbjct: 240 ELDARQYKELRMFRLGTDFR---DNYYEALP-TGVDITRVEV------WPVTNKIPLDLL 289
Query: 431 TAAVENDRGDNAVNININP 449
TA + N NI NP
Sbjct: 290 TALKKTRNYGNTRNIVGNP 308
>gnl|CDD|183558 PRK12495, PRK12495, hypothetical protein; Provisional.
Length = 226
Score = 28.7 bits (64), Expect = 7.7
Identities = 21/110 (19%), Positives = 32/110 (29%)
Query: 435 ENDRGDNAVNININPEEAKAGSSKLTELPNPDLKKKTNESQADDEGSEDSLSGCGSPTCR 494
A + + EA A S ++ D + E++A D+ + S +
Sbjct: 67 PVTEDGAAGDDAGDGAEATAPSDAGSQASPDDDAQPAAEAEAADQSAPPEASSTSATDEA 126
Query: 495 LLPEPTEYNAATTSVRPKSYPFDKRQSRNSGTWTPNVEKENPTGSDQDMG 544
P A + R S P V E PT S D
Sbjct: 127 ATDPPATAAARDGPTPDPTAQPATPDERRSPRQRPPVSGEPPTPSTPDAH 176
>gnl|CDD|227468 COG5139, COG5139, Uncharacterized conserved protein [Function
unknown].
Length = 397
Score = 28.9 bits (64), Expect = 7.9
Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 5/64 (7%)
Query: 419 SPNENVANNTNDTAAVENDRGDNAVNININPEEAKAGSSKLTELPNPDLKKKTNESQADD 478
+P + A++ T EN+ N ++ P+E G+S + +PD +K NE A D
Sbjct: 15 TPEDGTASSQKSTINAENENTKQ--NQSMEPQETSKGTS--NDTKDPDNGEK-NEEAAID 69
Query: 479 EGSE 482
E S
Sbjct: 70 ENSN 73
>gnl|CDD|143465 cd07147, ALDH_F21_RNP123, Aldehyde dehydrogenase family 21A1-like.
Aldehyde dehydrogenase ALDH21A1 (gene name RNP123) was
first described in the moss Tortula ruralis and is
believed to play an important role in the detoxification
of aldehydes generated in response to desiccation- and
salinity-stress, and ALDH21A1 expression represents a
unique stress tolerance mechanism. So far, of plants,
only the bryophyte sequence has been observed, but
similar protein sequences from bacteria and archaea are
also present in this CD.
Length = 452
Score = 28.8 bits (65), Expect = 8.0
Identities = 16/43 (37%), Positives = 23/43 (53%), Gaps = 6/43 (13%)
Query: 300 RICVQK---DEKQSRLVDY---LETGEPSNPETTTSNVISRPE 336
R+ V + DE +SRLV L+TG+P + T +IS E
Sbjct: 268 RVLVHRSVYDEFKSRLVARVKALKTGDPKDDATDVGPMISESE 310
>gnl|CDD|146930 pfam04534, Herpes_UL56, Herpesvirus UL56 protein. In herpes
simplex virus type 2, UL56 is thought to be a
tail-anchored type II membrane protein involved in
vesicular trafficking. The C terminal hydrophobic region
is required for association with the cytoplasmic
membrane, and the N terminal proline-rich region is
important for the translocation of UL56 to the Golgi
apparatus and cytoplasmic vesicles.
Length = 198
Score = 28.5 bits (63), Expect = 8.3
Identities = 15/38 (39%), Positives = 22/38 (57%), Gaps = 5/38 (13%)
Query: 497 PEPTEYN---AATTSVRPK--SYPFDKRQSRNSGTWTP 529
P Y AA T+ +P S+PFD+ +S++SG W P
Sbjct: 143 DHPPTYATVCAARTTEQPMGLSWPFDQPRSQSSGLWRP 180
>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 = 29.0 bits (65), Expect = 8.4
Identities = 8/29 (27%), Positives = 10/29 (34%)
Query: 488 CGSPTCRLLPEPTEYNAATTSVRPKSYPF 516
G+ R + N A S YPF
Sbjct: 77 GGTDYSRQRRFASLNNCAFVSTEDVVYPF 105
>gnl|CDD|227510 COG5183, SSM4, Protein involved in mRNA turnover and stability
[RNA processing and modification].
Length = 1175
Score = 29.2 bits (65), Expect = 8.5
Identities = 8/22 (36%), Positives = 9/22 (40%), Gaps = 1/22 (4%)
Query: 35 ICRICHCEVTPEASPDVSPAYC 56
CRIC E + P P C
Sbjct: 14 SCRICRTEDIRD-DPLFHPCKC 34
>gnl|CDD|213316 cd05969, MACS_like_4, Uncharacterized subfamily of Acetyl-CoA
synthetase like family (ACS). This family is most
similar to acetyl-CoA synthetase. Acetyl-CoA synthetase
(ACS) catalyzes the formation of acetyl-CoA from
acetate, CoA, and ATP. Synthesis of acetyl-CoA is
carried out in a two-step reaction. In the first step,
the enzyme catalyzes the synthesis of acetyl-AMP
intermediate from acetate and ATP. In the second step,
acetyl-AMP reacts with CoA to produce acetyl-CoA. This
enzyme is only present in bacteria.
Length = 443
Score = 28.9 bits (65), Expect = 8.6
Identities = 12/32 (37%), Positives = 13/32 (40%), Gaps = 2/32 (6%)
Query: 310 SRLVDYLETGEPSNPETT--TSNVISRPEHDN 339
S L GEP NPE V+ P HD
Sbjct: 207 SSLRHIASVGEPLNPEVVVWGEKVLGMPIHDT 238
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
0.313 0.129 0.393
Gapped
Lambda K H
0.267 0.0738 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 27,708,624
Number of extensions: 2623053
Number of successful extensions: 1600
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1600
Number of HSP's successfully gapped: 26
Length of query: 562
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 460
Effective length of database: 6,413,494
Effective search space: 2950207240
Effective search space used: 2950207240
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 62 (27.6 bits)