RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9124
(213 letters)
>gnl|CDD|216614 pfam01625, PMSR, Peptide methionine sulfoxide reductase. This
enzyme repairs damaged proteins. Methionine sulfoxide
in proteins is reduced to methionine.
Length = 147
Score = 78.4 bits (194), Expect = 1e-18
Identities = 27/58 (46%), Positives = 35/58 (60%), Gaps = 2/58 (3%)
Query: 15 KTAVLAMGCFWAPDGLFGTTKGVLRTKVGYSGGTTENPTYRNIPAFT--EQEVVVVEY 70
+TA A GCFW + +F GV+ T+VGY+GG TENPTY + + T E V V Y
Sbjct: 1 ETATFAGGCFWGVEAVFEKLPGVISTEVGYAGGDTENPTYEEVCSGTTGHAEAVRVTY 58
>gnl|CDD|223303 COG0225, MsrA, Peptide methionine sulfoxide reductase
[Posttranslational modification, protein turnover,
chaperones].
Length = 174
Score = 70.7 bits (174), Expect = 2e-15
Identities = 25/61 (40%), Positives = 30/61 (49%), Gaps = 2/61 (3%)
Query: 12 NNTKTAVLAMGCFWAPDGLFGTTKGVLRTKVGYSGGTTENPTYRNIPAFT--EQEVVVVE 69
+ A A GCFW + F GVL T GY+GG T NPTY + + T E V V
Sbjct: 4 AGMEKAYFAGGCFWGVEAYFEQIPGVLSTVSGYAGGHTPNPTYEEVCSGTTGHAEAVEVT 63
Query: 70 Y 70
Y
Sbjct: 64 Y 64
>gnl|CDD|237597 PRK14054, PRK14054, methionine sulfoxide reductase A;
Provisional.
Length = 172
Score = 70.2 bits (173), Expect = 3e-15
Identities = 24/44 (54%), Positives = 29/44 (65%)
Query: 12 NNTKTAVLAMGCFWAPDGLFGTTKGVLRTKVGYSGGTTENPTYR 55
+TAVLA GCFW + F KGV+ T+VGY+GG ENPTY
Sbjct: 1 MMMETAVLAGGCFWGMEAPFDRVKGVISTRVGYTGGHVENPTYE 44
>gnl|CDD|235499 PRK05550, PRK05550, bifunctional methionine sulfoxide reductase B/A
protein; Provisional.
Length = 283
Score = 68.0 bits (167), Expect = 1e-13
Identities = 25/60 (41%), Positives = 35/60 (58%), Gaps = 2/60 (3%)
Query: 13 NTKTAVLAMGCFWAPDGLFGTTKGVLRTKVGYSGGTTENPTYRNIPAFTEQ--EVVVVEY 70
+T+ A+ A GCFW + F GVL + GY+GG T+NPTY + + T E V VE+
Sbjct: 126 DTEEAIFAGGCFWGVEYYFKKLPGVLSVESGYTGGDTKNPTYEQVCSGTTGHAEAVRVEF 185
>gnl|CDD|237269 PRK13014, PRK13014, methionine sulfoxide reductase A;
Provisional.
Length = 186
Score = 61.6 bits (150), Expect = 5e-12
Identities = 24/61 (39%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 12 NNTKTAVLAMGCFWAPDGLFGTTKGVLRTKVGYSGGTTENPTYRNIPAFT--EQEVVVVE 69
+ +TA A GCFW +G+F GV+ GYSGG +NPTY + T E V +
Sbjct: 6 DGMETATFAGGCFWGVEGVFQHVPGVVSVVSGYSGGHVDNPTYEQVCTGTTGHAEAVQIT 65
Query: 70 Y 70
Y
Sbjct: 66 Y 66
>gnl|CDD|234604 PRK00058, PRK00058, methionine sulfoxide reductase A;
Provisional.
Length = 213
Score = 61.8 bits (151), Expect = 6e-12
Identities = 22/43 (51%), Positives = 26/43 (60%)
Query: 13 NTKTAVLAMGCFWAPDGLFGTTKGVLRTKVGYSGGTTENPTYR 55
+ A+ MGCFW + LF GV T VGY+GG T NPTYR
Sbjct: 44 GMEQAIFGMGCFWGAERLFWQLPGVYSTAVGYAGGYTPNPTYR 86
>gnl|CDD|129496 TIGR00401, msrA, methionine-S-sulfoxide reductase. This model
describes peptide methionine sulfoxide reductase
(MsrA), a repair enzyme for proteins that have been
inactivated by oxidation. The enzyme from E. coli is
coextensive with this model and has enzymatic activity.
However, in all completed genomes in which this module
is present, a second protein module, described in
TIGR00357, is also found, and in several cases as part
of the same polypeptide chain: N-terminal to this
module in Helicobacter pylori and Haemophilus
influenzae (as in PilB of Neisseria gonorrhoeae) but
C-terminal to it in Treponema pallidum. PilB,
containing both domains, has been shown to be important
for the expression of adhesins in certain pathogens
[Protein fate, Protein modification and repair,
Cellular processes, Adaptations to atypical
conditions].
Length = 149
Score = 58.2 bits (141), Expect = 5e-11
Identities = 23/58 (39%), Positives = 29/58 (50%), Gaps = 2/58 (3%)
Query: 15 KTAVLAMGCFWAPDGLFGTTKGVLRTKVGYSGGTTENPTYRNIPAFT--EQEVVVVEY 70
+ A A GCFW + F GV+ T VGY+ G T NPTY + + E V V Y
Sbjct: 1 EIATFAGGCFWGTEKYFRLIPGVVSTAVGYTNGYTPNPTYEEVCSGDTGHAEAVQVTY 58
>gnl|CDD|184456 PRK14018, PRK14018, trifunctional thioredoxin/methionine sulfoxide
reductase A/B protein; Provisional.
Length = 521
Score = 48.7 bits (116), Expect = 7e-07
Identities = 23/69 (33%), Positives = 34/69 (49%), Gaps = 1/69 (1%)
Query: 3 KTMSQTNGQNNTKTAVLAMGCFWAPDGLFGTTKGVLRTKVGYSGGTTENPTYRNIPAFT- 61
+ + NT+T LA GCFW + F GV+ GY+ G T+NP+Y ++ +
Sbjct: 187 DGQKKDSKIMNTRTIYLAGGCFWGLEAYFQRIDGVVDAVSGYANGNTKNPSYEDVYRHSG 246
Query: 62 EQEVVVVEY 70
E V V Y
Sbjct: 247 HAETVKVTY 255
>gnl|CDD|235497 PRK05528, PRK05528, methionine sulfoxide reductase A;
Provisional.
Length = 156
Score = 30.4 bits (69), Expect = 0.34
Identities = 13/36 (36%), Positives = 16/36 (44%)
Query: 16 TAVLAMGCFWAPDGLFGTTKGVLRTKVGYSGGTTEN 51
T A GC W F T GV+ T+ G + G T
Sbjct: 3 TVYFAGGCLWGVQAFFKTLPGVIHTEAGRANGRTST 38
>gnl|CDD|185081 PRK15127, PRK15127, multidrug efflux system protein AcrB;
Provisional.
Length = 1049
Score = 29.9 bits (67), Expect = 1.0
Identities = 17/68 (25%), Positives = 34/68 (50%), Gaps = 9/68 (13%)
Query: 90 NSSNMTQTFTYASHPHVHHHDNHDNDTQYTKFQENIEY-TVLMPGDLYRKTISMESSCST 148
++ + T T+ S D D + Q ++ L+P ++ ++ +S+E S S+
Sbjct: 84 STGTVQITLTFES--------GTDADIAQVQVQNKLQLAMPLLPQEVQQQGVSVEKSSSS 135
Query: 149 FLLVSGVL 156
FL+V GV+
Sbjct: 136 FLMVVGVI 143
>gnl|CDD|182881 PRK10983, PRK10983, putative inner membrane protein; Provisional.
Length = 368
Score = 29.2 bits (66), Expect = 1.7
Identities = 12/28 (42%), Positives = 17/28 (60%), Gaps = 3/28 (10%)
Query: 140 ISMESSCSTFLLVSGVLGGLLFISAFLM 167
I M + L++SGV+GGL+ AF M
Sbjct: 300 IRMGADLPMILILSGVIGGLI---AFGM 324
>gnl|CDD|225786 COG3247, HdeD, Uncharacterized conserved protein [Function
unknown].
Length = 185
Score = 28.7 bits (65), Expect = 1.7
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 150 LLVSGVLGGLLFISAFLMCYLASRLQTAL 178
LL+SG+L LL I A L + + T L
Sbjct: 78 LLLSGILSILLGILAGFNPGLGALVLTYL 106
>gnl|CDD|219062 pfam06496, DUF1097, Protein of unknown function (DUF1097). This
family consists of several bacterial putative membrane
proteins.
Length = 140
Score = 27.9 bits (63), Expect = 2.3
Identities = 13/30 (43%), Positives = 16/30 (53%), Gaps = 7/30 (23%)
Query: 150 LLVSGVLGG-------LLFISAFLMCYLAS 172
+L SG+LGG L I AF+MC A
Sbjct: 60 ILGSGLLGGNPLAGYILTGIVAFVMCLQAK 89
>gnl|CDD|219898 pfam08551, DUF1751, Eukaryotic integral membrane protein (DUF1751).
This domain is found in eukaryotic integral membrane
proteins. YOL107W, a Saccharomyces cerervisiae protein,
has been shown to localise COP II vesicles.
Length = 99
Score = 27.2 bits (61), Expect = 2.8
Identities = 10/37 (27%), Positives = 17/37 (45%)
Query: 149 FLLVSGVLGGLLFISAFLMCYLASRLQTALATRYHSN 185
F+LV V+ LL +L+ Y+ +R + L
Sbjct: 50 FILVVNVITNLLVFLYYLLLYMITRSERYLDVPISGG 86
>gnl|CDD|183603 PRK12574, PRK12574, putative monovalent cation/H+ antiporter
subunit B; Reviewed.
Length = 141
Score = 27.3 bits (61), Expect = 3.9
Identities = 10/18 (55%), Positives = 15/18 (83%)
Query: 154 GVLGGLLFISAFLMCYLA 171
G +GGL+F SAF++ +LA
Sbjct: 37 GFIGGLIFSSAFILMFLA 54
>gnl|CDD|234467 TIGR04094, adjacent_YSIRK, YSIRK-targeted surface antigen
transcriptional regulator. Bacteria whose genomes
encode only one protein with the YSIRK variant form of
signal peptide (TIGR01168) were examined for conserved
genes near that one tagged protein. This protein is
found adjacent to at various classes of repetitive or
low-complexity YSIRK proteins (whether unique in genome
or not), in a range of species (Enterococcus faecalis
X98, Ruminococcus torques, Coprobacillus sp. D7,
Lysinibacillus fusiformis ZC1, Streptococcus equi subsp.
equi 4047, etc). The affliated YSIRK proteins include
Streptococcal protective antigen (see PMID:19865839) and
proteins with the Rib/alpha/Esp surface antigen repeat
(see TIGR02331). The last quarter of this protein has an
AraC family helix-turn-helix (HTH)transcriptional
regulator domain.
Length = 383
Score = 27.7 bits (62), Expect = 4.4
Identities = 14/50 (28%), Positives = 19/50 (38%), Gaps = 1/50 (2%)
Query: 113 DNDTQYTKFQENIEYTVLMPGDLYRKTISMESSCSTFLLVSGVLGGLLFI 162
D D K E+ + T L+P D FL SG+L + I
Sbjct: 17 DKDFSVLKSYES-DRTKLLPYDFKLTLNKKSKETIQFLFFSGILNEMFLI 65
>gnl|CDD|220027 pfam08808, RES, RES domain. This presumed domain contains 3 highly
conserved polar groups that could form an active site.
These are an arginine, glutamate and serine, hence the
RES domain. The domain is found widely distributed in
bacteria. The domain is about 150 residues in length.
Length = 163
Score = 27.2 bits (60), Expect = 4.6
Identities = 9/29 (31%), Positives = 11/29 (37%), Gaps = 1/29 (3%)
Query: 167 MCYLASRLQTALA-TRYHSNNLDHFVREH 194
+ Y A L TALA H + R
Sbjct: 36 VLYAAESLATALAEVLVHGDPALLLTRYV 64
>gnl|CDD|222449 pfam13908, Shisa, Wnt and FGF inhibitory regulator. Shisa is a
transcription factor-type molecule that physically
interacts with immature forms of the Wnt receptor
Frizzled and the FGF receptor within the endoplasmic
reticulum to inhibit their post-translational maturation
and trafficking to the cell surface.
Length = 177
Score = 27.1 bits (60), Expect = 5.2
Identities = 7/58 (12%), Positives = 14/58 (24%), Gaps = 3/58 (5%)
Query: 65 VVVVEYCLDLFEPSGHGKRRRRRDSNSSNMTQTFTYASHPHVHHHDNHDNDTQYTKFQ 122
+++ C R +R + + T P QY +
Sbjct: 92 IIICFTCCCCCLEKAC---RPQRPVMTRATSTTVQTTPLPQPPSTAPSYPGPQYQGYH 146
>gnl|CDD|189020 cd00128, PIN_FEN1_EXO1-like, PIN domains of Flap Endonuclease-1
(FEN1)-like and Exonuclease-1 (EXO1)-like nucleases,
structure-specific, divalent-metal-ion dependent, 5'
nucleases. PIN (PilT N terminus) domain of Flap
Endonuclease-1 (FEN1) and Exonuclease-1 (EXO1)-like
nucleases: FEN1, EXO1, Mkt1, Gap endonuclease 1 (GEN1)
and Xeroderma pigmentosum complementation group G (XPG)
nuclease are members of the structure-specific, 5'
nuclease family that catalyzes hydrolysis of DNA
duplex-containing nucleic acid structures during DNA
replication, repair, and recombination. These nucleases
contain a PIN domain with a helical arch/clamp region (I
domain) of variable length (approximately 30 to 800
residues) and a H3TH (helix-3-turn-helix) domain, an
atypical helix-hairpin-helix-2-like region. Both the
H3TH domain (not included here) and the helical
arch/clamp region are involved in DNA binding. Most
nucleases within this family also have a carboxylate
rich active site that is involved in binding essential
divalent metal ion cofactors (Mg2+/Mn2+). Some nucleases
in this family have C-terminal extensions that act as
interaction sites for other proteins.
Length = 209
Score = 27.1 bits (60), Expect = 5.3
Identities = 12/57 (21%), Positives = 17/57 (29%), Gaps = 8/57 (14%)
Query: 81 GKRRRRRDSNSSNMTQT-----FTYASHPHVHHHD---NHDNDTQYTKFQENIEYTV 129
GKR R + T+ F A P + + + E I Y V
Sbjct: 87 GKRTEARAEAEISSTEASYIGQFIEAQKPFKRNVTITPKAYQNCKILLSLEGIPYVV 143
>gnl|CDD|145103 pfam01770, Folate_carrier, Reduced folate carrier. The reduced
folate carrier (a transmembrane glycoprotein) transports
reduced folate into mammalian cells via the carrier
mediated mechanism (as opposed to the receptor mediated
mechanism) it also transports cytotoxic folate analogues
used in chemotherapy, such as methotrexate (MTX).
Mammalian cells have an absolute requirement for
exogenous folates which are needed for growth, and
biosynthesis of macromolecules.
Length = 410
Score = 27.2 bits (61), Expect = 6.5
Identities = 8/25 (32%), Positives = 13/25 (52%), Gaps = 4/25 (16%)
Query: 151 LVSGVLGGLLFISAF----LMCYLA 171
+ S + GLLF+ F +CY+
Sbjct: 320 VFSALQAGLLFLMGFTRNIWVCYVG 344
>gnl|CDD|225401 COG2845, COG2845, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 354
Score = 27.1 bits (60), Expect = 8.6
Identities = 10/24 (41%), Positives = 11/24 (45%)
Query: 160 LFISAFLMCYLASRLQTALATRYH 183
L + LM LA L ALAT
Sbjct: 120 LVVGDSLMQGLAEGLDKALATSPG 143
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
0.319 0.131 0.396
Gapped
Lambda K H
0.267 0.0635 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,296,967
Number of extensions: 915277
Number of successful extensions: 964
Number of sequences better than 10.0: 1
Number of HSP's gapped: 962
Number of HSP's successfully gapped: 27
Length of query: 213
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 120
Effective length of database: 6,812,680
Effective search space: 817521600
Effective search space used: 817521600
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: 57 (25.9 bits)