RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3671
(266 letters)
>gnl|CDD|202989 pfam04379, DUF525, Protein of unknown function (DUF525). Members
of this family include the bacterial protein ApaG and
the C termini of some F-box proteins (pfam00646). F-box
proteins contain a carboxyl-terminal domain that
interacts with protein substrates, so this family may be
involved in protein-protein interaction. The function of
ApaG proteins is unknown, but mutations in the
Salmonella typhimurium ApaG homologue corD gives a
phenotype of low-level cobalt resistance and decreased
magnesium efflux by effects on the CorA magnesium
transport system.
Length = 90
Score = 99.9 bits (250), Expect = 5e-27
Identities = 37/78 (47%), Positives = 49/78 (62%), Gaps = 5/78 (6%)
Query: 191 SPTSSVYWWRYCIRLENLGELTVQLRERHWRIFSLSGTLETVRGRGVVGQEPVLSKSLP- 249
SP Y + Y I +ENLG TVQL RHW I +G +E VRG GVVG++P+L+ P
Sbjct: 6 SPEEGRYVFAYTITIENLGPETVQLLSRHWIITDANGKVEEVRGEGVVGEQPLLA---PG 62
Query: 250 -AFQYSSHVSLQAPSGHM 266
+F+Y+S L+ PSG M
Sbjct: 63 ESFEYTSGTPLETPSGSM 80
>gnl|CDD|180098 PRK05461, apaG, CO2+/MG2+ efflux protein ApaG; Reviewed.
Length = 127
Score = 96.8 bits (242), Expect = 2e-25
Identities = 40/96 (41%), Positives = 57/96 (59%), Gaps = 5/96 (5%)
Query: 173 TTENVRVTVIPFYMGCRDSPTSSVYWWRYCIRLENLGELTVQLRERHWRIFSLSGTLETV 232
T + V+V P Y+ + P Y + Y I +ENLG + VQL RHW I +G ++ V
Sbjct: 5 VTYGIEVSVQPRYLEEQSDPEEGRYVFAYTITIENLGRVPVQLLSRHWLITDANGRVQEV 64
Query: 233 RGRGVVGQEPVLSKSLP--AFQYSSHVSLQAPSGHM 266
RG GVVG++PVL+ P +F+Y+S L+ PSG M
Sbjct: 65 RGEGVVGEQPVLA---PGESFEYTSGAVLETPSGTM 97
>gnl|CDD|225515 COG2967, ApaG, Uncharacterized protein affecting Mg2+/Co2+
transport [Inorganic ion transport and metabolism].
Length = 126
Score = 82.4 bits (204), Expect = 8e-20
Identities = 35/94 (37%), Positives = 53/94 (56%), Gaps = 1/94 (1%)
Query: 173 TTENVRVTVIPFYMGCRDSPTSSVYWWRYCIRLENLGELTVQLRERHWRIFSLSGTLETV 232
++ ++ V V P Y+ + SP Y + Y + + NLGE+ VQL R+W I +G + V
Sbjct: 4 SSPDIEVQVQPRYLEEQSSPEEERYVFAYTVTIRNLGEVPVQLLSRYWLITDGNGRVTEV 63
Query: 233 RGRGVVGQEPVLSKSLPAFQYSSHVSLQAPSGHM 266
G GVVG++P+L +QY+S L PSG M
Sbjct: 64 EGEGVVGEQPLL-APGEEYQYTSGCPLDTPSGTM 96
>gnl|CDD|214961 smart00992, YccV-like, Hemimethylated DNA-binding protein YccV
like. YccV is a hemimethylated DNA binding protein
which has been shown to regulate dnaA gene expression.
The structure of one of the hypothetical proteins in
this family has been solved and it forms a beta sheet
structure with a terminating alpha helix.
Length = 98
Score = 60.7 bits (148), Expect = 3e-12
Identities = 27/127 (21%), Positives = 50/127 (39%), Gaps = 38/127 (29%)
Query: 13 QGKYSTGQLFLHRVFGYRGIVLFPWLARVYDRDIPNKRDKPSDVNGSVGKEVK-SKTHTF 71
K+ GQ+ H++FGYRG+V D + + + ++ + + F
Sbjct: 1 HAKFRIGQVVRHKLFGYRGVVF----------DWDPEFANTEEWYDEIPEDSRPPRDQPF 50
Query: 72 YQVLIDSRDCPYIRAQTEAVTFLGNQNSNKSLYAIPGLDYVAHEDILPYSCSH--EQPLH 129
Y VL+++ D Y+ YV+ +++ P + + PL
Sbjct: 51 YHVLVENDDSSYVA-------------------------YVSEQNLEPDTSGEPIDHPLL 85
Query: 130 HELFDKF 136
ELFD+F
Sbjct: 86 DELFDEF 92
>gnl|CDD|220004 pfam08755, YccV-like, Hemimethylated DNA-binding protein YccV like.
YccV is a hemimethylated DNA binding protein which has
been shown to regulate dnaA gene expression. The
structure of one of the hypothetical proteins in this
family has been solved and it forms a beta sheet
structure with a terminating alpha helix.
Length = 100
Score = 47.2 bits (113), Expect = 4e-07
Identities = 35/134 (26%), Positives = 48/134 (35%), Gaps = 56/134 (41%)
Query: 15 KYSTGQLFLHRVFGYRGIVL-----F----PWLARVYDRDIPNKRDKPSDVNGSVGKEVK 65
K+ GQ+ HR+FGYRG++ F W + D RD+P
Sbjct: 3 KFRIGQVVRHRLFGYRGVIFDVDPEFAASEEWYEAIP-EDRRPARDQP------------ 49
Query: 66 SKTHTFYQVLIDSRDCPYIRAQTEAVTFLGNQNSNKSLYAIPGLDYVAHEDILPYSCSHE 125
FY VL++ D Y+ YVA E++ P S E
Sbjct: 50 -----FYHVLVEDDDSSYVA-------------------------YVAEENLEP-DASGE 78
Query: 126 QPLH---HELFDKF 136
H ELFD+F
Sbjct: 79 PIRHPDLGELFDRF 92
>gnl|CDD|131152 TIGR02097, yccV, hemimethylated DNA binding domain. This model
describes the small protein from E. coli YccV and its
homologs in other Proteobacteria. YccV is now described
as a hemimethylated DNA binding protein. The model also
describes a domain in longer eukaryotic proteins.
Length = 101
Score = 36.2 bits (84), Expect = 0.003
Identities = 23/93 (24%), Positives = 35/93 (37%), Gaps = 33/93 (35%)
Query: 15 KYSTGQLFLHRVFGYRGIVL---------FPWLARVYDRDIPNKRDKPSDVNGSVGKEVK 65
K+ GQ+ H++FGYRG+V+ WL +I RD+P
Sbjct: 3 KFRIGQVVRHKLFGYRGVVIDVDPEYSNTEEWL-DAIPVEIRPLRDQP------------ 49
Query: 66 SKTHTFYQVLIDSRDCPYIRAQTEAVTFLGNQN 98
FY VL + + V ++ QN
Sbjct: 50 -----FYHVLAEDDEGLPY------VAYVAEQN 71
>gnl|CDD|226308 COG3785, COG3785, Uncharacterized conserved protein [Function
unknown].
Length = 116
Score = 31.7 bits (72), Expect = 0.14
Identities = 21/93 (22%), Positives = 34/93 (36%), Gaps = 34/93 (36%)
Query: 15 KYSTGQLFLHRVFGYRGIVL---------FPWLARVYDRDIPNKRDKPSDVNGSVGKEVK 65
K+ GQ+ HR+F +RG+V W + P RD+P
Sbjct: 14 KFGIGQVVRHRLFPFRGVVFDVDPEYANTEEWPDEIPVNIRP-LRDQP------------ 60
Query: 66 SKTHTFYQVLIDSRDCPYIRAQTEAVTFLGNQN 98
FY +L ++ + Y V ++ QN
Sbjct: 61 -----FYHLLAENDETEY-------VAYVSEQN 81
>gnl|CDD|225459 COG2907, COG2907, Predicted NAD/FAD-binding protein [General
function prediction only].
Length = 447
Score = 31.3 bits (71), Expect = 0.50
Identities = 14/58 (24%), Positives = 17/58 (29%), Gaps = 11/58 (18%)
Query: 114 HEDILPYSCSHEQPLHHELFDKFLVHMPDKDPPFV-AQQTLRTWQRKNHPWLELSDVH 170
+ P E+ H LF DP V AQQ L Q W +
Sbjct: 356 RPWVDPAHVIAERTYPHPLF----------DPEAVRAQQELWALQGARRTWFCGAYFG 403
>gnl|CDD|151689 pfam11247, DUF2675, Protein of unknown function (DUF2675). Members
in this family of proteins are annotated as Gene protein
5.5. Currently no function is known.
Length = 98
Score = 27.9 bits (62), Expect = 1.8
Identities = 12/53 (22%), Positives = 20/53 (37%)
Query: 127 PLHHELFDKFLVHMPDKDPPFVAQQTLRTWQRKNHPWLELSDVHKETTENVRV 179
P E+ + L H P+ FV +Q +R ++ K + VR
Sbjct: 44 PFDREMLVQGLTHGPEGAAAFVVKQGIREAIKEMLSEYSDQPSFKLSPATVRE 96
>gnl|CDD|235405 PRK05320, PRK05320, rhodanese superfamily protein; Provisional.
Length = 257
Score = 27.7 bits (62), Expect = 5.7
Identities = 15/56 (26%), Positives = 18/56 (32%), Gaps = 19/56 (33%)
Query: 120 YSCSHEQPLHHELFDKFLV---------HMPDKDP-----PFVAQQTLRTWQRKNH 161
S S QP F + LV P P P V TL+ W + H
Sbjct: 75 ESLSDSQP-----FRRMLVKLKREIITMKRPAIRPELGRAPSVDAATLKRWLDQGH 125
>gnl|CDD|232844 TIGR00143, hypF, [NiFe] hydrogenase maturation protein HypF. A
previously described regulatory effect of HypF
mutatation is attributable to loss of activity of a
regulatory hydrogenase. A zinc finger-like region
CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported
the regulatory hypothesis. However, more recent work
(PUBMED:11375153) shows the direct effect is on the
activity of expressed hydrogenases with nickel/iron
centers, rather than on expression [Protein fate,
Protein modification and repair].
Length = 711
Score = 28.2 bits (63), Expect = 5.7
Identities = 12/43 (27%), Positives = 15/43 (34%), Gaps = 14/43 (32%)
Query: 107 PGLDYVAHEDILPYSCSHEQPLHHELFDKFLVHMPDKDPPFVA 149
P L + +LPY+ PLHH L P V
Sbjct: 260 PNLPTIGV--MLPYT-----PLHHLLLQ-------LLAFPLVM 288
>gnl|CDD|224828 COG1916, COG1916, Uncharacterized homolog of PrgY (pheromone
shutdown protein) [Function unknown].
Length = 388
Score = 27.3 bits (61), Expect = 9.1
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 55 DVNGSVGKEVKSKTHTFYQVLIDSRD 80
DV ++ +E + + T Y+VLID RD
Sbjct: 166 DVLSALMQEFRRFSPTVYKVLIDERD 191
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 0.137 0.432
Gapped
Lambda K H
0.267 0.0767 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,463,433
Number of extensions: 1240459
Number of successful extensions: 890
Number of sequences better than 10.0: 1
Number of HSP's gapped: 882
Number of HSP's successfully gapped: 17
Length of query: 266
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 171
Effective length of database: 6,723,972
Effective search space: 1149799212
Effective search space used: 1149799212
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: 58 (26.0 bits)