RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13515
(526 letters)
>gnl|CDD|177288 PHA00616, PHA00616, hypothetical protein.
Length = 44
Score = 32.4 bits (74), Expect = 0.038
Identities = 12/26 (46%), Positives = 19/26 (73%)
Query: 410 VYQCYHCLKIFKRKKDLPRHIMSVHM 435
+YQC C IF++KK++ H++SVH
Sbjct: 1 MYQCLRCGGIFRKKKEVIEHLLSVHK 26
Score = 25.5 bits (56), Expect = 9.1
Identities = 8/25 (32%), Positives = 12/25 (48%)
Query: 466 YECENCSKIFNSKRKLYSHKRKDHM 490
Y+C C IF K+++ H H
Sbjct: 2 YQCLRCGGIFRKKKEVIEHLLSVHK 26
>gnl|CDD|215056 PLN00104, PLN00104, MYST -like histone acetyltransferase;
Provisional.
Length = 450
Score = 31.6 bits (72), Expect = 1.1
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 411 YQCYHCLKIFKRKKDLPRHIMSVHMR 436
Y C CLK KRK+ L RH+ ++
Sbjct: 199 YFCEFCLKFMKRKEQLQRHMKKCDLK 224
>gnl|CDD|238464 cd00924, Cyt_c_Oxidase_Vb, Cytochrome c oxidase subunit Vb.
Cytochrome c oxidase (CcO), the terminal oxidase in the
respiratory chains of eukaryotes and most bacteria, is a
multi-chain transmembrane protein located in the inner
membrane of mitochondria and the cell membrane of
prokaryotes. It catalyzes the reduction of O2 and
simultaneously pumps protons across the membrane. The
number of subunits varies from three to five in bacteria
and up to 13 in mammalian mitochondria. Subunits I, II,
and III of mammalian CcO are encoded within the
mitochondrial genome and the remaining 10 subunits are
encoded within the nuclear genome. Found only in
eukaryotes, subunit Vb is one of three mammalian
subunits that lacks a transmembrane region. Subunit Vb
is located on the matrix side of the membrane and binds
the regulatory subunit of protein kinase A. The
abnormally extended conformation is stable only in the
CcO assembly.
Length = 97
Score = 29.6 bits (67), Expect = 1.1
Identities = 15/44 (34%), Positives = 18/44 (40%), Gaps = 7/44 (15%)
Query: 184 NLIAHVHGKRF--CDICSQDYSTKYYLKLHKQVHEGKQHECEEC 225
NL+ KR C IC D ++ L K GK C EC
Sbjct: 47 NLVPSAFDKRIVGC-ICEPDSHDVIWMWLEK----GKPKRCPEC 85
Score = 27.6 bits (62), Expect = 5.0
Identities = 10/34 (29%), Positives = 13/34 (38%), Gaps = 4/34 (11%)
Query: 55 RYTCDICSQDYSTKYYLKLHKQVHEGKQHECEKC 88
R IC D ++ L K GK C +C
Sbjct: 56 RIVGCICEPDSHDVIWMWLEK----GKPKRCPEC 85
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 29.5 bits (66), Expect = 1.8
Identities = 23/79 (29%), Positives = 32/79 (40%), Gaps = 8/79 (10%)
Query: 89 PRLFPSSKMLYDHTMRSHKTRELFKCHQCSRKYMSKPSLRRHI-YATHINKGVRFSCHLC 147
P+L S LY K + C C + S SL++HI Y H C +C
Sbjct: 53 PQLLDESSYLYKLLTS--KAVSPYVCPLCLMPFSSSVSLKQHIRYTEHSKV-----CPVC 105
Query: 148 GKSFHREQSLRKHLREEEN 166
GK F S H+ ++ N
Sbjct: 106 GKEFRNTDSTLDHVCKKHN 124
Score = 28.7 bits (64), Expect = 3.2
Identities = 20/70 (28%), Positives = 29/70 (41%), Gaps = 4/70 (5%)
Query: 445 PREFQNKANLNHHLASHAGKTYECENCSKIFNSKRKLYSHKR-KDHMGLTYSCFMCNKTI 503
P+ + L L S A Y C C F+S L H R +H + C +C K
Sbjct: 53 PQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYTEH---SKVCPVCGKEF 109
Query: 504 TSKNSLRDHI 513
+ +S DH+
Sbjct: 110 RNTDSTLDHV 119
>gnl|CDD|239650 cd03678, MM_CoA_mutase_1, Coenzyme B12-dependent-methylmalonyl
coenzyme A (CoA) mutase (MCM) family, unknown subfamily
1; composed of uncharacterized bacterial proteins
containing a C-terminal MCM domain. MCM catalyzes the
isomerization of methylmalonyl-CoA to succinyl-CoA. The
reaction proceeds via radical intermediates beginning
with a substrate-induced homolytic cleavage of the Co-C
bond of coenzyme B12 to produce cob(II)alamin and the
deoxyadenosyl radical. MCM plays an important role in
the conversion of propionyl-CoA to succinyl-CoA during
the degradation of propionate for the Krebs cycle. In
some bacteria, MCM is involved in the reverse metabolic
reaction, the rearrangement of succinyl-CoA to
methylmalonyl-CoA. Members of this subfamily also
contain an N-terminal coenzyme B12 binding domain
followed by a domain similar to the E. coli ArgK
membrane ATPase.
Length = 495
Score = 30.2 bits (68), Expect = 2.8
Identities = 13/56 (23%), Positives = 26/56 (46%), Gaps = 8/56 (14%)
Query: 168 DQLHCDKCRYKTFLKSNLIAHVHGKRFCDICSQD-------YSTKYYLKLHKQVHE 216
DQ +K R + +++ + V G DI +D +ST++ L++ + E
Sbjct: 186 DQ-QVEKFRRENGIRAETLRSVRGTVQADILKEDQAQNTCIFSTEFALRMMGDIQE 240
>gnl|CDD|178635 PLN03086, PLN03086, PRLI-interacting factor K; Provisional.
Length = 567
Score = 29.8 bits (67), Expect = 3.6
Identities = 11/33 (33%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 298 LREEENQDQLHCDKCRYKTFLKSNLIAHVHGYH 330
LR EE ++ +HC+KC + F + + H+ +H
Sbjct: 445 LRVEEAKNHVHCEKCG-QAFQQGEMEKHMKVFH 476
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 29.3 bits (65), Expect = 6.5
Identities = 25/172 (14%), Positives = 40/172 (23%), Gaps = 40/172 (23%)
Query: 1 MKQSLAMHIKKMNREPEQHYDKPKQVEFPCVYCGKIFPRLGLLKEHTKTHHLKVRYTCDI 60
+ S + + + R + K P CGK+F R LK H H +
Sbjct: 297 ISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKL 356
Query: 61 -------------------------------------CSQDYSTKYYLKLHKQVHEGKQH 83
C +++ L LH H +
Sbjct: 357 LNSSSKFSPLLNNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRP 416
Query: 84 ECEKCPRLFPSSKMLYDHT--MRSHKTRELFKCHQCSRKYMSKPSLRRHIYA 133
K P S Y+ + H + + L H
Sbjct: 417 YNCKNPPCSKSFNRHYNLIPHKKIHTNHAPL-LCSILKSFRRDLDLSNHGKD 467
>gnl|CDD|222863 PHA02540, 61, DNA primase; Provisional.
Length = 337
Score = 28.8 bits (65), Expect = 7.4
Identities = 12/41 (29%), Positives = 16/41 (39%), Gaps = 6/41 (14%)
Query: 249 FKCHQC--SRKYMSKPSLRRHIYANHINKGVRFSCHLCGKS 287
F+C C S+K +K + G F CH CG
Sbjct: 28 FRCPICGDSQKDKNK----ARGWIYEKKDGGVFKCHNCGYH 64
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 25.1 bits (55), Expect = 8.4
Identities = 8/23 (34%), Positives = 14/23 (60%)
Query: 439 YPCTICPREFQNKANLNHHLASH 461
Y C C + F++K+ L H+ +H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
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
0.324 0.135 0.433
Gapped
Lambda K H
0.267 0.0722 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 25,002,912
Number of extensions: 2281436
Number of successful extensions: 2983
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2949
Number of HSP's successfully gapped: 140
Length of query: 526
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 425
Effective length of database: 6,457,848
Effective search space: 2744585400
Effective search space used: 2744585400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 61 (27.3 bits)