RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9551
(250 letters)
>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional.
Length = 1388
Score = 35.0 bits (81), Expect = 0.037
Identities = 30/219 (13%), Positives = 59/219 (26%), Gaps = 21/219 (9%)
Query: 2 ESPSPKTEDEIFWKPASGLRRKTTDTKNITLKKEDSEGEKSFVPPVRDEESETQRKAHAK 61
+ KT+ + L++K K + K V +E
Sbjct: 1156 QRLKSKTKGKASKLRKPKLKKKEKKKKKSSADKSKKASVVGNSKRVDSDEKRKLDDKPDN 1215
Query: 62 RVRETRRSTQG-----------VTLEELKSAEQLVKKKQQQQLVQASQQPSPEKETPDTS 110
+ + S Q +++ LKS + K + +S S E + +
Sbjct: 1216 KKSNSSGSDQEDDEEQKTKPKKSSVKRLKSKKNNSSKSSEDNDEFSSDDLSKEGKPKNAP 1275
Query: 111 EVSNSQPVAISATITPSPSPTINNSGERRPSWRLRVDNGVKFMLEDARDNPSSNDKTRSS 170
+ ++ + + S P+ K + + +
Sbjct: 1276 KRVSAVQYSPPPPSKRPDGESNGGSKPSSPT----KKKVKKRLEGSLAALKKKKKSEKKT 1331
Query: 171 SRGATDTAET------TVTIPLRRPGKLAVDSDKEQDKE 203
+R + LRRP K DS E D +
Sbjct: 1332 ARKKKSKTRVKQASASQSSRLLRRPRKKKSDSSSEDDDD 1370
>gnl|CDD|233870 TIGR02442, Cob-chelat-sub, cobaltochelatase subunit.
Cobaltochelatase is responsible for the insertion of
cobalt into the corrin ring of coenzyme B12 during its
biosynthesis. Two versions have been well described.
CbiK/CbiX is a monomeric, anaerobic version which acts
early in the biosynthesis (pfam06180). CobNST is a
trimeric, ATP-dependent, aerobic version which acts late
in the biosynthesis (TIGR02257/TIGR01650/TIGR01651). A
number of genomes (actinobacteria, cyanobacteria,
betaproteobacteria and pseudomonads) which apparently
biosynthesize B12, encode a cobN gene but are
demonstrably lacking cobS and cobT. These genomes do,
however contain a homolog (modelled here) of the
magnesium chelatase subunits BchI/BchD family. Aside
from the cyanobacteria (which have a separate magnesium
chelatase trimer), these species do not make chlorins,
so do not have any use for a magnesium chelatase.
Furthermore, in nearly all cases the members of this
family are proximal to either CobN itself or other genes
involved in cobalt transport or B12 biosynthesis.
Length = 633
Score = 32.7 bits (75), Expect = 0.15
Identities = 35/160 (21%), Positives = 48/160 (30%), Gaps = 27/160 (16%)
Query: 58 AHAKRVRETRRSTQGVTLEELKSAEQLVKK-------------KQQQQLVQASQQPSPEK 104
A A R + VT E+++ A +LV K ++ L + ++P P+
Sbjct: 277 ARAARALAALDGRRRVTAEDVREAAELVLPHRRRRKPFEQPQGKDEKDLEEKPEEPGPDP 336
Query: 105 ETPDTSEVSNSQPVAISATIT---------PSPSPTINNSGERRPSWRLRVDNGVKFMLE 155
E PD E Q P S R+
Sbjct: 337 EKPDEGEDDAEQSGPRGHPTPGNDDEKEPDPQEEADGQGSSTDPAGDIFRIRVLA-PPQA 395
Query: 156 DARDNPSSNDKTRSSSRGATDTAETTVTIPLRRPGKLAVD 195
AR +TRS SRG A P LAVD
Sbjct: 396 RARGASGRRSRTRSDSRGRYVRAR----RNRGPPDDLAVD 431
>gnl|CDD|215152 PLN02269, PLN02269, Pyruvate dehydrogenase E1 component subunit
alpha.
Length = 362
Score = 32.0 bits (73), Expect = 0.29
Identities = 17/59 (28%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 48 RDEESET-QRKAHAKRVRETRRSTQGVTLEELKSAEQLVKKKQQQQLVQASQQPSPEKE 105
RDE S Q + +RVR+ + + T ELK E+ ++K+ + +A + P P+
Sbjct: 276 RDEISGVRQERDPIERVRKLLLAHELATEAELKDIEKEIRKEVDDAVAKAKESPMPDPS 334
>gnl|CDD|219355 pfam07267, Nucleo_P87, Nucleopolyhedrovirus capsid protein P87.
This family consists of several Nucleopolyhedrovirus
capsid protein P87 sequences. P87 is expressed late in
infection and concentrated in infected cell nuclei.
Length = 606
Score = 31.0 bits (70), Expect = 0.61
Identities = 26/137 (18%), Positives = 42/137 (30%), Gaps = 18/137 (13%)
Query: 91 QQLVQASQQPSPEKETPDTSEVSNSQPVAISATITPSPSPTINN----SGERRPSWRLRV 146
+ +Q P+ TP T E+ + Q + + S + E R
Sbjct: 275 RSWQTPAQTPARRISTPMTEEIKSWQTPLQTPAMYSSDYQAPKPEPIYTWEELLRERFPS 334
Query: 147 DNGVKFMLEDARDNPSSNDKTRSSSRGATDTAETTVTIPLRRPGKLAVDSDKEQDKENDS 206
D L D+ S + TR R RR L S E + ++D
Sbjct: 335 DLFAISSLPDSDSEASDSGPTRKRKR--------------RRVPPLPEYSSDEDEDDSDE 380
Query: 207 RNAQATQAVIQRRKRPK 223
+ +RR+ K
Sbjct: 381 DEVDYEKERKRRREEDK 397
>gnl|CDD|227568 COG5243, HRD1, HRD ubiquitin ligase complex, ER membrane component
[Posttranslational modification, protein turnover,
chaperones].
Length = 491
Score = 29.2 bits (65), Expect = 2.0
Identities = 28/146 (19%), Positives = 45/146 (30%), Gaps = 27/146 (18%)
Query: 45 PPVRDEESETQRKAHAKRVRETRRSTQGVTLEELKSAEQLVKKKQQQQLVQASQQPSPEK 104
P + D+ S T + VR T+ +TQ + + + +S Q P+
Sbjct: 343 PVIFDQSSPT---PASPNVRNTQIATQVPNPDNTPTT------TAVPGITNSSNQGDPQA 393
Query: 105 ETPDTSEVSNSQPVAISATITPSPSPTINNSGERRPSWRLRVDNGVKFMLEDARDNPSSN 164
T + +NS A S P W + + R S
Sbjct: 394 STFNGVPNANSSGFAAHTQDLSSVIPG----------WTM-------LPIPGTRRISQST 436
Query: 165 DKTRSSSRGAT-DTAETTVTIPLRRP 189
T S+ T D + +T P P
Sbjct: 437 STTNPSATPTTGDPSNSTYGGPQTFP 462
>gnl|CDD|234977 PRK01741, PRK01741, cell division protein ZipA; Provisional.
Length = 332
Score = 28.9 bits (65), Expect = 2.4
Identities = 13/109 (11%), Positives = 38/109 (34%), Gaps = 12/109 (11%)
Query: 30 ITLKKEDSEGEKSFVPPVRDEESETQRKAHAKRVRETRRSTQGVTLEELKSAEQLVKKKQ 89
ITL ++ + ++ Q ++ T+ + +T+EE +S ++
Sbjct: 103 ITLPNQEPAYYMQNHRSEPIQPTQPQYQS------PTQTNVASMTIEETQSPNVPIEGIN 156
Query: 90 ------QQQLVQASQQPSPEKETPDTSEVSNSQPVAISATITPSPSPTI 132
+ +L + + + + + +P A + + + I
Sbjct: 157 SSSEQLRVELAELAAEIYSDASHRVELAKNFMEPQAETEAQPEATTNFI 205
>gnl|CDD|149648 pfam08662, eIF2A, Eukaryotic translation initiation factor eIF2A.
This is a family of eukaryotic translation initiation
factors.
Length = 194
Score = 28.4 bits (64), Expect = 3.1
Identities = 9/12 (75%), Positives = 9/12 (75%)
Query: 141 SWRLRVDNGVKF 152
S RLRVDNG K
Sbjct: 164 SPRLRVDNGFKI 175
>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase
component YidC; Validated.
Length = 429
Score = 28.7 bits (64), Expect = 3.4
Identities = 20/87 (22%), Positives = 40/87 (45%), Gaps = 6/87 (6%)
Query: 48 RDEESETQRKAHAKRVRETRRSTQGVTLEELKSAEQLVKKKQQQQLVQASQQ----PSPE 103
E++ ++K A++ R R +E +A + + ++ V+A ++ SP
Sbjct: 339 EKNEAKARKKEIAQKRRAAEREINREARQERAAAMA--RARARRAAVKAKKKGLIDASPN 396
Query: 104 KETPDTSEVSNSQPVAISATITPSPSP 130
++TP +E S P + AT T P+
Sbjct: 397 EDTPSENEESKGSPPQVEATTTAEPNR 423
>gnl|CDD|233256 TIGR01063, gyrA, DNA gyrase, A subunit. This model describes the
common type II DNA topoisomerase (DNA gyrase). Two
apparently independently arising families, one in the
Proteobacteria and one in Gram-positive lineages, are
both designated toposisomerase IV [DNA metabolism, DNA
replication, recombination, and repair].
Length = 800
Score = 28.4 bits (64), Expect = 4.4
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 60 AKRVRETRRSTQGVTLEELKSAEQLV 85
+ V E R+TQGV L L ++LV
Sbjct: 768 VQDVSEQGRNTQGVRLIRLDEDDKLV 793
>gnl|CDD|235502 PRK05560, PRK05560, DNA gyrase subunit A; Validated.
Length = 805
Score = 28.5 bits (65), Expect = 4.6
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 63 VRETRRSTQGVTLEELKSAEQLV 85
+ T R+TQGV L L +++V
Sbjct: 774 ISITGRNTQGVRLIRLDEGDKVV 796
>gnl|CDD|240622 cd05198, formate_dh_like, Formate/glycerate and related
dehydrogenases of the D-specific 2-hydroxy acid
dehydrogenase family. Formate dehydrogenase, D-specific
2-hydroxy acid dehydrogenase, Phosphoglycerate
Dehydrogenase, Lactate dehydrogenase, Thermostable
Phosphite Dehydrogenase, and Hydroxy(phenyl)pyruvate
reductase, among others, share a characteristic
arrangement of 2 similar subdomains of the alpha/beta
Rossmann fold NAD+ binding form. 2-hydroxyacid
dehydrogenases are enzymes that catalyze the conversion
of a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
The NAD+ binding domain is inserted within the linear
sequence of the mostly N-terminal catalytic domain,
which has a similar domain structure to the internal NAD
binding domain. Structurally, these domains are
connected by extended alpha helices and create a cleft
in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence. Formate dehydrogenase
(FDH) catalyzes the NAD+-dependent oxidation of formate
ion to carbon dioxide with the concomitant reduction of
NAD+ to NADH. FDHs of this family contain no metal ions
or prosthetic groups. Catalysis occurs though direct
transfer of hydride ion to NAD+ without the stages of
acid-base catalysis typically found in related
dehydrogenases. FDHs are found in all methylotrophic
microorganisms in energy production and in the stress
responses of plants. Formate/glycerate and related
dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-Adenosylhomocysteine Hydrolase,
among others. While many members of this family are
dimeric, alanine DH is hexameric and phosphoglycerate DH
is tetrameric.
Length = 302
Score = 28.0 bits (63), Expect = 5.2
Identities = 10/34 (29%), Positives = 15/34 (44%), Gaps = 3/34 (8%)
Query: 211 ATQAVIQRRKRPK---RRSTGVVHVDLDEILDRG 241
T V+ + + K GV ++DLD RG
Sbjct: 53 VTAEVLAKAPKLKFIQVAGAGVDNIDLDAAKKRG 86
>gnl|CDD|238153 cd00249, AGE, AGE domain; N-acyl-D-glucosamine 2-epimerase domain;
Responsible for intermediate epimerization during
biosynthesis of N-acetylneuraminic acid. Catalytic
mechanism is believed to be via nucleotide elimination
and readdition and is ATP modulated. AGE is structurally
and mechanistically distinct from the other four types
of epimerases. The AGE domain monomer is composed of an
alpha(6)/alpha(6)-barrel, the structure of which is also
found in glucoamylase and cellulase. The active form is
a homodimer. The alignment also contains subtype III
mannose 6-phosphate isomerases.
Length = 384
Score = 27.7 bits (62), Expect = 6.0
Identities = 6/22 (27%), Positives = 12/22 (54%)
Query: 138 RRPSWRLRVDNGVKFMLEDARD 159
RP W ++G++++ RD
Sbjct: 70 WRPEWLEAAEHGLEYLDRHGRD 91
>gnl|CDD|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional.
Length = 1355
Score = 27.7 bits (61), Expect = 7.7
Identities = 17/92 (18%), Positives = 30/92 (32%), Gaps = 2/92 (2%)
Query: 51 ESETQRKAHAKRVRETRRSTQGVTLEELKSAEQLVKKKQQQQLV--QASQQPSPEKETPD 108
E Q+ +A + + E A + ++QQ Q++ Q + P
Sbjct: 413 EQPAQQPYYAPAPEQPAQQPYYAPAPEQPVAGNAWQAEEQQSTFAPQSTYQTEQTYQQPA 472
Query: 109 TSEVSNSQPVAISATITPSPSPTINNSGERRP 140
E QP + P P + + RP
Sbjct: 473 AQEPLYQQPQPVEQQPVVEPEPVVEETKPARP 504
>gnl|CDD|220633 pfam10214, Rrn6, RNA polymerase I-specific transcription-initiation
factor. RNA polymerase I-specific
transcription-initiation factor Rrn6 and Rrn7 represent
components of a multisubunit transcription factor
essential for the initiation of rDNA transcription by
Pol I. These proteins are found in fungi.
Length = 753
Score = 27.4 bits (61), Expect = 8.2
Identities = 12/75 (16%), Positives = 21/75 (28%), Gaps = 3/75 (4%)
Query: 48 RDEESETQRKAHAKRVRETRRSTQGVTLEELKSAEQLVKKKQQQQLVQASQQPSPEKETP 107
+ E+Q + R + T+ + SA + Q S P +
Sbjct: 658 DSSQLESQSQIPTIRSSQQVSQTRKGGSSVVPSAPAPRLAQSSQPPTSQSSSDLPPSSSQ 717
Query: 108 DTSEV---SNSQPVA 119
S SQ +
Sbjct: 718 AFSLSDLPMQSQSES 732
>gnl|CDD|215521 PLN02967, PLN02967, kinase.
Length = 581
Score = 27.3 bits (60), Expect = 8.3
Identities = 25/103 (24%), Positives = 39/103 (37%), Gaps = 8/103 (7%)
Query: 154 LEDARDNPSSNDKTRSSSRGATDTAETTVTIPLRRPGKLAVDSDKEQDKENDSRN----- 208
D S TRS R T + PL +L V+ D DKE+
Sbjct: 61 EPDENGAVSKKKPTRSVKRATKKTVVEI-SEPLEEGSELVVNEDAALDKESKKTPRRTRR 119
Query: 209 --AQATQAVIQRRKRPKRRSTGVVHVDLDEILDRGGENEETNH 249
A A+ V + + K R V +++ D+G E+E ++
Sbjct: 120 KAAAASSDVEEEKTEKKVRKRRKVKKMDEDVEDQGSESEVSDV 162
>gnl|CDD|224557 COG1643, HrpA, HrpA-like helicases [DNA replication, recombination,
and repair].
Length = 845
Score = 27.3 bits (61), Expect = 8.5
Identities = 20/68 (29%), Positives = 31/68 (45%), Gaps = 15/68 (22%)
Query: 174 ATDTAETTVTIPLRRPGKLAVDSDKEQDKENDSRN----------AQATQAVIQRRKRPK 223
AT+ AET++TIP R +DS ++K D R ++A + QR R
Sbjct: 319 ATNIAETSLTIPGIRY---VIDSGLAKEKRYDPRTGLTRLETEPISKA--SADQRAGRAG 373
Query: 224 RRSTGVVH 231
R G+ +
Sbjct: 374 RTGPGICY 381
>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed.
Length = 1068
Score = 27.3 bits (61), Expect = 9.0
Identities = 17/125 (13%), Positives = 44/125 (35%), Gaps = 22/125 (17%)
Query: 23 KTTDTKNITLKKEDSEGEKSFVPPVRDEESETQRKAHAKRVRETRRSTQ----------- 71
+ T + + E +E ++ +DE+ + R+ +R + +R Q
Sbjct: 648 QQTAETRESQQAEVTEKART-----QDEQQQAPRRERQRRRNDEKRQAQQEAKALNVEEQ 702
Query: 72 -GVTLEELKSAEQLVKKKQQQQL-----VQASQQPSPEKETPDTSEVSNSQPVAISATIT 125
E+ + +Q+ +++Q+QL ++ S + + + + A T
Sbjct: 703 SVQETEQEERVQQVQPRRKQRQLNQKVRIEQSVAEEAVAPVVEETVAAEPVVQEVPAPRT 762
Query: 126 PSPSP 130
Sbjct: 763 ELVKV 767
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
0.304 0.121 0.326
Gapped
Lambda K H
0.267 0.0675 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,096,322
Number of extensions: 1088410
Number of successful extensions: 1046
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1007
Number of HSP's successfully gapped: 103
Length of query: 250
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 155
Effective length of database: 6,723,972
Effective search space: 1042215660
Effective search space used: 1042215660
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 43 (21.9 bits)
S2: 58 (26.2 bits)