RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15895
(124 letters)
>gnl|CDD|235366 PRK05218, PRK05218, heat shock protein 90; Provisional.
Length = 613
Score = 162 bits (413), Expect = 2e-48
Identities = 58/103 (56%), Positives = 77/103 (74%), Gaps = 3/103 (2%)
Query: 22 NAEKHEFQAETRMLLDIVAKSLYSDKEVFIRELISNASDALEKLRYNQLSEVMPFPTDHD 81
E EFQAE + LL ++ SLYS+KE+F+RELISNASDA++KLR+ L++ P +
Sbjct: 2 AMETGEFQAEVKQLLHLMIHSLYSNKEIFLRELISNASDAIDKLRFEALTD--PALYE-G 58
Query: 82 HGKLEIRISTDKQNRILTIQDSGIGMTKEELKSNLGTIARSGS 124
G L+IRIS DK+ R LTI D+GIGMT+EE+ NLGTIA+SG+
Sbjct: 59 DGDLKIRISFDKEARTLTISDNGIGMTREEVIENLGTIAKSGT 101
>gnl|CDD|223403 COG0326, HtpG, Molecular chaperone, HSP90 family [Posttranslational
modification, protein turnover, chaperones].
Length = 623
Score = 139 bits (352), Expect = 9e-40
Identities = 56/101 (55%), Positives = 73/101 (72%), Gaps = 3/101 (2%)
Query: 24 EKHEFQAETRMLLDIVAKSLYSDKEVFIRELISNASDALEKLRYNQLSEVMPFPTDHDHG 83
E FQAE + LLD++ SLYS+KE+F+RELISNASDA++KLR+ + P +
Sbjct: 5 ETRGFQAEVKQLLDLMIHSLYSNKEIFLRELISNASDAIDKLRF--EALSDPELGE-GDS 61
Query: 84 KLEIRISTDKQNRILTIQDSGIGMTKEELKSNLGTIARSGS 124
L IRIS DK N+ LTI D+GIGMTK+E+ NLGTIA+SG+
Sbjct: 62 DLRIRISFDKDNKTLTISDNGIGMTKDEVIENLGTIAKSGT 102
>gnl|CDD|185466 PTZ00130, PTZ00130, heat shock protein 90; Provisional.
Length = 814
Score = 107 bits (267), Expect = 4e-28
Identities = 57/101 (56%), Positives = 77/101 (76%), Gaps = 3/101 (2%)
Query: 24 EKHEFQAETRMLLDIVAKSLYSDKEVFIRELISNASDALEKLRYNQLSEVMPFPTDHDHG 83
E+H++Q E L+DI+ SLY+ KEVF+RELISNA+DALEK+R+ LS+ +
Sbjct: 66 EQHQYQTEVTRLMDIIVNSLYTQKEVFLRELISNAADALEKIRFLSLSDESVL---GEEK 122
Query: 84 KLEIRISTDKQNRILTIQDSGIGMTKEELKSNLGTIARSGS 124
KLEIRIS +K+ IL+I D+GIGMTKE+L +NLGTIA+SG+
Sbjct: 123 KLEIRISANKEKNILSITDTGIGMTKEDLINNLGTIAKSGT 163
>gnl|CDD|240341 PTZ00272, PTZ00272, heat shock protein 83 kDa (Hsp83); Provisional.
Length = 701
Score = 99.0 bits (246), Expect = 3e-25
Identities = 50/101 (49%), Positives = 72/101 (71%), Gaps = 3/101 (2%)
Query: 24 EKHEFQAETRMLLDIVAKSLYSDKEVFIRELISNASDALEKLRYNQLSEVMPFPTDHDHG 83
E FQAE L+ ++ + YS+KE+F+RELISNASDA +K+RY L++ +
Sbjct: 3 ETFAFQAEINQLMSLIINTFYSNKEIFLRELISNASDACDKIRYQSLTDPSVL---GESP 59
Query: 84 KLEIRISTDKQNRILTIQDSGIGMTKEELKSNLGTIARSGS 124
+L IR+ DK+N+ LT++D+GIGMTK +L +NLGTIARSG+
Sbjct: 60 RLCIRVVPDKENKTLTVEDNGIGMTKADLVNNLGTIARSGT 100
>gnl|CDD|237603 PRK14083, PRK14083, HSP90 family protein; Provisional.
Length = 601
Score = 66.5 bits (163), Expect = 5e-14
Identities = 35/98 (35%), Positives = 55/98 (56%), Gaps = 12/98 (12%)
Query: 26 HEFQAETRMLLDIVAKSLYSDKEVFIRELISNASDALEKLRYNQLSEVMPFPTDHDH-GK 84
H FQ + R ++D++++ LYS V++REL+ NA DA+ R D G+
Sbjct: 3 HRFQVDLRGVIDLLSRHLYSSPRVYVRELLQNAVDAITARRA----------LDPTAPGR 52
Query: 85 LEIRISTDKQNRILTIQDSGIGMTKEELKSNLGTIARS 122
+ I + TD L ++D+GIG+T+EE+ L TI RS
Sbjct: 53 IRIEL-TDAGGGTLIVEDNGIGLTEEEVHEFLATIGRS 89
>gnl|CDD|238030 cd00075, HATPase_c, Histidine kinase-like ATPases; This family
includes several ATP-binding proteins for example:
histidine kinase, DNA gyrase B, topoisomerases, heat
shock protein HSP90, phytochrome-like ATPases and DNA
mismatch repair proteins.
Length = 103
Score = 46.5 bits (111), Expect = 9e-08
Identities = 13/75 (17%), Positives = 28/75 (37%), Gaps = 16/75 (21%)
Query: 50 FIRELISNASDALEKLRYNQLSEVMPFPTDHDHGKLEIRISTDKQNRILTIQDSGIGMTK 109
+ L+SNA T G++ I + D + + ++D+G G+ +
Sbjct: 4 VLLNLLSNAIKH----------------TPEGGGRITISVERDGDHLEIRVEDNGPGIPE 47
Query: 110 EELKSNLGTIARSGS 124
E+L+ +
Sbjct: 48 EDLERIFERFSDGSR 62
>gnl|CDD|214643 smart00387, HATPase_c, Histidine kinase-like ATPases. Histidine
kinase-, DNA gyrase B-, phytochrome-like ATPases.
Length = 111
Score = 39.6 bits (93), Expect = 4e-05
Identities = 13/66 (19%), Positives = 30/66 (45%), Gaps = 13/66 (19%)
Query: 48 EVFIRELISNASDALEKLRYNQLSEVMPFPTDHDHGKLEIRISTDKQNRILTIQDSGIGM 107
+R+++SN D K + G++ + + D + +T++D+G G+
Sbjct: 3 PDRLRQVLSNLLDNAIKYT-------------PEGGRITVTLERDGDHVEITVEDNGPGI 49
Query: 108 TKEELK 113
E+L+
Sbjct: 50 PPEDLE 55
>gnl|CDD|217081 pfam02518, HATPase_c, Histidine kinase-, DNA gyrase B-, and
HSP90-like ATPase. This family represents the
structurally related ATPase domains of histidine kinase,
DNA gyrase B and HSP90.
Length = 111
Score = 38.1 bits (89), Expect = 1e-04
Identities = 13/62 (20%), Positives = 28/62 (45%), Gaps = 17/62 (27%)
Query: 51 IRELISNASDALEKLRYNQLSEVMPFPTDHDHGKLEIRISTDKQNRILTIQDSGIGMTKE 110
+ L+ NA +++ G++E+ + D +T++D+GIG+ E
Sbjct: 10 LSNLLDNA------IKHA-----------PAGGEIEVTLERDGGRLRITVEDNGIGIPPE 52
Query: 111 EL 112
+L
Sbjct: 53 DL 54
>gnl|CDD|222246 pfam13589, HATPase_c_3, Histidine kinase-, DNA gyrase B-, and
HSP90-like ATPase. This family represents,
additionally, the structurally related ATPase domains of
histidine kinase, DNA gyrase B and HSP90.
Length = 134
Score = 33.8 bits (78), Expect = 0.007
Identities = 22/72 (30%), Positives = 34/72 (47%), Gaps = 20/72 (27%)
Query: 51 IRELISNASDALEKLRYNQLSEVMPFPTDHDHGKLEIRISTDKQNRILTIQDSGIGMTKE 110
I ELI N+ DA D ++I I D+ ++I+D+G GM+ E
Sbjct: 7 IAELIDNSIDA-------------------DATNVKISIDPDRGEDGISIEDNGGGMSYE 47
Query: 111 ELKSNLGTIARS 122
EL++ L + RS
Sbjct: 48 ELRNAL-KLGRS 58
>gnl|CDD|223715 COG0642, BaeS, Signal transduction histidine kinase [Signal
transduction mechanisms].
Length = 336
Score = 31.6 bits (71), Expect = 0.069
Identities = 9/34 (26%), Positives = 21/34 (61%)
Query: 80 HDHGKLEIRISTDKQNRILTIQDSGIGMTKEELK 113
G++ I + D + ++++D+G G+ +EEL+
Sbjct: 244 TPGGEITISVRQDDEQVTISVEDTGPGIPEEELE 277
>gnl|CDD|234630 PRK00095, mutL, DNA mismatch repair protein; Reviewed.
Length = 617
Score = 30.2 bits (69), Expect = 0.23
Identities = 16/64 (25%), Positives = 27/64 (42%), Gaps = 24/64 (37%)
Query: 51 IRELISNASDALEKLRYNQLSEVMPFPTDHDHGKLEIRISTDK--QNRILTIQDSGIGMT 108
++EL+ NA DA G I I ++ I ++D+G G++
Sbjct: 27 VKELVENALDA---------------------GATRIDIEIEEGGLKLI-RVRDNGCGIS 64
Query: 109 KEEL 112
KE+L
Sbjct: 65 KEDL 68
>gnl|CDD|235246 PRK04184, PRK04184, DNA topoisomerase VI subunit B; Validated.
Length = 535
Score = 30.2 bits (69), Expect = 0.24
Identities = 19/74 (25%), Positives = 39/74 (52%), Gaps = 17/74 (22%)
Query: 40 AKSLYSDKEVFIRELISNASDALEKLRYNQLSEVMPFPTDHDHGKLEIRISTDKQNRI-L 98
A++LY ++EL+ N+ DA E + ++P K+EI+ + ++ +
Sbjct: 34 ARALY----TTVKELVDNSLDACE------EAGILPDI------KIEIKRVDEGKDHYRV 77
Query: 99 TIQDSGIGMTKEEL 112
T++D+G G+ EE+
Sbjct: 78 TVEDNGPGIPPEEI 91
>gnl|CDD|182539 PRK10549, PRK10549, signal transduction histidine-protein kinase
BaeS; Provisional.
Length = 466
Score = 30.0 bits (68), Expect = 0.25
Identities = 15/48 (31%), Positives = 19/48 (39%), Gaps = 11/48 (22%)
Query: 65 LRYNQLSEVMPFPTDHDHGKLEIRISTDKQNRILTIQDSGIGMTKEEL 112
LRY TD G L I + LT DS G++ E+L
Sbjct: 365 LRY----------TD-SGGSLHISAEQRDKTLRLTFADSAPGVSDEQL 401
>gnl|CDD|227077 COG4734, ArdA, Antirestriction protein [General function prediction
only].
Length = 193
Score = 29.2 bits (65), Expect = 0.48
Identities = 16/53 (30%), Positives = 25/53 (47%)
Query: 7 FNHHYSTQAEAASNDNAEKHEFQAETRMLLDIVAKSLYSDKEVFIRELISNAS 59
F+ Y +AE+ + E E + D + S Y D E + R+L S+AS
Sbjct: 128 FDEAYRGEAESEEDFAQEMVEDNGLLNEVPDPLRSSQYFDFEAYARDLFSSAS 180
>gnl|CDD|224307 COG1389, COG1389, DNA topoisomerase VI, subunit B [DNA replication,
recombination, and repair].
Length = 538
Score = 28.5 bits (64), Expect = 0.91
Identities = 21/88 (23%), Positives = 43/88 (48%), Gaps = 19/88 (21%)
Query: 27 EFQAETRMLL--DIVAKSLYSDKEVFIRELISNASDALEKLRYNQLSEVMPFPTDHDHGK 84
EF + + +L D +SL + + EL++N+ DA E+ L ++ K
Sbjct: 19 EFFRKNKEMLGFDGPIRSLTT----TVHELVTNSLDACEE--AGILPDI----------K 62
Query: 85 LEIRISTDKQNRILTIQDSGIGMTKEEL 112
+EI K + + ++D+G G+ +E++
Sbjct: 63 VEIER-IGKDHYKVIVEDNGPGIPEEQI 89
>gnl|CDD|223400 COG0323, MutL, DNA mismatch repair enzyme (predicted ATPase) [DNA
replication, recombination, and repair].
Length = 638
Score = 28.1 bits (63), Expect = 1.2
Identities = 14/64 (21%), Positives = 27/64 (42%), Gaps = 22/64 (34%)
Query: 51 IRELISNASDALEKLRYNQLSEVMPFPTDHDHGKLEIRISTDKQN-RILTIQDSGIGMTK 109
++EL+ N+ DA G I I + +++ ++D+G G+ K
Sbjct: 28 VKELVENSLDA---------------------GATRIDIEVEGGGLKLIRVRDNGSGIDK 66
Query: 110 EELK 113
E+L
Sbjct: 67 EDLP 70
>gnl|CDD|236945 PRK11644, PRK11644, sensory histidine kinase UhpB; Provisional.
Length = 495
Score = 28.0 bits (63), Expect = 1.3
Identities = 6/32 (18%), Positives = 13/32 (40%)
Query: 86 EIRISTDKQNRILTIQDSGIGMTKEELKSNLG 117
++ + +L I+D G G+ + G
Sbjct: 432 TLQGWQQDERLMLVIEDDGSGLPPGSGQQGFG 463
>gnl|CDD|235198 PRK04011, PRK04011, peptide chain release factor 1; Provisional.
Length = 411
Score = 27.9 bits (63), Expect = 1.6
Identities = 10/31 (32%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 44 YSDKEVFIRELISNASDALEKLRYNQLSEVM 74
Y+ E +REL+ ASD L++ + ++M
Sbjct: 254 YTG-ESGLRELVDKASDLLKEQELVKEKKLM 283
>gnl|CDD|234058 TIGR02916, PEP_his_kin, putative PEP-CTERM system histidine kinase.
Members of this protein family have a novel N-terminal
domain, a single predicted membrane-spanning helix, and
a predicted cystosolic histidine kinase domain. We
designate this protein PrsK, and its companion
DNA-binding response regulator protein (TIGR02915) PrsR.
These predicted signal-transducing proteins appear to
enable enhancer-dependent transcriptional activation.
The prsK gene is often associated with exopolysaccharide
biosynthesis genes [Protein fate, Protein and peptide
secretion and trafficking, Signal transduction,
Two-component systems].
Length = 679
Score = 27.8 bits (62), Expect = 1.8
Identities = 10/34 (29%), Positives = 19/34 (55%)
Query: 83 GKLEIRISTDKQNRILTIQDSGIGMTKEELKSNL 116
G++ IR+ + + I+DSG GM+ ++ L
Sbjct: 599 GRVAIRVERECGAARIEIEDSGCGMSPAFIRERL 632
>gnl|CDD|206770 cd11365, RNase_PH_archRRP42, RRP42 subunit of archaeal exosome.
The RRP42 subunit of the archaeal exosome is a member of
the RNase_PH family, named after the bacterial
Ribonuclease PH, a 3'-5' exoribonuclease. Structurally
all members of this family form hexameric rings (trimers
of dimers). In archaea, the ring is formed by three
Rrp41:Rrp42 dimers. The central chamber within the ring
contains three phosphorolytic active sites located in an
Rrp41 pocket at the interface between Rrp42 and Rrp41.
The ring is capped by three copies of Rrp4 and/or Csl4
which contain putative RNA interaction domains. The
archaeal exosome degrades single-stranded RNA (ssRNA) in
the 3'-5' direction, but also can catalyze the reverse
reaction of adding nucleoside diphosphates to the 3'-end
of RNA which has been shown to lead to the formation of
poly-A-rich tails on RNA. It is required for 3'
processing of the 5.8S rRNA.
Length = 256
Score = 27.6 bits (62), Expect = 1.8
Identities = 10/38 (26%), Positives = 16/38 (42%)
Query: 87 IRISTDKQNRILTIQDSGIGMTKEELKSNLGTIARSGS 124
I I+ D+ I+ +Q G G E+ IA +
Sbjct: 213 ITITIDEDGNIVALQKGGGGSFTEDEIDKAIDIALEKA 250
>gnl|CDD|226654 COG4191, COG4191, Signal transduction histidine kinase regulating
C4-dicarboxylate transport system [Signal transduction
mechanisms].
Length = 603
Score = 27.3 bits (61), Expect = 2.1
Identities = 13/53 (24%), Positives = 22/53 (41%), Gaps = 15/53 (28%)
Query: 54 LISNASDALEKLRYNQLSEVMPFPTDHDHGKLEIRISTDKQNRILTIQDSGIG 106
L+ NA DA+ + +L IR + +LT++D+G G
Sbjct: 505 LLQNALDAMA---------------GQEDRRLSIRAQREGGQVVLTVRDNGPG 542
>gnl|CDD|234307 TIGR03676, aRF1/eRF1, peptide chain release factor 1, archaeal and
eukaryotic forms. Directs the termination of nascent
peptide synthesis (translation) in response to the
termination codons UAA, UAG and UGA. This model
identifies both archaeal (aRF1) and eukaryotic (eRF1) of
the protein. Also known as translation termination
factor 1 [Protein synthesis, Translation factors].
Length = 357
Score = 27.2 bits (61), Expect = 2.3
Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 5/49 (10%)
Query: 26 HEFQAETRMLLDIVAKSLYSDKEVFIRELISNASDALEKLRYNQLSEVM 74
+E + + ++ + S Y+ E +REL+ A D L+ L Y + ++M
Sbjct: 232 YELK---KKIIGLFDVS-YTG-ESGLRELVEKAEDLLKDLEYMKEKKLM 275
>gnl|CDD|226951 COG4585, COG4585, Signal transduction histidine kinase [Signal
transduction mechanisms].
Length = 365
Score = 27.1 bits (60), Expect = 2.9
Identities = 15/101 (14%), Positives = 34/101 (33%), Gaps = 24/101 (23%)
Query: 23 AEKHEFQAETRMLLDIVAKSLYSDKEV------FIRELISNASDALEKLRYNQLSEVMPF 76
E + + L + ++ E ++E ++NA +R+ Q +EV
Sbjct: 250 LADFEERTGITVDLSLGSELERLPPEAEDALFRIVQEALTNA------IRHAQATEV--- 300
Query: 77 PTDHDHGKLEIRISTDKQNRILTIQDSGIGMTKEELKSNLG 117
+ + L + D+G+G ++ G
Sbjct: 301 ---------RVTLERTDDELRLEVIDNGVGFDPDKEGGGFG 332
>gnl|CDD|235268 PRK04282, PRK04282, exosome complex RNA-binding protein Rrp42;
Provisional.
Length = 271
Score = 26.8 bits (60), Expect = 3.0
Identities = 15/38 (39%), Positives = 19/38 (50%)
Query: 87 IRISTDKQNRILTIQDSGIGMTKEELKSNLGTIARSGS 124
I I+TD+ I+ IQ SGIG EE IA +
Sbjct: 221 ITITTDEDGNIVAIQKSGIGSFTEEEVDKAIDIALEKA 258
>gnl|CDD|233250 TIGR01052, top6b, DNA topoisomerase VI, B subunit. This model
describes DNA topoisomerase VI, an archaeal type II DNA
topoisomerase (DNA gyrase) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 488
Score = 26.3 bits (58), Expect = 5.0
Identities = 18/83 (21%), Positives = 39/83 (46%), Gaps = 23/83 (27%)
Query: 40 AKSLYSDKEVFIRELISNASDALEKLRYNQLSEVMPFPTDHDHGKLEIRIS---TDKQNR 96
+SL + I EL++N+ DA E+ + ++P +I++ K +
Sbjct: 26 IRSLTT----VIHELVTNSLDACEE------AGILP----------DIKVEIEKIGKDHY 65
Query: 97 ILTIQDSGIGMTKEELKSNLGTI 119
+T++D+G G+ +E + G +
Sbjct: 66 KVTVEDNGPGIPEEYIPKVFGKM 88
>gnl|CDD|223896 COG0826, COG0826, Collagenase and related proteases
[Posttranslational modification, protein turnover,
chaperones].
Length = 347
Score = 26.1 bits (58), Expect = 5.6
Identities = 19/59 (32%), Positives = 27/59 (45%), Gaps = 12/59 (20%)
Query: 5 PNFNHHYSTQAEAASNDNAEKHEFQAE---TRMLLDIVAKSLYSDKEVFIRELISNASD 60
P+ H STQA NAE +F E R++L + L S +E I+E+ D
Sbjct: 112 PDLPIHVSTQANV---TNAETAKFWKELGAKRVVL---PREL-SLEE--IKEIKEQTPD 161
>gnl|CDD|224493 COG1577, ERG12, Mevalonate kinase [Lipid metabolism].
Length = 307
Score = 25.7 bits (57), Expect = 6.7
Identities = 23/90 (25%), Positives = 40/90 (44%), Gaps = 12/90 (13%)
Query: 28 FQAETRMLLDIVAKSLYSDKEVF------IRELISNASDALEKLRYNQLSEVMPFPTDHD 81
T+ L+ VAK L + EV I EL+ A AL+ + +L E+M + +
Sbjct: 180 VPGSTKELVAGVAKLLEEEPEVIDPILDAIGELVQEAEAALQTGDFEELGELM----NIN 235
Query: 82 HGKL-EIRISTDKQNRILTI-QDSGIGMTK 109
G L + +ST + + ++ + G K
Sbjct: 236 QGLLKALGVSTPELDELVEAARSLGALGAK 265
>gnl|CDD|236842 PRK11091, PRK11091, aerobic respiration control sensor protein
ArcB; Provisional.
Length = 779
Score = 26.1 bits (58), Expect = 7.3
Identities = 9/31 (29%), Positives = 21/31 (67%), Gaps = 1/31 (3%)
Query: 83 GKLEIRISTDKQNRIL-TIQDSGIGMTKEEL 112
G + +R+ ++ + + ++DSGIG+ ++EL
Sbjct: 417 GGVTVRVRYEEGDMLTFEVEDSGIGIPEDEL 447
>gnl|CDD|233017 TIGR00549, mevalon_kin, mevalonate kinase. This model represents
mevalonate kinase, the third step in the mevalonate
pathway of isopentanyl pyrophosphate (IPP) biosynthesis.
IPP is a common intermediate for a number of pathways
including cholesterol biosynthesis. This model covers
enzymes from eukaryotes, archaea and bacteria. The
related enzyme from the same pathway, phosphmevalonate
kinase, serves as an outgroup for this clade. Paracoccus
exhibits two genes within the
phosphomevalonate/mevalonate kinase family, one of which
falls between trusted and noise cutoffs of this model.
The degree of divergence is high, but if the trees
created from this model are correct, the proper names of
these genes have been swapped [Central intermediary
metabolism, Other].
Length = 274
Score = 25.7 bits (57), Expect = 8.1
Identities = 19/77 (24%), Positives = 32/77 (41%), Gaps = 11/77 (14%)
Query: 31 ETRMLLDIVAKSLYSDKEVF------IRELISNASDALEKLRYNQLSEVMPFPTDHDHGK 84
T+ + V + L E+ I EL A ALE L E+M + + G
Sbjct: 179 STKEAVARVRQLLERFPELIDSIMDAIGELTLEAKAALEDGDVESLGELM----NINQGL 234
Query: 85 L-EIRISTDKQNRILTI 100
L + +S K ++++ I
Sbjct: 235 LKALGVSHPKLDQLVEI 251
>gnl|CDD|132720 cd02584, RNAP_II_Rpb1_C, Largest subunit (Rpb1) of Eukaryotic RNA
polymerase II (RNAP II), C-terminal domain. RNA
polymerase II (RNAP II) is a large multi-subunit complex
responsible for the synthesis of mRNA. RNAP II consists
of a 10-subunit core enzyme and a peripheral heterodimer
of two subunits. The largest core subunit (Rpb1) of
yeast RNAP II is the best characterized member of this
family. Structure studies suggest that RNAP complexes
from different organisms share a crab-claw-shape
structure. In yeast, Rpb1 and Rpb2, the largest and the
second largest subunits, each makes up one clamp, one
jaw, and part of the cleft. Rpb1 interacts with Rpb2 to
form the DNA entry and RNA exit channels in addition to
the catalytic center of RNA synthesis. The C-terminal
domain of Rpb1 makes up part of the foot and jaw
structures.
Length = 410
Score = 25.2 bits (56), Expect = 9.8
Identities = 11/42 (26%), Positives = 20/42 (47%)
Query: 12 STQAEAASNDNAEKHEFQAETRMLLDIVAKSLYSDKEVFIRE 53
+ E + + + E+ ML D+ K + ++VFIRE
Sbjct: 208 NDDEEKEEDSEDDVFLKKIESNMLSDMTLKGIEGIRKVFIRE 249
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
0.312 0.128 0.344
Gapped
Lambda K H
0.267 0.0753 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,989,871
Number of extensions: 517125
Number of successful extensions: 365
Number of sequences better than 10.0: 1
Number of HSP's gapped: 355
Number of HSP's successfully gapped: 53
Length of query: 124
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 39
Effective length of database: 7,167,512
Effective search space: 279532968
Effective search space used: 279532968
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: 53 (24.1 bits)