RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11137
(831 letters)
>gnl|CDD|113931 pfam05179, CDC73, RNA pol II accessory factor, Cdc73 family.
Length = 273
Score = 139 bits (351), Expect = 1e-36
Identities = 61/121 (50%), Positives = 73/121 (60%), Gaps = 18/121 (14%)
Query: 4 LPSGAPSPSHQKRISRTPIIIIPAANTSLITM-----------FVTTEAKRAAGSKRENE 52
PS K+ SR PII+IP+A +SLITM +V +AKR G ++
Sbjct: 105 DKQNGPS----KKGSRDPIILIPSAASSLITMYNIKDFLQEGKYVPVDAKRKQGCQKPEL 160
Query: 53 ILIQRSKG--DGTTVPYRVIDNPLKLARTDWDRVVAVFVMGPAWQFKGWPWDANPVEIFS 110
I IQR TV YRV+DNP KL DWDRVVAVFV GPAWQFKGWPW+ +PV+IF
Sbjct: 161 IAIQRKFSRSKFVTVRYRVVDNPEKLKPDDWDRVVAVFVTGPAWQFKGWPWN-SPVDIFH 219
Query: 111 K 111
K
Sbjct: 220 K 220
Score = 86.4 bits (214), Expect = 1e-18
Identities = 45/120 (37%), Positives = 56/120 (46%), Gaps = 9/120 (7%)
Query: 346 TRTSIFHTSGKIF-SKNIFAILQSIKAREEGRHRPAPPTPLVPSTPVNKSVPQPIV---Y 401
TRT + ++G +F +I A LQ REEGR P P + + P Y
Sbjct: 1 TRTEVLISNGTLFERLDIIASLQGASLREEGRLEKPVPVPTDKPEDMRVDLHSPQEEAKY 60
Query: 402 NRYDQERFIKSREETEGFKIDTMGTYHGMTLKSVTEGNTPRKPALTPSTPAHQTPSATPN 461
NRY QERF S EETEGFKIDT G+ G LKS+ G K + PS +
Sbjct: 61 NRYAQERF--SGEETEGFKIDTFGSLRGSVLKSIHAG---PKATASARADKQNGPSKKGS 115
Score = 65.2 bits (159), Expect = 2e-11
Identities = 37/87 (42%), Positives = 44/87 (50%), Gaps = 6/87 (6%)
Query: 703 TRTSIFHTSGKIF-SKNIFAILQSIKAREEGRHRPAPPTPLVPSTPVNKSVPQPIV---Y 758
TRT + ++G +F +I A LQ REEGR P P + + P Y
Sbjct: 1 TRTEVLISNGTLFERLDIIASLQGASLREEGRLEKPVPVPTDKPEDMRVDLHSPQEEAKY 60
Query: 759 NRYDQERFIKSREETEGFKIDTMGKGH 785
NRY QERF S EETEGFKIDT G
Sbjct: 61 NRYAQERF--SGEETEGFKIDTFGSLR 85
>gnl|CDD|227486 COG5157, CDC73, RNA polymerase II assessory factor [Transcription].
Length = 362
Score = 55.8 bits (134), Expect = 4e-08
Identities = 27/107 (25%), Positives = 47/107 (43%), Gaps = 14/107 (13%)
Query: 15 KRISRTPIIIIPAANTSLITM-----------FVT-TEAKRAAGSKRENEILIQRSKGDG 62
K ++ PII++P + +S +T+ +V + R +E+ DG
Sbjct: 200 KYYAKDPIILVPQSASSPLTLSNIKEFLEEGKYVNPRNLPSCSDGIRISEVEKVELDLDG 259
Query: 63 TTVPYRVIDNPLKLARTDWDRVVAVFVMGPAWQFKGWPWDANPVEIF 109
+ ++D+ WDRVV +F G WQF + W +P E+F
Sbjct: 260 P-FRFIIVDDTGGFKPEYWDRVVCIFTTGSKWQFGRYNWR-DPGELF 304
>gnl|CDD|214470 smart00013, LRRNT, Leucine rich repeat N-terminal domain.
Length = 33
Score = 32.3 bits (74), Expect = 0.046
Identities = 13/32 (40%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 799 QCPFRCICFRTTVRCMFQHLEYVPR-VSNDTT 829
CP C C T V C + L VP + DTT
Sbjct: 1 ACPAPCNCSGTAVDCSGRGLTEVPLDLPPDTT 32
>gnl|CDD|201808 pfam01462, LRRNT, Leucine rich repeat N-terminal domain. Leucine
Rich Repeats pfam00560 are short sequence motifs present
in a number of proteins with diverse functions and
cellular locations. Leucine Rich Repeats are often
flanked by cysteine rich domains. This domain is often
found at the N-terminus of tandem leucine rich repeats.
Length = 28
Score = 29.1 bits (66), Expect = 0.56
Identities = 11/26 (42%), Positives = 13/26 (50%)
Query: 799 QCPFRCICFRTTVRCMFQHLEYVPRV 824
CP C+C T V C + L VPR
Sbjct: 1 ACPAPCVCSGTVVDCSGRGLTEVPRD 26
>gnl|CDD|215641 PLN03237, PLN03237, DNA topoisomerase 2; Provisional.
Length = 1465
Score = 32.1 bits (73), Expect = 1.7
Identities = 27/144 (18%), Positives = 47/144 (32%), Gaps = 15/144 (10%)
Query: 179 RKAAASNIPVVPRPYRKDILAYLNGEVATSASIDKTAPLEIPTQVKRVGTEELETPAKKP 238
RK AA+N P A AT + ++ T++ + +P KK
Sbjct: 1336 RKPAAANKKAAKPP-----AAAKKRGPAT-----VQSGQKLLTEMLKPAEAIGISPEKKV 1385
Query: 239 RLEDSVHLQHVKQQLAARLDAPKEASVTLDNIKFGPGSLTEAMSVEKIAAIKAKRLAKKR 298
R + + R KE + +N+ S + E + K + R
Sbjct: 1386 RKMRASPFNKKSGSVLGRAATNKETE-SSENVSGSSSSEKD----EIDVSAKPRPQRANR 1440
Query: 299 TTIKRVATDTDGTDIGDKDAEKDN 322
V +D++ D D + D
Sbjct: 1441 KQTTYVLSDSESESADDSDFDDDE 1464
Score = 32.1 bits (73), Expect = 1.7
Identities = 27/144 (18%), Positives = 47/144 (32%), Gaps = 15/144 (10%)
Query: 536 RKAAASNIPVVPRPYRKDILAYLNGEVATSASIDKTAPLEIPTQVKRVGTEELETPAKKP 595
RK AA+N P A AT + ++ T++ + +P KK
Sbjct: 1336 RKPAAANKKAAKPP-----AAAKKRGPAT-----VQSGQKLLTEMLKPAEAIGISPEKKV 1385
Query: 596 RLEDSVHLQHVKQQLAARLDAPKEASVTLDNIKFGPGSLTEAMSVEKIAAIKAKRLAKKR 655
R + + R KE + +N+ S + E + K + R
Sbjct: 1386 RKMRASPFNKKSGSVLGRAATNKETE-SSENVSGSSSSEKD----EIDVSAKPRPQRANR 1440
Query: 656 TTIKRVATDTDGTDIGDKDAEKDN 679
V +D++ D D + D
Sbjct: 1441 KQTTYVLSDSESESADDSDFDDDE 1464
>gnl|CDD|192486 pfam10224, DUF2205, Predicted coiled-coil protein (DUF2205). This
entry represent a highly conserved 100 residue region
which is likely to be a coiled-coil structure. The exact
function is unknown.
Length = 80
Score = 28.6 bits (64), Expect = 2.6
Identities = 17/80 (21%), Positives = 37/80 (46%), Gaps = 1/80 (1%)
Query: 219 IPTQVKRVGTEELETPAKKPRLEDSVHLQHVKQQLAARLDAPKEASVTLDN-IKFGPGSL 277
+ + E LE A++ +E ++ LQ + L+ R++A KE ++ L + +F +
Sbjct: 1 MSPRRDSEDLEALEKEARQRLIEQALELQDSLEDLSQRVEAVKEENLKLRSENQFLQQYI 60
Query: 278 TEAMSVEKIAAIKAKRLAKK 297
MS + + ++ K
Sbjct: 61 ENLMSNSSVTQSTSPKIKNK 80
Score = 28.6 bits (64), Expect = 2.6
Identities = 17/80 (21%), Positives = 37/80 (46%), Gaps = 1/80 (1%)
Query: 576 IPTQVKRVGTEELETPAKKPRLEDSVHLQHVKQQLAARLDAPKEASVTLDN-IKFGPGSL 634
+ + E LE A++ +E ++ LQ + L+ R++A KE ++ L + +F +
Sbjct: 1 MSPRRDSEDLEALEKEARQRLIEQALELQDSLEDLSQRVEAVKEENLKLRSENQFLQQYI 60
Query: 635 TEAMSVEKIAAIKAKRLAKK 654
MS + + ++ K
Sbjct: 61 ENLMSNSSVTQSTSPKIKNK 80
>gnl|CDD|111576 pfam02691, VacA, Vacuolating cyotoxin. This family consists of
Vacuolating cyotoxin proteins form Proteobacteria. These
proteins are an important virulence determinate in H.
pylori and induce cytoplasmic vacuolation in a variety
of mammalian cell lines.
Length = 1002
Score = 31.2 bits (70), Expect = 2.7
Identities = 23/87 (26%), Positives = 36/87 (41%), Gaps = 5/87 (5%)
Query: 429 GMTLKSVTEGNTPRKPALTPSTPAHQT---PSATPNANAAASPAPYNINKKEIIERENQI 485
G+ + + EG KP PS + S+ N+N + K EI + Q+
Sbjct: 290 GLNIIAPPEGGYEDKPKDNPSQSGAKNDKQESSQNNSNTQVINPKNDAQKTEI--QPTQV 347
Query: 486 IFGEFSWPKDVNTNYLHYQSSREGAVK 512
I G F+ KD N H + +G +K
Sbjct: 348 IDGPFAGGKDTVVNIDHINTKADGTIK 374
>gnl|CDD|180523 PRK06305, PRK06305, DNA polymerase III subunits gamma and tau;
Validated.
Length = 451
Score = 30.9 bits (70), Expect = 3.2
Identities = 13/76 (17%), Positives = 25/76 (32%), Gaps = 2/76 (2%)
Query: 348 TSIFHTSGKIFSKNIFAILQSIKAREEGRHRPAPPTPLVPSTPVN--KSVPQPIVYNRYD 405
T I H + ++ IK+ + R P + S+ S PQP + +
Sbjct: 341 TVIIHLIRIYQRPTLSQLVSQIKSPAFTQLRLESCPPQIKSSNSQQTVSSPQPQPVAKLE 400
Query: 406 QERFIKSREETEGFKI 421
Q + + +
Sbjct: 401 QGSLLTAASPQTKKET 416
Score = 30.9 bits (70), Expect = 3.2
Identities = 13/76 (17%), Positives = 25/76 (32%), Gaps = 2/76 (2%)
Query: 705 TSIFHTSGKIFSKNIFAILQSIKAREEGRHRPAPPTPLVPSTPVN--KSVPQPIVYNRYD 762
T I H + ++ IK+ + R P + S+ S PQP + +
Sbjct: 341 TVIIHLIRIYQRPTLSQLVSQIKSPAFTQLRLESCPPQIKSSNSQQTVSSPQPQPVAKLE 400
Query: 763 QERFIKSREETEGFKI 778
Q + + +
Sbjct: 401 QGSLLTAASPQTKKET 416
>gnl|CDD|223722 COG0649, NuoD, NADH:ubiquinone oxidoreductase 49 kD subunit 7
[Energy production and conversion].
Length = 398
Score = 29.9 bits (68), Expect = 6.1
Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 5/50 (10%)
Query: 184 SNIPVVPRPYRKDILAYLNGEVATSASIDKTAPLEIP--TQVKRVGTEEL 231
NIP R D L+ +N E+A +++K +E+P Q RV EL
Sbjct: 66 QNIPYTDRL---DYLSAMNNELAYVLAVEKLLGIEVPERAQYIRVMLSEL 112
Score = 29.9 bits (68), Expect = 6.1
Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 5/50 (10%)
Query: 541 SNIPVVPRPYRKDILAYLNGEVATSASIDKTAPLEIP--TQVKRVGTEEL 588
NIP R D L+ +N E+A +++K +E+P Q RV EL
Sbjct: 66 QNIPYTDRL---DYLSAMNNELAYVLAVEKLLGIEVPERAQYIRVMLSEL 112
>gnl|CDD|225093 COG2182, MalE, Maltose-binding periplasmic proteins/domains
[Carbohydrate transport and metabolism].
Length = 420
Score = 29.6 bits (67), Expect = 7.6
Identities = 9/46 (19%), Positives = 13/46 (28%)
Query: 70 IDNPLKLARTDWDRVVAVFVMGPAWQFKGWPWDANPVEIFSKNLAV 115
L D ++F G A PW + + N V
Sbjct: 240 YKKGLIPEDVAGDFAQSLFTEGKAAAIINGPWSISAYKDAGINYGV 285
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
0.316 0.131 0.381
Gapped
Lambda K H
0.267 0.0726 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 42,019,315
Number of extensions: 4134330
Number of successful extensions: 4075
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4063
Number of HSP's successfully gapped: 37
Length of query: 831
Length of database: 10,937,602
Length adjustment: 105
Effective length of query: 726
Effective length of database: 6,280,432
Effective search space: 4559593632
Effective search space used: 4559593632
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 63 (28.1 bits)