RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy876
(179 letters)
>gnl|CDD|233047 TIGR00604, rad3, DNA repair helicase (rad3). All proteins in this
family for which funcitons are known are DNA-DNA
helicases that funciton in the initiation of
transcription and nucleotide excision repair as part of
the TFIIH complex. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 705
Score = 59.7 bits (145), Expect = 6e-11
Identities = 21/69 (30%), Positives = 36/69 (52%)
Query: 82 KYTLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELGTQFPIKLEANHVIDKDQ 141
L F CL+ + + E RSVIL SGTL+P+D+F LG + H++ ++
Sbjct: 420 NPILKFMCLDPSIALKPLFERVRSVILASGTLSPLDAFPRNLGFNPVSQDSPTHILKREN 479
Query: 142 VFIGVLGQG 150
+ ++ +G
Sbjct: 480 LLTLIVTRG 488
Score = 27.8 bits (62), Expect = 3.8
Identities = 11/30 (36%), Positives = 19/30 (63%), Gaps = 2/30 (6%)
Query: 4 LSSRKHTCINDEVLKAK--ENINDLCQELK 31
L+SRK+ C++ EV K + + +N C +L
Sbjct: 102 LASRKNLCLHPEVSKERQGKVVNGKCIKLT 131
>gnl|CDD|219153 pfam06733, DEAD_2, DEAD_2. This represents a conserved region
within a number of RAD3-like DNA-binding helicases that
are seemingly ubiquitous - members include proteins of
eukaryotic, bacterial and archaeal origin. RAD3 is
involved in nucleotide excision repair, and forms part
of the transcription factor TFIIH in yeast.
Length = 168
Score = 44.3 bits (105), Expect = 5e-06
Identities = 18/33 (54%), Positives = 23/33 (69%), Gaps = 2/33 (6%)
Query: 1 MTILSSRKHTCINDEVLKAK--ENINDLCQELK 31
IL SRK+ CIN EV K + E+IN+ C+ELK
Sbjct: 27 GVILGSRKNLCINPEVKKLRKGEDINEKCKELK 59
>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA
replication, recombination, and repair].
Length = 654
Score = 37.1 bits (86), Expect = 0.003
Identities = 15/38 (39%), Positives = 21/38 (55%)
Query: 87 FWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELG 124
L + ++ SV+LTS TL+P+DSF S LG
Sbjct: 387 LPLLVPSKLLEELFSKVASVVLTSATLSPLDSFSSLLG 424
>gnl|CDD|214693 smart00488, DEXDc2, DEAD-like helicases superfamily.
Length = 289
Score = 32.4 bits (74), Expect = 0.089
Identities = 12/33 (36%), Positives = 19/33 (57%), Gaps = 3/33 (9%)
Query: 2 TILSSRKHTCINDEVLKAKE--NIND-LCQELK 31
L+SRK+ C+N EV K+ + D +C+ L
Sbjct: 116 LSLTSRKNLCLNPEVRTLKQNGLVVDEVCRSLT 148
>gnl|CDD|236148 PRK08074, PRK08074, bifunctional ATP-dependent DNA helicase/DNA
polymerase III subunit epsilon; Validated.
Length = 928
Score = 29.1 bits (66), Expect = 1.5
Identities = 12/24 (50%), Positives = 13/24 (54%), Gaps = 3/24 (12%)
Query: 104 RSVILTSGTLAPVDSFQ---SELG 124
+SVILTS TL SF LG
Sbjct: 673 KSVILTSATLTVNGSFDYIIERLG 696
>gnl|CDD|217658 pfam03650, UPF0041, Uncharacterized protein family (UPF0041).
Length = 120
Score = 27.9 bits (62), Expect = 1.6
Identities = 13/42 (30%), Positives = 17/42 (40%), Gaps = 3/42 (7%)
Query: 72 YRKDRTPMSIKYTLHFW--CLNSGLVFSDIRESARSVILTSG 111
R K T+HFW L GLV + + + R SG
Sbjct: 7 KRFWNHEAGPK-TVHFWAPTLKWGLVLAGLGDLKRPPEKISG 47
>gnl|CDD|222991 PHA03119, PHA03119, helicase-primase primase subunit; Provisional.
Length = 1085
Score = 27.6 bits (61), Expect = 4.2
Identities = 18/52 (34%), Positives = 21/52 (40%), Gaps = 4/52 (7%)
Query: 75 DRTPMSIKYTLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELGTQ 126
DR + Y HF C N IR+ R+V LT L P S LG
Sbjct: 343 DREFVDYIYLAHFECFNR----KQIRDHLRAVTLTDIALIPDVVSASSLGRS 390
>gnl|CDD|220478 pfam09935, DUF2167, Protein of unknown function (DUF2167). This
domain, found in various hypothetical membrane-anchored
prokaryotic proteins, has no known function.
Length = 241
Score = 27.3 bits (61), Expect = 4.7
Identities = 16/58 (27%), Positives = 26/58 (44%), Gaps = 12/58 (20%)
Query: 19 AKENINDLCQELKETEGESNRWYRKDRTPMRGIEPVVSQG----PHADEYQGESNRWY 72
AK + +DL + +KE E N+ + +G E + G PH D ++R Y
Sbjct: 78 AKIDYDDLLKSMKEGTEEDNKEREE-----QGYEAIELVGWAEKPHYDA---ATHRLY 127
>gnl|CDD|185333 PRK15435, PRK15435, bifunctional DNA-binding transcriptional dual
regulator/O6-methylguanine-DNA methyltransferase;
Provisional.
Length = 353
Score = 27.1 bits (60), Expect = 5.7
Identities = 21/71 (29%), Positives = 30/71 (42%), Gaps = 9/71 (12%)
Query: 60 HADEYQGESNRWYRKDRTPMSIKYTLHFWCLNSGLVFSDIRESARSV--ILTSGTLAPVD 117
ADE G + + +R ++++Y L L LV ES R + IL A
Sbjct: 168 KADETLGMTAKQFRHGGENLAVRYALADCELGRCLV----AESERGICAILLGDDDA--- 220
Query: 118 SFQSELGTQFP 128
+ SEL FP
Sbjct: 221 ALISELQQMFP 231
>gnl|CDD|199844 cd03860, M14_CP_A-B_like, Peptidase M14 carboxypeptidase subfamily
A/B-like. The Peptidase M14 Carboxypeptidase (CP) A/B
subfamily is one of two main M14 CP subfamilies defined
by sequence and structural homology, the other being the
N/E subfamily. CPs hydrolyze single, C-terminal amino
acids from polypeptide chains. They have a recognition
site for the free C-terminal carboxyl group, which is a
key determinant of specificity. Enzymes belonging to the
A/B subfamily are normally synthesized as inactive
precursors containing preceding signal peptide, followed
by a globular N-terminal pro-region linked to the
enzyme; these proenzymes are called
procarboxypeptidases. The A/B enzymes can be further
divided based on their substrate specificity;
Carboxypeptidase A-like (CPA-like) enzymes favor
hydrophobic residues while carboxypeptidase B-like
(CPB-like) enzymes only cleave the basic residues lysine
or arginine. There are nine members in the A/B family:
CPA1, CPA2, CPA3, CPA4, CPA5, CPA6, CPB, CPO and CPU.
CPA1, CPA2 and CPB are produced by the pancreas. The A
forms have slightly different specificities, with CPA1
preferring aliphatic and small aromatic residues, and
CPA2 preferring the bulkier aromatic side chains. CPA3
is found in secretory granules of mast cells and
functions in inflammatory processes. CPA4 is detected in
hormone-regulated tissues, and is thought to play a role
in prostate cancer. CPA5 is present in discrete regions
of pituitary and other tissues, and cleaves aliphatic
C-terminal residues. CPA6 is highly expressed in
embryonic brain and optic muscle, suggesting that it may
play a specific role in cell migration and axonal
guidance. CPU (also called CPB2) is produced and
secreted by the liver as the inactive precursor, PCPU,
commonly referred to as thrombin-activatable
fibrinolysis inhibitor (TAFI). Little is known about CPO
but it has been suggested to have specificity for acidic
residues.
Length = 293
Score = 26.7 bits (60), Expect = 6.7
Identities = 11/48 (22%), Positives = 18/48 (37%), Gaps = 15/48 (31%)
Query: 36 ESNRWYRKDRTPMRGI---------------EPVVSQGPHADEYQGES 68
++R +RK+R+P G S P ++ Y G S
Sbjct: 109 TTDRLWRKNRSPNGGGCVGVDLNRNFDFHWGGEGASSNPCSETYAGPS 156
>gnl|CDD|173971 cd08206, RuBisCO_large_I_II_III, Ribulose bisphosphate carboxylase
large chain, Form I,II,III. Ribulose bisphosphate
carboxylase (Rubisco) plays an important role in the
Calvin reductive pentose phosphate pathway. It catalyzes
the primary CO2 fixation step. Rubisco is activated by
carbamylation of an active site lysine, stabilized by a
divalent cation, which then catalyzes the proton
abstraction from the substrate ribulose 1,5 bisphosphate
(RuBP) and leads to the formation of two molecules of
3-phosphoglycerate. Members of the Rubisco family can be
divided into 4 subgroups, Form I-IV, which differ in
their taxonomic distribution and subunit composition.
Form I-III have Rubisco activity, while Form IV, also
called Rubico-like proteins (RLP), are missing critical
active site residues.
Length = 414
Score = 26.8 bits (60), Expect = 7.4
Identities = 11/40 (27%), Positives = 19/40 (47%)
Query: 22 NINDLCQELKETEGESNRWYRKDRTPMRGIEPVVSQGPHA 61
I D+ +E + S ++ +D M+ + PV S G H
Sbjct: 309 GIADMLREDEVEGDLSRIFFNQDWGGMKPVFPVASGGLHP 348
>gnl|CDD|224618 COG1704, LemA, Uncharacterized conserved protein [Function
unknown].
Length = 185
Score = 26.1 bits (58), Expect = 8.1
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 17 LKAKENINDLCQELKETEGE 36
LKA EN +L +L+ TE
Sbjct: 114 LKANENFLELQSQLEGTENR 133
>gnl|CDD|227127 COG4789, EscV, Type III secretory pathway, component EscV
[Intracellular trafficking and secretion].
Length = 689
Score = 26.5 bits (59), Expect = 8.9
Identities = 14/33 (42%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 98 DIRESARSVILTSGTLAPVDSFQSELGTQFPIK 130
DIR R +I +S PV S+Q ELG + I+
Sbjct: 650 DIRRYVRKLIESSFPDLPVLSYQ-ELGEEINIQ 681
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
0.317 0.135 0.405
Gapped
Lambda K H
0.267 0.0696 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,749,645
Number of extensions: 772039
Number of successful extensions: 613
Number of sequences better than 10.0: 1
Number of HSP's gapped: 612
Number of HSP's successfully gapped: 23
Length of query: 179
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 88
Effective length of database: 6,901,388
Effective search space: 607322144
Effective search space used: 607322144
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 (21.7 bits)
S2: 56 (25.4 bits)