RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8909
(138 letters)
>gnl|CDD|163611 pfam10046, BLOC1_2, Biogenesis of lysosome-related organelles
complex-1 subunit 2. Members of this family of proteins
play a role in cellular proliferation, as well as in the
biogenesis of specialized organelles of the
endosomal-lysosomal system.
Length = 99
Score = 85.4 bits (212), Expect = 9e-23
Identities = 44/99 (44%), Positives = 59/99 (59%)
Query: 37 ATNMFKKTADYLIGELNSTQADYEVLEKMNNATITKYSDMKQITVNISNSIEEQNQRYKQ 96
A MF K + Y+ EL + D ++LEKMN T KY M+Q + IE NQ+Y++
Sbjct: 1 AEKMFNKISKYVEAELEISVEDLKLLEKMNENTALKYKKMRQSAKGLRVEIEALNQKYEE 60
Query: 97 LIPQLEQIDQIYDSVLKLEQAAYKLDHYAKRLEAKFKQL 135
L P L+QID I V LE+A Y+LD Y+K LE+K K L
Sbjct: 61 LKPYLQQIDAIEQQVTTLEEAVYELDEYSKELESKVKSL 99
>gnl|CDD|223571 COG0497, RecN, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 557
Score = 31.0 bits (71), Expect = 0.16
Identities = 31/154 (20%), Positives = 62/154 (40%), Gaps = 29/154 (18%)
Query: 4 NVENSLSNKMTSLSTSTSSFEPMISHDPRLNELATNMFKKTADYLIGE--------LNST 55
+ E+ + ++ L + + E + +D +L+ELA + A Y + E L+
Sbjct: 235 SGEDDTVSALSLLGRALEALEDLSEYDGKLSELAE--LLEEALYELEEASEELRAYLDEL 292
Query: 56 QADYEVLEKMNNATITKYSDMKQITVNISNSIEEQNQRYKQLIPQLEQIDQIYDSVLKLE 115
+ D LE++ + +K + +IE+ + ++ +L Q+D +S+ LE
Sbjct: 293 EFDPNRLEEVE----ERLFALKSLARKYGVTIEDLLEYLDKIKEELAQLDNSEESLEALE 348
Query: 116 -----------QAAYKLD----HYAKRLEAKFKQ 134
+AA L AK LE +
Sbjct: 349 KEVKKLKAELLEAAEALSAIRKKAAKELEKEVTA 382
Score = 26.4 bits (59), Expect = 6.0
Identities = 12/53 (22%), Positives = 24/53 (45%), Gaps = 6/53 (11%)
Query: 85 NSIEEQNQRYKQLIPQLEQIDQIYDSVLKLEQAAYKLDHYAKRLEAKFKQLEK 137
+ E + + +L E +++ LE+A+ +L Y LE +LE+
Sbjct: 255 EDLSEYDGKLSEL---AELLEEALYE---LEEASEELRAYLDELEFDPNRLEE 301
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 30.4 bits (69), Expect = 0.25
Identities = 24/92 (26%), Positives = 41/92 (44%), Gaps = 3/92 (3%)
Query: 48 LIGELNSTQADYEVLEKMNNATITKYSDMKQITVNISNSIEEQNQRYKQLIPQLEQIDQI 107
L EL+S Q++ +E + + SD + I IE+ Q ++L +LE++ +
Sbjct: 686 LKRELSSLQSELRRIENRLDELSQELSDASRKIGEIEKEIEQLEQEEEKLKERLEEL-EE 744
Query: 108 YDSVLKLEQAAYK--LDHYAKRLEAKFKQLEK 137
S L+ E K L R+E + L K
Sbjct: 745 DLSSLEQEIENVKSELKELEARIEELEEDLHK 776
>gnl|CDD|129705 TIGR00618, sbcc, exonuclease SbcC. All proteins in this family for
which functions are known are part of an exonuclease
complex with sbcD homologs. This complex is involved in
the initiation of recombination to regulate the levels
of palindromic sequences in DNA. 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 = 1042
Score = 30.3 bits (68), Expect = 0.36
Identities = 20/99 (20%), Positives = 35/99 (35%)
Query: 40 MFKKTADYLIGELNSTQADYEVLEKMNNATITKYSDMKQITVNISNSIEEQNQRYKQLIP 99
M L G+ ++L Y + KQ+ + E Q+ +Q
Sbjct: 184 MEFAKKKSLHGKAELLTLRSQLLTLCTPCMPDTYHERKQVLEKELKHLREALQQTQQSHA 243
Query: 100 QLEQIDQIYDSVLKLEQAAYKLDHYAKRLEAKFKQLEKQ 138
L Q + + LK +Q +L + L A+ LE+
Sbjct: 244 YLTQKREAQEEQLKKQQLLKQLRARIEELRAQEAVLEET 282
>gnl|CDD|234501 TIGR04211, SH3_and_anchor, SH3 domain protein. Members of this
protein family have a signal peptide, a strongly
conserved SH3 domain, a variable region, and then a
C-terminal hydrophobic transmembrane alpha helix region.
Length = 198
Score = 29.6 bits (67), Expect = 0.44
Identities = 14/72 (19%), Positives = 34/72 (47%), Gaps = 2/72 (2%)
Query: 32 RLNELATNMFKKTADYLIGELNSTQADYEVLEKMNNATITKYSDMKQITVNISNSIEEQN 91
L E + ++ A+ L E + + LE + + +KQ++ N ++E+N
Sbjct: 77 ELQEELAELQEQLAE-LQQENQELKQELSTLEAELERLQKELARIKQLSANAIE-LDEEN 134
Query: 92 QRYKQLIPQLEQ 103
+ ++ + +L+Q
Sbjct: 135 RELREELAELKQ 146
>gnl|CDD|234342 TIGR03752, conj_TIGR03752, integrating conjugative element protein,
PFL_4705 family. Members of this protein family are
found occasionally on plasmids such as the Pseudomonas
putida toluene catabolic TOL plasmid pWWO_p085. Usually,
however, they are found on the bacterial main chromosome
in regions flanked by markers of conjugative transfer
and/or transposition [Mobile and extrachromosomal
element functions, Plasmid functions].
Length = 472
Score = 29.2 bits (66), Expect = 0.62
Identities = 19/116 (16%), Positives = 45/116 (38%), Gaps = 4/116 (3%)
Query: 7 NSLSNKMTSLSTSTSSFEPMISHDPRLNELATNMFKKTADYLIGELNSTQADYEVLEKMN 66
S S + TS ++ + + + + + T L+ E+ + L N
Sbjct: 23 KSFSGSGSPEPTSDTALAELSPEELKALGIEGDTPADTLRTLVAEVKELRKRLAKLISEN 82
Query: 67 NATITKYSDMKQITVNISNSIEEQNQRYKQLIPQL-EQIDQIYDSVLKLEQAAYKL 121
A + +++ +I I++ Q Q +L ++I+Q+ +L+ +L
Sbjct: 83 EALKAENERLQKREQSIDQQIQQAVQSETQ---ELTKEIEQLKSERQQLQGLIDQL 135
>gnl|CDD|212087 cd11518, SLC6sbd_SIT1, Na(+)- and Cl(-)-dependent imino acid
transporter SIT1; solute-binding domain. SIT1 (also
called XTRP3, XT3, IMINO) transports imino acids, such
as proline, pipecolate, MeAIB, and sarcosine. It has
weak affinity for neutral amino acids such as
phenylalanine. Human SIT1 is encoded by the SLC6A20
gene. SIT1 is expressed in brain, kidney, small
intestine, thymus, spleen, ovary, and lung. SLC6A20 is a
candidate gene for the rare disorder iminoglycinuria.
This subgroup belongs to the solute carrier 6 (SLC6)
transporter family.
Length = 576
Score = 28.3 bits (63), Expect = 1.6
Identities = 16/38 (42%), Positives = 23/38 (60%), Gaps = 3/38 (7%)
Query: 52 LNSTQADYEVLEKMNNATITKYSDMKQITVNISNSIEE 89
LNS + Y E+ A+ T+Y ++ T+NIS SIEE
Sbjct: 127 LNSNRTGYT--EECEKASPTQYFWYRE-TLNISPSIEE 161
>gnl|CDD|220441 pfam09849, DUF2076, Uncharacterized protein conserved in bacteria
(DUF2076). This domain, found in various hypothetical
prokaryotic proteins, has no known function. The domain,
however, is found in various periplasmic ligand-binding
sensor proteins.
Length = 234
Score = 27.3 bits (61), Expect = 2.2
Identities = 8/30 (26%), Positives = 14/30 (46%)
Query: 109 DSVLKLEQAAYKLDHYAKRLEAKFKQLEKQ 138
D+ L Q + K+ A+ ++LE Q
Sbjct: 41 DAPYYLVQTILVQEAALKQANARIEELEAQ 70
>gnl|CDD|226809 COG4372, COG4372, Uncharacterized protein conserved in bacteria
with the myosin-like domain [Function unknown].
Length = 499
Score = 27.7 bits (61), Expect = 2.4
Identities = 17/92 (18%), Positives = 37/92 (40%), Gaps = 4/92 (4%)
Query: 51 ELNSTQADYEVLEKMNNATITKYSDMKQITVNISNSIEEQNQRYKQLIPQ----LEQIDQ 106
EL + + E + + A + +Q ++ ++ R K L Q Q
Sbjct: 110 ELQKARQEREAVRQELAAARQNLAKAQQELARLTKQAQDLQTRLKTLAEQRRQLEAQAQS 169
Query: 107 IYDSVLKLEQAAYKLDHYAKRLEAKFKQLEKQ 138
+ S +L+ +A +L L+ + Q+E++
Sbjct: 170 LQASQKQLQASATQLKSQVLDLKLRSAQIEQE 201
>gnl|CDD|131884 TIGR02837, spore_II_R, stage II sporulation protein R. A
comparative genome analysis of all sequenced genomes of
shows a number of proteins conserved strictly among the
endospore-forming subset of the Firmicutes. This
protein, a member of this panel, is designated stage II
sporulation protein R [Cellular processes, Sporulation
and germination].
Length = 168
Score = 27.0 bits (60), Expect = 3.2
Identities = 15/46 (32%), Positives = 28/46 (60%), Gaps = 5/46 (10%)
Query: 77 KQIT--VNISNSIEEQNQRYKQLIPQLEQIDQIYDSVLKLEQAAYK 120
K+I ++ S+EE + ++ +P +I++I +SV+K E A YK
Sbjct: 66 KEIRPWLSGLKSLEEARRVIRENLP---EIERIAESVIKAEGADYK 108
>gnl|CDD|224486 COG1570, XseA, Exonuclease VII, large subunit [DNA replication,
recombination, and repair].
Length = 440
Score = 27.2 bits (61), Expect = 3.5
Identities = 16/69 (23%), Positives = 34/69 (49%), Gaps = 3/69 (4%)
Query: 63 EKMNNATITKYSDMKQITVNISNSIEEQNQRYKQLIPQLE-QIDQIYDSVLKLEQAAYKL 121
++ A + + KQ ++ + Q QR +Q + QLE ++D+ LK + +L
Sbjct: 320 IRLRRALENQLALKKQRLERLTQRLNPQIQRQQQRLQQLERRLDKALRRQLK--RKRERL 377
Query: 122 DHYAKRLEA 130
+ ++LE+
Sbjct: 378 EALVEQLES 386
>gnl|CDD|226513 COG4026, COG4026, Uncharacterized protein containing TOPRIM domain,
potential nuclease [General function prediction only].
Length = 290
Score = 26.8 bits (59), Expect = 4.0
Identities = 15/73 (20%), Positives = 39/73 (53%), Gaps = 4/73 (5%)
Query: 70 ITKYSDMKQITVNISNSIEEQNQRYKQLIPQLE----QIDQIYDSVLKLEQAAYKLDHYA 125
+ +Y D+K+ + +EE + ++L+ +LE + +++ + + +LE +L+
Sbjct: 127 VPEYMDLKEDYEELKEKLEELQKEKEELLKELEELEAEYEEVQERLKRLEVENSRLEEML 186
Query: 126 KRLEAKFKQLEKQ 138
K+L + L+K+
Sbjct: 187 KKLPGEVYDLKKR 199
>gnl|CDD|181419 PRK08418, PRK08418, chlorohydrolase; Provisional.
Length = 408
Score = 26.9 bits (60), Expect = 4.6
Identities = 14/83 (16%), Positives = 32/83 (38%), Gaps = 11/83 (13%)
Query: 26 MISHDPRLNELATNMFKKTADYLIGELNSTQADYEVLEKMNNATITKYSDMKQITVNISN 85
+ + L ELA + L++T+ + L +NN I + D +
Sbjct: 330 LTHANMPLLELAKILL----------LSATRYGAKAL-GLNNGEIKEGKDADLSVFELPE 378
Query: 86 SIEEQNQRYKQLIPQLEQIDQIY 108
++ Q Q I +++ +++
Sbjct: 379 ECTKKEQLPLQFILHAKEVKKLF 401
>gnl|CDD|219791 pfam08317, Spc7, Spc7 kinetochore protein. This domain is found in
cell division proteins which are required for
kinetochore-spindle association.
Length = 321
Score = 26.5 bits (59), Expect = 4.8
Identities = 22/89 (24%), Positives = 39/89 (43%), Gaps = 9/89 (10%)
Query: 48 LIGELNSTQADYEVLEKMNNATITKYSDMKQITVNISNSIEEQNQRYKQLIPQLEQIDQI 107
L L + D E+L K + + +K +++E+ +QL +L D
Sbjct: 152 LEENLEGMKRDEELLNK----DLNLINSIKPKLRKKLQALKEEIASLRQLADELNLCDP- 206
Query: 108 YDSVLKLEQAAYKLDHYAKRLEAKFKQLE 136
L+LE+A +L + ++ K KQLE
Sbjct: 207 ----LELEKARQELRSLSVKISEKRKQLE 231
>gnl|CDD|223450 COG0373, HemA, Glutamyl-tRNA reductase [Coenzyme metabolism].
Length = 414
Score = 26.4 bits (59), Expect = 5.6
Identities = 16/80 (20%), Positives = 38/80 (47%), Gaps = 5/80 (6%)
Query: 22 SFEPMISHDPRLNELATNMFKKTADYLIGELNSTQADYEVLEKMNNATITKYSDMKQITV 81
P I L E A ++ ++ + + +L + + + EVLEK+ + + K + TV
Sbjct: 334 EVVPTIRA---LREQAEDVREEELEKALKKLPNGEDEEEVLEKLARSLVNKL--LHAPTV 388
Query: 82 NISNSIEEQNQRYKQLIPQL 101
+ + +E ++ + + +L
Sbjct: 389 RLKEAAKEGSEELLRALREL 408
>gnl|CDD|236912 PRK11448, hsdR, type I restriction enzyme EcoKI subunit R;
Provisional.
Length = 1123
Score = 26.5 bits (59), Expect = 6.9
Identities = 12/58 (20%), Positives = 28/58 (48%), Gaps = 1/58 (1%)
Query: 82 NISNSIEEQNQRYKQLIPQLEQIDQIYDSVLKLEQA-AYKLDHYAKRLEAKFKQLEKQ 138
N+ ++++++ KQ + + ++ + +Q L+ A LE K ++LE Q
Sbjct: 142 NLLHALQQEVLTLKQQLELQAREKAQSQALAEAQQQELVALEGLAAELEEKQQELEAQ 199
>gnl|CDD|222290 pfam13654, AAA_32, AAA domain. This family includes a wide variety
of AAA domains including some that have lost essential
nucleotide binding residues in the P-loop.
Length = 509
Score = 26.3 bits (59), Expect = 7.0
Identities = 11/56 (19%), Positives = 28/56 (50%), Gaps = 4/56 (7%)
Query: 84 SNSIEEQNQRYKQLIPQLEQIDQIYDSVLKLEQ--AAYKLDHYAKRLEAKFKQLEK 137
+ +EE+ Q + + +LE+ + + + +L++ A + + L+ K+ L K
Sbjct: 184 IDELEEELQEILRQLRELER--EAREKLRELDREVALFAVGPLLDELKEKYADLPK 237
>gnl|CDD|240319 PTZ00226, PTZ00226, fumarate hydratase; Provisional.
Length = 570
Score = 26.2 bits (58), Expect = 7.1
Identities = 13/39 (33%), Positives = 18/39 (46%)
Query: 61 VLEKMNNATITKYSDMKQITVNISNSIEEQNQRYKQLIP 99
VL K T D K ++ + N+ +N RY QL P
Sbjct: 142 VLGKRGELIWTGGEDEKALSKGVYNAYTNRNLRYSQLAP 180
>gnl|CDD|216531 pfam01496, V_ATPase_I, V-type ATPase 116kDa subunit family. This
family consists of the 116kDa V-type ATPase (vacuolar
(H+)-ATPases) subunits, as well as V-type ATP synthase
subunit i. The V-type ATPases family are proton pumps
that acidify intracellular compartments in eukaryotic
cells for example yeast central vacuoles,
clathrin-coated and synaptic vesicles. They have
important roles in membrane trafficking processes. The
116kDa subunit (subunit a) in the V-type ATPase is part
of the V0 functional domain responsible for proton
transport. The a subunit is a transmembrane glycoprotein
with multiple putative transmembrane helices it has a
hydrophilic amino terminal and a hydrophobic carboxy
terminal. It has roles in proton transport and assembly
of the V-type ATPase complex. This subunit is encoded by
two homologous gene in yeast VPH1 and STV1.
Length = 707
Score = 25.8 bits (57), Expect = 8.6
Identities = 8/41 (19%), Positives = 21/41 (51%)
Query: 98 IPQLEQIDQIYDSVLKLEQAAYKLDHYAKRLEAKFKQLEKQ 138
+P ++ + + +L LE +++ + LE + +LE+
Sbjct: 63 VPPSKEFLDLEEEILDLEAEIKEVEENLESLEKEINELEEW 103
>gnl|CDD|239296 cd02998, PDI_a_ERp38, PDIa family, endoplasmic reticulum protein
38 (ERp38) subfamily; composed of proteins similar to
the P5-like protein first isolated from alfalfa, which
contains two redox active TRX (a) domains at the
N-terminus, like human P5, and a C-terminal domain with
homology to the C-terminal domain of ERp29, unlike
human P5. The cDNA clone of this protein (named G1) was
isolated from an alfalfa cDNA library by screening with
human protein disulfide isomerase (PDI) cDNA. The G1
protein is constitutively expressed in all major organs
of the plant and its expression is induced by treatment
with tunicamycin, indicating that it may be a
glucose-regulated protein. The G1 homolog in the
eukaryotic social amoeba Dictyostelium discoideum is
also described as a P5-like protein, which is located
in the endoplasmic reticulum (ER) despite the absence
of an ER-retrieval signal. G1 homologs from Aspergillus
niger and Neurospora crassa have also been
characterized, and are named TIGA and ERp38,
respectively. Also included in the alignment is an
atypical PDI from Leishmania donovani containing a
single a domain, and the C-terminal a domain of a
P5-like protein from Entamoeba histolytica.
Length = 105
Score = 25.3 bits (56), Expect = 8.6
Identities = 8/34 (23%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 31 PRLNELATNMFKKTADYLIGELNSTQADYEVLEK 64
P +LA +F D +I ++++ +A+ ++ +K
Sbjct: 38 PEYEKLA-AVFANEDDVVIAKVDADEANKDLAKK 70
>gnl|CDD|204614 pfam11221, Med21, Subunit 21 of Mediator complex. Med21 has been
known as Srb7 in yeasts, hSrb7 in humans and Trap 19 in
Drosophila. The heterodimer of the two subunits Med7 and
Med21 appears to act as a hinge between the middle and
the tail regions of Mediator.
Length = 132
Score = 25.3 bits (56), Expect = 9.3
Identities = 16/67 (23%), Positives = 34/67 (50%), Gaps = 12/67 (17%)
Query: 77 KQITVNIS------NSIEEQNQRYKQLIPQLEQIDQIYDSVLKLEQAAYKLDHYAKRLEA 130
+QI I +S EEQ +R K+L +L +++ + E+A + + K++EA
Sbjct: 71 QQIEYLIDSLPGIESSEEEQLRRIKELEEELREVEA------EREEAVKEKEKLLKKVEA 124
Query: 131 KFKQLEK 137
+++ +
Sbjct: 125 LLREIAR 131
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
0.308 0.123 0.316
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: 6,454,145
Number of extensions: 561673
Number of successful extensions: 816
Number of sequences better than 10.0: 1
Number of HSP's gapped: 793
Number of HSP's successfully gapped: 139
Length of query: 138
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 51
Effective length of database: 7,078,804
Effective search space: 361019004
Effective search space used: 361019004
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 54 (24.6 bits)