RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14254
(210 letters)
>gnl|CDD|218703 pfam05700, BCAS2, Breast carcinoma amplified sequence 2 (BCAS2).
This family consists of several eukaryotic sequences of
unknown function. The mammalian members of this family
are annotated as breast carcinoma amplified sequence 2
(BCAS2) proteins. BCAS2 is a putative spliceosome
associated protein.
Length = 221
Score = 233 bits (595), Expect = 4e-78
Identities = 109/210 (51%), Positives = 150/210 (71%), Gaps = 3/210 (1%)
Query: 4 EVLVDALPYIDQGYDDPGVREAALAMVEEETRRYRPTKNYLEHIPPL---DINKFETEIM 60
EV+VDALPYID YD+PGVREAA A+VEEE +RYRPTKNYLEH+P L D + FET ++
Sbjct: 6 EVVVDALPYIDDDYDEPGVREAADALVEEEMKRYRPTKNYLEHLPSLQGPDYSLFETPLL 65
Query: 61 RKDFERIQQRLPMEPLSMIRYKLPQPPTGKMSDIAAWTECVENSMSQLEHQSTRIVNLQL 120
R +FER+Q PM+ L M RY+LP+PP GK +D AW + N+ +QLEHQ RI+NL+L
Sbjct: 66 RNEFERVQAGQPMKGLDMSRYELPEPPAGKANDDKAWKAALNNARAQLEHQLIRIINLEL 125
Query: 121 MLEYGPETWKEYLQTLVNCVSQAQSKLIQLRKEIQEINWERKVMQIKGGEQLKKLEADWV 180
+ +YG W Y + L + + + +L +L++EI+E+N +RK Q + GE+L+ LE WV
Sbjct: 126 LSKYGKNAWLVYNEQLEALLKRLEKELAELKEEIEEVNRQRKYSQEEAGEKLRSLEQRWV 185
Query: 181 GLVSKNYEIEQACVLLEKKIQILQAEKAKR 210
LVSKN EIE AC LE++I+ L+ +KA+
Sbjct: 186 DLVSKNLEIEVACAELEQEIEQLKRKKAEL 215
>gnl|CDD|213286 cd05919, BCL_like, Benzoate CoA ligase (BCL) and similar adenylate
forming enzymes. This family contains benzoate CoA
ligase (BCL) and related ligases that catalyze the
acylation of benzoate derivatives, 2-aminobenzoate and
4-hydroxybenzoate. Aromatic compounds represent the
second most abundant class of organic carbon compounds
after carbohydrates. Xenobiotic aromatic compounds are
also a major class of man-made pollutants. Some bacteria
use benzoate as the sole source of carbon and energy
through benzoate degradation. Benzoate degradation
starts with its activation to benzoyl-CoA by benzoate
CoA ligase. The reaction catalyzed by benzoate CoA
ligase proceeds via a two-step process; the first
ATP-dependent step forms an acyl-AMP intermediate, and
the second step forms the acyl-CoA ester with release of
the AMP.
Length = 436
Score = 33.1 bits (76), Expect = 0.086
Identities = 20/77 (25%), Positives = 32/77 (41%), Gaps = 9/77 (11%)
Query: 19 DPGVREAALAMVEEETRRYRPTKNYLEHIPPLDIN-KFETEIMRKDFERIQQRLP--MEP 75
P V EAA+ V +E R ++ P I E ++ R +++RL P
Sbjct: 359 HPAVAEAAVVAVPDEDGLVRLKA-FVVPRPGEAIQQLLERDLHR----FLRERLAPYKCP 413
Query: 76 LSM-IRYKLPQPPTGKM 91
+ LP+ TGK+
Sbjct: 414 RQIEFLDTLPRTATGKL 430
>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y. Members of this family are
RNase Y, an endoribonuclease. The member from Bacillus
subtilis, YmdA, has been shown to be involved in
turnover of yitJ riboswitch [Transcription, Degradation
of RNA].
Length = 514
Score = 30.3 bits (69), Expect = 0.66
Identities = 29/125 (23%), Positives = 55/125 (44%), Gaps = 15/125 (12%)
Query: 56 ETEIMRKDFERIQQRLPMEPLSMIRYKLPQPPTGKMSDIAAWTECVENSMSQLEHQSTRI 115
E + R + +R+++RL ++ R KM + E +E +L ++ +
Sbjct: 70 ELKERRNELQRLERRLLQREETLDR---------KMESLDKKEENLEKKEKELSNKEKNL 120
Query: 116 VNLQLMLEYGPETWKEYLQTL--VNCVSQAQSKLIQLRKEIQEINWERKVMQIKGGEQLK 173
+ LE E E + L ++ ++Q ++K I L + +E E + IK E+
Sbjct: 121 DEKEEELE---ELIAEQREELERISGLTQEEAKEILLEEVEEEARHEAAKL-IKEIEEEA 176
Query: 174 KLEAD 178
K EAD
Sbjct: 177 KEEAD 181
>gnl|CDD|226330 COG3808, OVP1, Inorganic pyrophosphatase [Energy production and
conversion].
Length = 703
Score = 30.5 bits (69), Expect = 0.68
Identities = 15/38 (39%), Positives = 22/38 (57%)
Query: 1 MAGEVLVDALPYIDQGYDDPGVREAALAMVEEETRRYR 38
+AG +L LPY+ G V AA+ +VEE R++R
Sbjct: 524 VAGLLLGGLLPYLFSGITMTAVGRAAMEVVEEVRRQFR 561
>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 = 30.0 bits (68), Expect = 0.72
Identities = 21/101 (20%), Positives = 42/101 (41%), Gaps = 12/101 (11%)
Query: 106 SQLEHQSTRIVNLQLMLEYGPETWKEYLQTLVNCVSQAQSKLIQLRKEIQEINWERKVMQ 165
+L + LQ L E E Q + + +L L E++ + E
Sbjct: 66 ERLPELQQELAELQEELAELQEQLAELQQEN----QELKQELSTLEAELERLQKEL---- 117
Query: 166 IKGGEQLKKLEADWVGLVSKNYEIEQACVLLEKKIQILQAE 206
++K+L A+ + L +N E+ + L+++ + L+AE
Sbjct: 118 ----ARIKQLSANAIELDEENRELREELAELKQENEALEAE 154
>gnl|CDD|177060 CHL00138, rps5, ribosomal protein S5; Validated.
Length = 143
Score = 29.2 bits (66), Expect = 0.76
Identities = 20/59 (33%), Positives = 27/59 (45%), Gaps = 21/59 (35%)
Query: 152 KEIQEINWERKVMQI-------KGGEQLKKL----------EADWVGL-VSKNYEIEQA 192
I+E WE +V+QI KGG KKL E WVG+ V K +++ A
Sbjct: 17 SNIKENKWEERVIQIKRVSKVVKGG---KKLSFRAIVVIGNENGWVGVGVGKADDVQNA 72
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 29.7 bits (67), Expect = 1.3
Identities = 15/84 (17%), Positives = 41/84 (48%)
Query: 127 ETWKEYLQTLVNCVSQAQSKLIQLRKEIQEINWERKVMQIKGGEQLKKLEADWVGLVSKN 186
E +E L L +++ +++L +L++EI+ + + + + + ++L+ L
Sbjct: 379 EALREELAELEAELAEIRNELEELKREIESLEERLERLSERLEDLKEELKELEAELEELQ 438
Query: 187 YEIEQACVLLEKKIQILQAEKAKR 210
E+E+ LE+ + L+ + +
Sbjct: 439 TELEELNEELEELEEQLEELRDRL 462
>gnl|CDD|215364 PLN02678, PLN02678, seryl-tRNA synthetase.
Length = 448
Score = 29.3 bits (66), Expect = 1.3
Identities = 17/65 (26%), Positives = 31/65 (47%), Gaps = 8/65 (12%)
Query: 142 QAQSKLIQLRKEIQEINWERKVMQIKGGEQLKKLEADWVGLVSKNYEIEQACVLLEKKIQ 201
Q Q +L LRKE ++N K +LK + D L+++ E+++ E ++Q
Sbjct: 44 QRQFELDSLRKEFNKLN--------KEVAKLKIAKEDATELIAETKELKKEITEKEAEVQ 95
Query: 202 ILQAE 206
+A
Sbjct: 96 EAKAA 100
>gnl|CDD|225309 COG2511, GatE, Archaeal Glu-tRNAGln amidotransferase subunit E
(contains GAD domain) [Translation, ribosomal structure
and biogenesis].
Length = 631
Score = 29.6 bits (67), Expect = 1.4
Identities = 22/75 (29%), Positives = 30/75 (40%), Gaps = 9/75 (12%)
Query: 24 EAALAMVEEETRRYRP--TKNYLEHIPPLDINKFETEIMRKDFERIQQRLPMEPLSMIRY 81
+ A+ V EETR P T YL +P ET+I R+ E L I+
Sbjct: 398 KEAIEGVPEETRGALPDGTTVYLRPLPGAARMYPETDIP-------PIRIDEELLEKIKE 450
Query: 82 KLPQPPTGKMSDIAA 96
LP+ P K+
Sbjct: 451 NLPELPEEKVERYVK 465
>gnl|CDD|222417 pfam13851, GAS, Growth-arrest specific micro-tubule binding. This
family is the highly conserved central region of a
number of metazoan proteins referred to as growth-arrest
proteins. In mouse, Gas8 is predominantly a testicular
protein, whose expression is developmentally regulated
during puberty and spermatogenesis. In humans, it is
absent in infertile males who lack the ability to
generate gametes. The localisation of Gas8 in the
motility apparatus of post-meiotic gametocytes and
mature spermatozoa, together with the detection of Gas8
also in cilia at the apical surfaces of epithelial cells
lining the pulmonary bronchi and Fallopian tubes
suggests that the Gas8 protein may have a role in the
functioning of motile cellular appendages. Gas8 is a
microtubule-binding protein localised to regions of
dynein regulation in mammalian cells.
Length = 201
Score = 28.7 bits (65), Expect = 1.8
Identities = 19/77 (24%), Positives = 42/77 (54%), Gaps = 12/77 (15%)
Query: 142 QAQSKLIQLRKEIQEINWERKVMQIKGGEQLKKLEADWVGLVSKN----YEIEQAC---- 193
+++L +L KE++ + WE +V++ ++ +K+E + L K +++Q
Sbjct: 90 NLKARLKELEKELKNLKWESEVLE----QRFEKVERERDELYDKFEAAIQDVQQKTGLKN 145
Query: 194 VLLEKKIQILQAEKAKR 210
+LLE+K++ L E K+
Sbjct: 146 LLLEQKLEALNEELEKK 162
>gnl|CDD|191668 pfam07011, DUF1313, Protein of unknown function (DUF1313). This
family consists of several hypothetical plant proteins
of around 100 residues in length. The function of this
family is unknown.
Length = 89
Score = 27.0 bits (60), Expect = 2.7
Identities = 13/26 (50%), Positives = 13/26 (50%)
Query: 133 LQTLVNCVSQAQSKLIQLRKEIQEIN 158
QT Q QS L Q R IQEIN
Sbjct: 9 WQTFQRSFVQVQSVLDQNRLLIQEIN 34
>gnl|CDD|153088 cd01679, RNR_I, Class I ribonucleotide reductase. Ribonucleotide
reductase (RNR) catalyzes the reductive synthesis of
deoxyribonucleotides from their corresponding
ribonucleotides. It provides the precursors necessary
for DNA synthesis. RNRs are separated into three classes
based on their metallocofactor usage. Class I RNRs,
found in eukaryotes, bacteria, and many viruses, use a
diiron-tyrosyl radical. Class II RNRs, found in
bacteria, bacteriophage, algae and archaea, use coenzyme
B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found
in anaerobic bacteria, bacteriophages, and archaea, use
an FeS cluster and S-adenosylmethionine to generate a
glycyl radical. Many organisms have more than one class
of RNR present in their genomes. All three RNRs have a
ten-stranded alpha-beta barrel domain that is
structurally similar to the domain of PFL (pyruvate
formate lyase). Class I RNR is oxygen-dependent and can
be subdivided into classes Ia (eukaryotes, prokaryotes,
viruses and phages) and Ib (which is found in
prokaryotes only). It is a tetrameric enzyme of two
alpha and two beta subunits; this model covers the major
part of the alpha or large subunit, called R1 in class
Ia and R1E in class Ib.
Length = 460
Score = 27.9 bits (63), Expect = 3.9
Identities = 17/68 (25%), Positives = 27/68 (39%), Gaps = 10/68 (14%)
Query: 87 PTGKMSDIAAWTECVENSMSQLEHQS-----TRIVN---LQLMLEYGPE-TWKEYLQ-TL 136
PT +S I T +E S + + +VN + + EYG T E Q L
Sbjct: 351 PTASISQILGATPSIEPITSNIYVRRVLSGEFPVVNPHLEKDLWEYGLYKTAYEIDQRWL 410
Query: 137 VNCVSQAQ 144
++ + Q
Sbjct: 411 IDLAADRQ 418
>gnl|CDD|221737 pfam12726, SEN1_N, SEN1 N terminal. This domain is found at the
N terminal of the helicase SEN1. SEN1 is a Pol II
termination factor for noncoding RNA genes. The N
terminal of SEN1, unlike the C terminal, is not
required for growth.
Length = 724
Score = 28.0 bits (63), Expect = 4.0
Identities = 8/31 (25%), Positives = 15/31 (48%)
Query: 41 KNYLEHIPPLDINKFETEIMRKDFERIQQRL 71
+ ++ P ++ KF +I D +RI L
Sbjct: 29 QRFIRSFPIENVQKFMEKIDEWDIQRILPGL 59
>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial 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. This family
represents the SMC protein of most bacteria. The smc
gene is often associated with scpB (TIGR00281) and scpA
genes, where scp stands for segregation and condensation
protein. SMC was shown (in Caulobacter crescentus) to be
induced early in S phase but present and bound to DNA
throughout the cell cycle [Cellular processes, Cell
division, DNA metabolism, Chromosome-associated
proteins].
Length = 1179
Score = 27.7 bits (62), Expect = 5.0
Identities = 21/110 (19%), Positives = 43/110 (39%), Gaps = 3/110 (2%)
Query: 51 DINKFETEIMRKDFERIQQRLPMEPLSMIRYKLPQPPTGKMSDIAAWT---ECVENSMSQ 107
+I++ E + +E L +L ++A E ++ +
Sbjct: 296 EISRLEQQKQILRERLANLERQLEELEAQLEELESKLDELAEELAELEEKLEELKEELES 355
Query: 108 LEHQSTRIVNLQLMLEYGPETWKEYLQTLVNCVSQAQSKLIQLRKEIQEI 157
LE + + LE E +E L+TL + V+Q + ++ L EI+ +
Sbjct: 356 LEAELEELEAELEELESRLEELEEQLETLRSKVAQLELQIASLNNEIERL 405
>gnl|CDD|238347 cd00636, TroA-like, Helical backbone metal receptor (TroA-like
domain). These proteins have been shown to function in
the ABC transport of ferric siderophores and metal ions
such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand
binding site is formed in the interface between two
globular domains linked by a single helix. Many of
these proteins also possess a low complexity region
containing a metal-binding histidine-rich motif
(repetitive HDH sequence). The TroA-like proteins
differ in their fold and ligand-binding mechanism from
the PBPI and PBPII proteins, but are structurally
similar, however, to the beta-subunit of the nitrogenase
molybdenum-iron protein MoFe. Most TroA-like proteins
are encoded by ABC-type operons and appear to function
as periplasmic components of ABC transporters in metal
ion uptake.
Length = 148
Score = 26.4 bits (58), Expect = 7.4
Identities = 12/67 (17%), Positives = 27/67 (40%), Gaps = 3/67 (4%)
Query: 94 IAAWTECVENSMSQLEHQSTRIVNLQLMLEYGPETWKEYLQTL---VNCVSQAQSKLIQL 150
I A +E + +L + +V + E E KE ++ + + A+ + +L
Sbjct: 65 IIANGSGLEAWLDKLSKIAIPVVVVDEASELSLENIKESIRLIGKALGKEENAEELIAEL 124
Query: 151 RKEIQEI 157
+ E+
Sbjct: 125 DARLAEL 131
>gnl|CDD|205977 pfam13804, HERV-K_env_2, Retro-transcribing viruses envelope
glycoprotein. This family comes from human endogenous
retrovirus K envelope glycoproteins.
Length = 170
Score = 26.5 bits (58), Expect = 8.1
Identities = 16/60 (26%), Positives = 25/60 (41%), Gaps = 10/60 (16%)
Query: 86 PPTGKMSDIAAWTECVENSMSQLEHQSTRIVNLQLMLEYGPETWKEYLQTLVNCVSQAQS 145
P K +++ W ECV NS L++ + +++ P Q NC Q QS
Sbjct: 119 PKESKNTEVLVWEECVANSAVILQNNEFGTI-----IDWAPRG-----QFYHNCSGQTQS 168
>gnl|CDD|188997 cd06459, M3B_PepF, Peptidase family M3B Oligopeptidase F (PepF).
Peptidase family M3B Oligopeptidase F (PepF;
Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and
includes oligoendopeptidase F from Lactococcus lactis.
This enzyme hydrolyzes peptides containing between 7 and
17 amino acids with fairly broad specificity. The PepF
gene is duplicated in L. lactis on the plasmid that
bears it, while a shortened second copy is found in
Bacillus subtilis. Most bacterial PepFs are cytoplasmic
endopeptidases; however, the PepF Bacillus
amyloliquefaciens oligopeptidase is a secreted protein
and may facilitate the process of sporulation.
Specifically, the yjbG gene encoding the homolog of the
PepF1 and PepF2 oligoendopeptidases of Lactococcus
lactis has been identified in Bacillus subtilis as an
inhibitor of sporulation initiation when over expressed
from a multicopy plasmid.
Length = 450
Score = 27.1 bits (60), Expect = 8.9
Identities = 24/100 (24%), Positives = 31/100 (31%), Gaps = 17/100 (17%)
Query: 16 GYDDPGVREAALAMVEEETRRYRPTKNYLEHIPPLDINKFETEIMRKDFERIQQRLPMEP 75
G+D LA E ++ EH PL K ER Q+RL +E
Sbjct: 111 GFDS--FLSLGLANNGERDXVAGYRRDVKEHNVPL---------AAKFRERKQRRLGLEK 159
Query: 76 LSM--IRYKLPQPPTGKMSDIAAWTECVENSMSQLEHQST 113
L + LP K + E V N S
Sbjct: 160 LYFYDVPAPLPTGNEPKGT----ADEAVNNIREXYSRLSP 195
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 0.133 0.383
Gapped
Lambda K H
0.267 0.0634 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,956,245
Number of extensions: 1016798
Number of successful extensions: 1181
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1170
Number of HSP's successfully gapped: 61
Length of query: 210
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 117
Effective length of database: 6,812,680
Effective search space: 797083560
Effective search space used: 797083560
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: 57 (25.9 bits)