RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4021
(65 letters)
>gnl|CDD|204784 pfam11932, DUF3450, Protein of unknown function (DUF3450). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria and eukaryotes.
Proteins in this family are about 260 amino acids in
length.
Length = 250
Score = 28.0 bits (63), Expect = 0.24
Identities = 11/38 (28%), Positives = 22/38 (57%)
Query: 3 IKVLQFQNKKLAQRLEQKNRAEAELRSRIEQLEKRQTQ 40
I+ L+ N +L + + + + A L+ +IEQ+EK +
Sbjct: 66 IENLRVYNDQLQRLVANQQQEIASLQQQIEQIEKTRQG 103
>gnl|CDD|183233 PRK11616, PRK11616, hypothetical protein; Provisional.
Length = 109
Score = 26.7 bits (59), Expect = 0.62
Identities = 8/25 (32%), Positives = 16/25 (64%)
Query: 22 RAEAELRSRIEQLEKRQTQDDAVLN 46
R ++ +RSR+E+ E + +AV+
Sbjct: 78 RKDSSVRSRVEKSEAQNQATNAVIP 102
>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 = 26.8 bits (60), Expect = 0.65
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 6 LQFQNKKLAQRLEQKNRAEAELRSRIEQLEKRQTQ 40
LQ ++L QR E +R L + E LEK++ +
Sbjct: 78 LQRLERRLLQREETLDRKMESLDKKEENLEKKEKE 112
>gnl|CDD|236976 PRK11773, uvrD, DNA-dependent helicase II; Provisional.
Length = 721
Score = 26.0 bits (58), Expect = 1.5
Identities = 10/14 (71%), Positives = 12/14 (85%)
Query: 21 NRAEAELRSRIEQL 34
N+A AE+R RIEQL
Sbjct: 64 NKAAAEMRHRIEQL 77
>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 = 25.4 bits (56), Expect = 2.2
Identities = 12/44 (27%), Positives = 23/44 (52%), Gaps = 4/44 (9%)
Query: 9 QNKKLAQRLEQKNRAEAELRSRIEQLEKRQTQ-DDAVLNVVVNE 51
+ +K +L +N A L++ E+L+KR+ D + V +E
Sbjct: 70 ELRKRLAKLISENEA---LKAENERLQKREQSIDQQIQQAVQSE 110
Score = 24.2 bits (53), Expect = 5.1
Identities = 8/44 (18%), Positives = 19/44 (43%), Gaps = 3/44 (6%)
Query: 2 DIKVLQFQNKKLAQRLEQKNRAEAELRSRIEQL---EKRQTQDD 42
+ L +N+ L E+ + E + +I+Q E ++ +
Sbjct: 74 RLAKLISENEALKAENERLQKREQSIDQQIQQAVQSETQELTKE 117
>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed.
Length = 1068
Score = 25.4 bits (56), Expect = 2.4
Identities = 14/42 (33%), Positives = 18/42 (42%), Gaps = 3/42 (7%)
Query: 12 KLAQRLEQKNRAEAELRSRIEQLEKRQTQDDAVLNVVVNESV 53
+ +Q R E R R EKRQ Q +A V +SV
Sbjct: 666 RTQDEQQQAPRRE---RQRRRNDEKRQAQQEAKALNVEEQSV 704
>gnl|CDD|236648 PRK10078, PRK10078, ribose 1,5-bisphosphokinase; Provisional.
Length = 186
Score = 25.1 bits (55), Expect = 2.5
Identities = 15/42 (35%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 6 LQFQNKKLAQRLEQKNR-AEAELRSRIEQLEKRQTQDDAVLN 46
LQ + L QRLE + R +E+ +R+ + + Q QD LN
Sbjct: 117 LQVSPEILRQRLENRGRENASEINARLARAARYQPQDCHTLN 158
>gnl|CDD|181271 PRK08179, prfH, peptide chain release factor-like protein;
Reviewed.
Length = 200
Score = 25.0 bits (55), Expect = 3.0
Identities = 8/33 (24%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 7 QFQNKKLA-QRLEQKNRAEAELRSRIEQLEKRQ 38
Q NK+LA + K + + +S + ++R
Sbjct: 150 QHANKRLARLLIAWKLEQQQQEQSAALKSQRRM 182
>gnl|CDD|223266 COG0188, GyrA, Type IIA topoisomerase (DNA gyrase/topo II,
topoisomerase IV), A subunit [DNA replication,
recombination, and repair].
Length = 804
Score = 24.9 bits (55), Expect = 3.1
Identities = 13/48 (27%), Positives = 24/48 (50%), Gaps = 1/48 (2%)
Query: 5 VLQFQNKKLAQRLEQKNRAE-AELRSRIEQLEKRQTQDDAVLNVVVNE 51
+L + ++L E+K E EL I LEK ++ +L+++ E
Sbjct: 423 ILDLRLRRLTGLEEEKIEKELKELEKEIADLEKILASEERLLDIIKKE 470
>gnl|CDD|217914 pfam04129, Vps52, Vps52 / Sac2 family. Vps52 complexes with
Vps53 and Vps54 to form a multi- subunit complex
involved in regulating membrane trafficking events.
Length = 511
Score = 24.7 bits (54), Expect = 3.4
Identities = 15/50 (30%), Positives = 27/50 (54%)
Query: 2 DIKVLQFQNKKLAQRLEQKNRAEAELRSRIEQLEKRQTQDDAVLNVVVNE 51
DIK LQ ++ ++ RLE + E++L ++ L D +++ VNE
Sbjct: 50 DIKFLQEKSNEMQLRLENRQAVESKLSQFVDDLIVPPELIDTIIDGDVNE 99
>gnl|CDD|234306 TIGR03674, fen_arch, flap structure-specific endonuclease.
Endonuclease that cleaves the 5'-overhanging flap
structure that is generated by displacement synthesis
when DNA polymerase encounters the 5'-end of a
downstream Okazaki fragment. Has 5'-endo-/exonuclease
and 5'-pseudo-Y-endonuclease activities. Cleaves the
junction between single and double-stranded regions of
flap DNA.
Length = 338
Score = 24.5 bits (54), Expect = 3.7
Identities = 8/32 (25%), Positives = 16/32 (50%)
Query: 2 DIKVLQFQNKKLAQRLEQKNRAEAELRSRIEQ 33
D K + + + L +R E + AE + +E+
Sbjct: 80 DGKPPELKAETLEERREIREEAEEKWEEALEK 111
>gnl|CDD|226232 COG3709, COG3709, Uncharacterized component of phosphonate
metabolism [Inorganic ion transport and metabolism].
Length = 192
Score = 24.6 bits (54), Expect = 4.3
Identities = 9/36 (25%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 13 LAQRLEQKNR-AEAELRSRIEQLEKRQTQDDAVLNV 47
LAQRL ++ R + E+ +R+ + + V +
Sbjct: 128 LAQRLAERGRESREEILARLARAARYTAGPGDVTTI 163
>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 = 24.6 bits (54), Expect = 4.3
Identities = 12/40 (30%), Positives = 20/40 (50%), Gaps = 3/40 (7%)
Query: 4 KVLQFQNKKLAQRLEQKNRAEAE---LRSRIEQLEKRQTQ 40
+ L+ K+AQ Q E L +R+E+LE R+ +
Sbjct: 379 EQLETLRSKVAQLELQIASLNNEIERLEARLERLEDRRER 418
>gnl|CDD|235316 PRK04863, mukB, cell division protein MukB; Provisional.
Length = 1486
Score = 24.5 bits (54), Expect = 5.0
Identities = 13/36 (36%), Positives = 20/36 (55%)
Query: 10 NKKLAQRLEQKNRAEAELRSRIEQLEKRQTQDDAVL 45
N+KL QRLEQ + R ++ Q + + Q + VL
Sbjct: 987 NEKLRQRLEQAEQERTRAREQLRQAQAQLAQYNQVL 1022
>gnl|CDD|219419 pfam07462, MSP1_C, Merozoite surface protein 1 (MSP1) C-terminus.
This family represents the C-terminal region of
merozoite surface protein 1 (MSP1) which are found in a
number of Plasmodium species. MSP-1 is a 200-kDa protein
expressed on the surface of the P. vivax merozoite.
MSP-1 of Plasmodium species is synthesised as a
high-molecular-weight precursor and then processed into
several fragments. At the time of red cell invasion by
the merozoite, only the 19-kDa C-terminal fragment
(MSP-119), which contains two epidermal growth
factor-like domains, remains on the surface. Antibodies
against MSP-119 inhibit merozoite entry into red cells,
and immunisation with MSP-119 protects monkeys from
challenging infections. Hence, MSP-119 is considered a
promising vaccine candidate.
Length = 574
Score = 24.5 bits (53), Expect = 5.1
Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 3 IKVLQFQNKKLAQRLEQKNRAEAELRSRIEQLEKRQTQDDAVLNVVVNESVYF 55
+K+ + NKK +++ Q +L E+LEKR+ + V+ N S +F
Sbjct: 82 LKLERLYNKK--EQIGQSKMQIKKLTLLKERLEKRKNSLNNPFYVLSNFSNFF 132
>gnl|CDD|233821 TIGR02322, phosphon_PhnN, phosphonate metabolism
protein/1,5-bisphosphokinase (PRPP-forming) PhnN.
Members of this family resemble PhnN of phosphonate
utilization operons, where different such operons confer
the ability to use somewhat different profiles of C-P
bond-containing compounds (see PMID:15231805), including
phosphites as well as phosphonates. PhnN in E. coli
shows considerable homology to guanylate kinases (EC
2.7.4.8), and has actually been shown to act as a ribose
1,5-bisphosphokinase (PRPP forming). This suggests an
analogous kinase reaction for phosphonate metabolism,
converting 5-phosphoalpha-1-(methylphosphono)ribose to
methylphosphono-PRPP [Central intermediary metabolism,
Phosphorus compounds].
Length = 179
Score = 24.2 bits (53), Expect = 5.4
Identities = 11/29 (37%), Positives = 14/29 (48%), Gaps = 3/29 (10%)
Query: 13 LAQRLEQKNRAEAELRSRIEQLEKRQTQD 41
LAQRL + R E R IE+ R +
Sbjct: 124 LAQRLAARGR---ESREEIEERLARSARF 149
>gnl|CDD|236842 PRK11091, PRK11091, aerobic respiration control sensor protein
ArcB; Provisional.
Length = 779
Score = 24.1 bits (53), Expect = 5.5
Identities = 8/31 (25%), Positives = 16/31 (51%)
Query: 6 LQFQNKKLAQRLEQKNRAEAELRSRIEQLEK 36
L+ +L Q + ++ +AE + EQL+
Sbjct: 108 LKDNIAQLNQEIAEREKAEEARQEAFEQLKN 138
>gnl|CDD|236992 PRK11819, PRK11819, putative ABC transporter ATP-binding protein;
Reviewed.
Length = 556
Score = 23.9 bits (53), Expect = 6.3
Identities = 8/23 (34%), Positives = 15/23 (65%), Gaps = 1/23 (4%)
Query: 14 AQRLEQKNRAEAELRSRIEQ-LE 35
A+RL Q+ + EA + +++ LE
Sbjct: 253 AKRLAQEEKQEAARQKALKRELE 275
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 23.6 bits (52), Expect = 8.2
Identities = 13/33 (39%), Positives = 19/33 (57%)
Query: 6 LQFQNKKLAQRLEQKNRAEAELRSRIEQLEKRQ 38
LQ K+L Q+ E +R L R E+LEK++
Sbjct: 84 LQKLEKRLLQKEENLDRKLELLEKREEELEKKE 116
>gnl|CDD|214395 CHL00204, ycf1, Ycf1; Provisional.
Length = 1832
Score = 23.9 bits (52), Expect = 8.8
Identities = 8/40 (20%), Positives = 18/40 (45%)
Query: 4 KVLQFQNKKLAQRLEQKNRAEAELRSRIEQLEKRQTQDDA 43
K N+K + +E +N+ E E + E ++ + +
Sbjct: 1507 KGFIPSNEKKSIEIENRNQEEKEPAGQGELESDKEKKGNL 1546
>gnl|CDD|233973 TIGR02680, TIGR02680, TIGR02680 family protein. Members of this
protein family belong to a conserved gene four-gene
neighborhood found sporadically in a phylogenetically
broad range of bacteria: Nocardia farcinica,
Symbiobacterium thermophilum, and Streptomyces
avermitilis (Actinobacteria), Geobacillus kaustophilus
(Firmicutes), Azoarcus sp. EbN1 and Ralstonia
solanacearum (Betaproteobacteria). Proteins in this
family average over 1400 amino acids in length
[Hypothetical proteins, Conserved].
Length = 1353
Score = 23.6 bits (51), Expect = 8.8
Identities = 11/42 (26%), Positives = 14/42 (33%)
Query: 13 LAQRLEQKNRAEAELRSRIEQLEKRQTQDDAVLNVVVNESVY 54
LE E EL +R E LE+ L + Y
Sbjct: 288 ARDELETAREEERELDARTEALEREADALRTRLEALQGSPAY 329
>gnl|CDD|226654 COG4191, COG4191, Signal transduction histidine kinase regulating
C4-dicarboxylate transport system [Signal transduction
mechanisms].
Length = 603
Score = 23.8 bits (52), Expect = 9.1
Identities = 11/39 (28%), Positives = 18/39 (46%), Gaps = 9/39 (23%)
Query: 6 LQFQNKKLAQRLEQKNRAEAELRSRIEQLEKRQTQDDAV 44
L N +L + ++ +AEA L R+ QD+ V
Sbjct: 347 LTRANARLQAEIAEREQAEAAL---------RRAQDELV 376
>gnl|CDD|221937 pfam13148, DUF3987, Protein of unknown function (DUF3987). A
family of uncharacterized proteins found by clustering
human gut metagenomic sequences.
Length = 379
Score = 23.4 bits (51), Expect = 9.9
Identities = 7/42 (16%), Positives = 17/42 (40%), Gaps = 3/42 (7%)
Query: 5 VLQFQNKKLAQRLEQKNRAEAELR---SRIEQLEKRQTQDDA 43
+ + + + + E+ EAE + + LEK+ +
Sbjct: 63 LEEIEEELREEYEEELKEYEAEKEIWEAEKKGLEKKAKKAIK 104
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
0.319 0.132 0.356
Gapped
Lambda K H
0.267 0.0719 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,137,157
Number of extensions: 229471
Number of successful extensions: 1034
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1023
Number of HSP's successfully gapped: 162
Length of query: 65
Length of database: 10,937,602
Length adjustment: 36
Effective length of query: 29
Effective length of database: 9,340,858
Effective search space: 270884882
Effective search space used: 270884882
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (24.2 bits)