RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1989
(82 letters)
>gnl|CDD|201054 pfam00170, bZIP_1, bZIP transcription factor. The Pfam entry
includes the basic region and the leucine zipper
region.
Length = 64
Score = 50.4 bits (121), Expect = 3e-10
Identities = 21/48 (43%), Positives = 30/48 (62%)
Query: 35 EAAKECRRKKKEYIKCLENRVAILENQNKALIDELKSLKELYCQQEME 82
EAA+ R +KK YI+ LE +V LE +NK L EL+ LK+ + + E
Sbjct: 15 EAARRSRLRKKAYIEELEEKVKELEAENKTLRSELERLKKECAKLKSE 62
>gnl|CDD|197664 smart00338, BRLZ, basic region leucin zipper.
Length = 65
Score = 40.6 bits (96), Expect = 2e-06
Identities = 16/42 (38%), Positives = 25/42 (59%)
Query: 35 EAAKECRRKKKEYIKCLENRVAILENQNKALIDELKSLKELY 76
EAA+ R +KK I+ LE +V LE +N+ L E++ L+
Sbjct: 15 EAARRSRERKKAEIEELERKVEQLEAENERLKKEIERLRREL 56
>gnl|CDD|213400 cd12193, B_zip1, basic leucine zipper DNA-binding and
multimerization region of GCN4 and related proteins.
Basic leucine zipper (bZIP) transcription factors act
in networks of homo- and hetero-dimers in the
regulation in a diverse set of cellular pathways.
Classical leucine zippers have alpha helices with
leucine residues 7 amino acids apart, which stabilize
dimerization with a parallel leucine zipper domain.
Dimerization creates a pair of basic regions that bind
DNA and undergo conformational change. GCN4 was
identified in Saccharomyces cerevisiae from mutations
in a deficiency in activation with the general amino
acid control pathway. GCN4 encodes a trans-activator of
amino acid biosynthetic genes containing 2 acidic
activation domains and a C-terminal bZIP domain,
comprised of a basic alpha-helical DNA-binding region
and a coiled-coil dimerization region.
Length = 54
Score = 39.2 bits (92), Expect = 6e-06
Identities = 17/43 (39%), Positives = 26/43 (60%)
Query: 35 EAAKECRRKKKEYIKCLENRVAILENQNKALIDELKSLKELYC 77
EAA+ R +K E +K LE++V L ++N L DE+ LK+
Sbjct: 12 EAARRSRARKMERMKQLEDKVEELTSENSDLEDEVDRLKKALA 54
>gnl|CDD|203738 pfam07716, bZIP_2, Basic region leucine zipper.
Length = 54
Score = 33.0 bits (76), Expect = 0.002
Identities = 16/39 (41%), Positives = 24/39 (61%)
Query: 35 EAAKECRRKKKEYIKCLENRVAILENQNKALIDELKSLK 73
EAA+ R KKK+ + LE RV LE +N L +++ L+
Sbjct: 14 EAARRSREKKKQREEELEERVKELEEENAQLRQKVEQLE 52
>gnl|CDD|235600 PRK05771, PRK05771, V-type ATP synthase subunit I; Validated.
Length = 646
Score = 28.7 bits (65), Expect = 0.24
Identities = 9/32 (28%), Positives = 20/32 (62%)
Query: 45 KEYIKCLENRVAILENQNKALIDELKSLKELY 76
E I+ ++ + +E + ++L++ELK L + Y
Sbjct: 214 SELIREIKEELEEIEKERESLLEELKELAKKY 245
>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 = 27.3 bits (61), Expect = 0.83
Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 7/59 (11%)
Query: 25 KISVPGSVWMEAAKECRRKKKEYIKCLENRVAILENQNKAL-------IDELKSLKELY 76
++S S+ +E A+ K ++ + R+ LEN+ K L I+E + LKE Y
Sbjct: 944 RLSEEYSLTLEEAEALENKIEDDEEEARRRLKRLENKIKELGPVNLAAIEEYEELKERY 1002
>gnl|CDD|235549 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated.
Length = 619
Score = 26.7 bits (60), Expect = 1.3
Identities = 11/42 (26%), Positives = 18/42 (42%)
Query: 34 MEAAKECRRKKKEYIKCLENRVAILENQNKALIDELKSLKEL 75
+E K ++ K+ K E +V Q+K + LKE
Sbjct: 221 LEKFKALAKQYKKLRKAQEKKVEGRLAQHKKYAKLREKLKEE 262
>gnl|CDD|224705 COG1792, MreC, Cell shape-determining protein [Cell envelope
biogenesis, outer membrane].
Length = 284
Score = 26.6 bits (59), Expect = 1.4
Identities = 9/38 (23%), Positives = 16/38 (42%)
Query: 42 RKKKEYIKCLENRVAILENQNKALIDELKSLKELYCQQ 79
+K+ ++ L V LE +NK L + L +
Sbjct: 79 KKELAELEQLLEEVESLEEENKRLKELLDFKESSSDYD 116
>gnl|CDD|234701 PRK00252, alaS, alanyl-tRNA synthetase; Reviewed.
Length = 865
Score = 26.2 bits (59), Expect = 1.8
Identities = 10/24 (41%), Positives = 12/24 (50%)
Query: 51 LENRVAILENQNKALIDELKSLKE 74
L RV L + K L EL+ LK
Sbjct: 717 LPERVEALLEELKELEKELEQLKA 740
>gnl|CDD|238111 cd00187, TOP4c, DNA Topoisomerase, subtype IIA; domain A';
bacterial DNA topoisomerase IV (C subunit, ParC),
bacterial DNA gyrases (A subunit, GyrA),mammalian DNA
toposiomerases II. DNA topoisomerases are essential
enzymes that regulate the conformational changes in DNA
topology by catalysing the concerted breakage and
rejoining of DNA strands during normal cellular growth.
Length = 445
Score = 26.4 bits (59), Expect = 1.8
Identities = 14/35 (40%), Positives = 21/35 (60%), Gaps = 3/35 (8%)
Query: 42 RKKKEY-IKCLENRVAILENQNKAL--IDELKSLK 73
++KEY + E R+ ILE KA+ IDE+ +L
Sbjct: 333 TRRKEYELGKAEARLHILEGLLKAILNIDEVINLI 367
>gnl|CDD|182597 PRK10626, PRK10626, hypothetical protein; Provisional.
Length = 239
Score = 26.2 bits (58), Expect = 2.0
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 53 NRVAILENQNKALIDELK 70
+RV LE+Q KAL+ LK
Sbjct: 222 SRVVTLEDQRKALVGSLK 239
>gnl|CDD|234352 TIGR03779, Bac_Flav_CT_M, Bacteroides conjugative transposon TraM
protein. Members of this protein family are designated
TraM and are found in a proposed transfer region of a
class of conjugative transposon found in the Bacteroides
lineage [Cellular processes, DNA transformation].
Length = 410
Score = 25.5 bits (56), Expect = 3.3
Identities = 11/25 (44%), Positives = 13/25 (52%)
Query: 15 IQVGPEDSLPKISVPGSVWMEAAKE 39
+ V D I VPGS +AAKE
Sbjct: 324 LSVYDTDGQEGIYVPGSAERDAAKE 348
>gnl|CDD|234972 PRK01688, PRK01688, histidinol-phosphate aminotransferase;
Provisional.
Length = 351
Score = 25.7 bits (57), Expect = 3.4
Identities = 8/28 (28%), Positives = 13/28 (46%)
Query: 45 KEYIKCLENRVAILENQNKALIDELKSL 72
+ I + RVA + + LI LK +
Sbjct: 258 PQGIAAMRERVAEINANRQWLIAALKEI 285
>gnl|CDD|240229 PTZ00014, PTZ00014, myosin-A; Provisional.
Length = 821
Score = 25.4 bits (56), Expect = 3.8
Identities = 13/41 (31%), Positives = 25/41 (60%), Gaps = 4/41 (9%)
Query: 35 EAAKECRRKKKEYIKCLENRVAILENQNKALIDELKSLKEL 75
+AAKE + ++E + E V++LE ALI ++K +++
Sbjct: 760 DAAKELTQIQREKLAAWEPLVSVLE----ALILKIKKKRKV 796
>gnl|CDD|222255 pfam13600, DUF4140, N-terminal domain of unknown function
(DUF4140). This family is often found at the N-terminus
of its member proteins, with DUF4139, pfam13598, at the
C-terminus.
Length = 101
Score = 24.6 bits (54), Expect = 4.8
Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 13/66 (19%)
Query: 20 EDSLPKISVPGSVWM------------EAAKECRRKKKEYIKCLENRVAILENQNKALID 67
DSL ++S PG+ + EA + +E ++ LE+ +A LE + +AL
Sbjct: 37 PDSL-RVSGPGNATILSVSVRRDYLPDEATSPALAELEEELRALEDELAALEAEKEALEA 95
Query: 68 ELKSLK 73
++K L
Sbjct: 96 QIKFLS 101
>gnl|CDD|218738 pfam05766, NinG, Bacteriophage Lambda NinG protein. NinG or Rap is
involved in recombination. Rap (recombination adept with
plasmid) increases lambda-by-plasmid recombination
catalyzed by Escherichia coli's RecBCD pathway.
Length = 188
Score = 25.0 bits (55), Expect = 4.8
Identities = 11/26 (42%), Positives = 16/26 (61%), Gaps = 3/26 (11%)
Query: 54 RVAILENQNKAL---IDELKSLKELY 76
RV LE ++ I+ELK++K LY
Sbjct: 151 RVEWLEGPHRPRKWTIEELKAIKALY 176
>gnl|CDD|232924 TIGR00334, 5S_RNA_mat_M5, ribonuclease M5. This family of
orthologous proteins shows a weak but significant
similarity to the central region of the DnaG-type DNA
primase. The region of similarity is termed the Toprim
(topoisomerase-primase) domain and is also shared by
RecR, OLD family nucleases, and type IA and II
topoisomerases [Transcription, RNA processing].
Length = 174
Score = 24.8 bits (54), Expect = 4.9
Identities = 5/22 (22%), Positives = 8/22 (36%)
Query: 44 KKEYIKCLENRVAILENQNKAL 65
+ I LEN + Q +
Sbjct: 98 VEAIIAALENVHEETKAQQSDI 119
>gnl|CDD|133384 cd01109, HTH_YyaN, Helix-Turn-Helix DNA binding domain of the
MerR-like transcription regulators YyaN and YraB.
Putative helix-turn-helix (HTH) MerR-like transcription
regulators of Bacillus subtilis, YyaN and YraB, and
related proteins; N-terminal domain. Based on sequence
similarity, these proteins are predicted to function as
transcription regulators that mediate responses to
stress in eubacteria. They belong to the MerR
superfamily of transcription regulators that promote
transcription of various stress regulons by
reconfiguring the operator sequence located between the
-35 and -10 promoter elements. A typical MerR regulator
is comprised of distinct domains that harbor the
regulatory (effector-binding) site and the active
(DNA-binding) site. Their N-terminal domains are
homologous and contain a DNA-binding winged HTH motif,
while the C-terminal domains are often dissimilar and
bind specific coactivator molecules such as metal ions,
drugs, and organic substrates.
Length = 113
Score = 24.7 bits (55), Expect = 5.0
Identities = 9/37 (24%), Positives = 18/37 (48%), Gaps = 7/37 (18%)
Query: 45 KEYIKC-------LENRVAILENQNKALIDELKSLKE 74
KEY + + R+ +LE + L +++ L+E
Sbjct: 64 KEYAELRREGDSTIPERLELLEEHREELEEQIAELQE 100
>gnl|CDD|224549 COG1634, COG1634, Uncharacterized Rossmann fold enzyme [General
function prediction only].
Length = 232
Score = 24.7 bits (54), Expect = 6.0
Identities = 14/39 (35%), Positives = 19/39 (48%)
Query: 19 PEDSLPKISVPGSVWMEAAKECRRKKKEYIKCLENRVAI 57
+ K S PGS + A E +RKK E+ K L +A
Sbjct: 182 FGIPVTKYSKPGSRRVVRADEIKRKKLEWAKRLIEWLAR 220
>gnl|CDD|180117 PRK05483, rplN, 50S ribosomal protein L14; Validated.
Length = 122
Score = 24.3 bits (54), Expect = 6.0
Identities = 8/26 (30%), Positives = 11/26 (42%)
Query: 37 AKECRRKKKEYIKCLENRVAILENQN 62
K RR YI+ +N +L N
Sbjct: 66 KKGVRRPDGSYIRFDDNAAVLLNNDG 91
>gnl|CDD|215153 PLN02271, PLN02271, serine hydroxymethyltransferase.
Length = 586
Score = 24.8 bits (54), Expect = 6.1
Identities = 9/26 (34%), Positives = 18/26 (69%)
Query: 38 KECRRKKKEYIKCLENRVAILENQNK 63
+E + +KE++K L+N I+E +N+
Sbjct: 546 REHGKLQKEFLKGLQNNKDIVELRNR 571
>gnl|CDD|205299 pfam13118, DUF3972, Protein of unknown function (DUF3972). This is
a Proteobacterial family of unknown function. Some of
the proteins in this family are annotated as being
kinesin-like proteins.
Length = 126
Score = 24.6 bits (54), Expect = 6.1
Identities = 10/26 (38%), Positives = 17/26 (65%)
Query: 51 LENRVAILENQNKALIDELKSLKELY 76
+ + L+N+NK L + L S++ELY
Sbjct: 83 KDETIEALKNENKFLKEALYSMQELY 108
>gnl|CDD|202837 pfam03980, Nnf1, Nnf1. NNF1 is an essential yeast gene that is
necessary for chromosome segregation. It is associated
with the spindle poles and forms part of a kinetochore
subcomplex called MIND.
Length = 108
Score = 24.5 bits (54), Expect = 6.5
Identities = 9/31 (29%), Positives = 19/31 (61%)
Query: 44 KKEYIKCLENRVAILENQNKALIDELKSLKE 74
+ + L R+ ++ +N AL DE+++L+E
Sbjct: 77 LLKQLDELNARLQKIQAENAALADEIQALRE 107
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 24.8 bits (55), Expect = 6.9
Identities = 15/40 (37%), Positives = 25/40 (62%)
Query: 34 MEAAKECRRKKKEYIKCLENRVAILENQNKALIDELKSLK 73
+EA +E + +E I+ LE ++ LE +N+ L EL+ LK
Sbjct: 3 LEALEERNSELEEQIRQLELKLRDLEAENEKLERELERLK 42
>gnl|CDD|221611 pfam12508, DUF3714, Protein of unknown function (DUF3714). This
domain family is found in bacteria, and is approximately
200 amino acids in length.
Length = 200
Score = 24.5 bits (54), Expect = 7.1
Identities = 11/19 (57%), Positives = 11/19 (57%)
Query: 21 DSLPKISVPGSVWMEAAKE 39
D I VPGS EAAKE
Sbjct: 127 DGQEGIYVPGSAEREAAKE 145
>gnl|CDD|221864 pfam12932, Sec16, Vesicle coat trafficking protein Sec16
mid-region. Sec16 is a multi-domain vesicle coat
protein. This central region is the functional part of
the molecules and thus is vital for the family's role
in mediating the movement of protein-cargo between the
organelles of the secretory pathway.
Length = 104
Score = 23.8 bits (52), Expect = 8.6
Identities = 16/31 (51%), Positives = 21/31 (67%), Gaps = 1/31 (3%)
Query: 43 KKKEYIKCLENRVAILENQNKALID-ELKSL 72
KKK+ IK LE+++A LEN N +L E K L
Sbjct: 65 KKKDVIKWLESKIAELENSNDSLKRKEDKLL 95
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
0.315 0.129 0.387
Gapped
Lambda K H
0.267 0.0753 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,059,403
Number of extensions: 306972
Number of successful extensions: 524
Number of sequences better than 10.0: 1
Number of HSP's gapped: 522
Number of HSP's successfully gapped: 59
Length of query: 82
Length of database: 10,937,602
Length adjustment: 51
Effective length of query: 31
Effective length of database: 8,675,548
Effective search space: 268941988
Effective search space used: 268941988
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: 53 (24.1 bits)