RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7463
(319 letters)
>gnl|CDD|223840 COG0769, MurE, UDP-N-acetylmuramyl tripeptide synthase [Cell
envelope biogenesis, outer membrane].
Length = 475
Score = 36.1 bits (84), Expect = 0.019
Identities = 17/99 (17%), Positives = 25/99 (25%), Gaps = 19/99 (19%)
Query: 82 LMRDHLVTHIPPEHRGKVSDAFFNKKQTALLTHYLKRNGIKLQCNLCADTFCPRSNMLRH 141
L RDHL H G + K + + + D +
Sbjct: 190 LSRDHLDYH------GTMEYYGAAKAVLFESLPHS-GEAV-----INPD--DGHGLDYKE 235
Query: 142 YLLKHRGDKVFYACDRCDKRFSLLQNLKRHLAIHERIAY 180
L GD + Y CD F R + +
Sbjct: 236 RLKNALGDYITYGCD-----FKRPDLDYRGIEESSSGSD 269
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 35.4 bits (81), Expect = 0.037
Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 3/54 (5%)
Query: 153 YACDRCDKRFSLLQNLKRHLAIHERIA-YQCNV--CDKKYSRLSDYKIHMNMHN 203
+C C FS L++L RH+ H QC+ CDK +SR + H+ H+
Sbjct: 34 DSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTHH 87
Score = 29.3 bits (65), Expect = 2.7
Identities = 17/80 (21%), Positives = 27/80 (33%), Gaps = 7/80 (8%)
Query: 130 DTFCPRSNMLRHYLLKHRGDKVFYACDRCDKRFSLLQNLKRHL-----AIHERIAYQCNV 184
S+ +G + +C+ FS L RHL + + C
Sbjct: 267 TASSQSSSPNESDSSSEKGFSLPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPY 326
Query: 185 --CDKKYSRLSDYKIHMNMH 202
C K +SR K H+ +H
Sbjct: 327 SLCGKLFSRNDALKRHILLH 346
Score = 29.3 bits (65), Expect = 3.4
Identities = 20/53 (37%), Positives = 25/53 (47%), Gaps = 4/53 (7%)
Query: 125 CNLCADTFCPRSNMLRHYLLKHRGDKVFYACDR--CDKRFSLLQNLKRHLAIH 175
C C D+F ++ RH + H G+K C CDK FS L RHL H
Sbjct: 36 CPNCTDSFSRLEHLTRH-IRSHTGEKPS-QCSYSGCDKSFSRPLELSRHLRTH 86
Score = 27.7 bits (61), Expect = 8.2
Identities = 25/164 (15%), Positives = 40/164 (24%), Gaps = 32/164 (19%)
Query: 73 LCGEKFE-KSLMRDHLVTHIPPEHRGKVSDA-------FFNKKQTALLTHYLKRNGIKLQ 124
LCG+ F ++ H++ H + N + L Y K
Sbjct: 328 LCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLLNNEPPQSLQQYKDLKNDKK- 386
Query: 125 CNLCADTFCPRSNMLRHYLLKHRGDKVFYACDRCDKRFSLLQNLKRHLAIHERIAYQCNV 184
+ C R+ L H + + C
Sbjct: 387 -SETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCK----------------------NPP 423
Query: 185 CDKKYSRLSDYKIHMNMHNGFKYQCHICLKCTSRKNYLKRHIIM 228
C K ++R + H +H LK R L H
Sbjct: 424 CSKSFNRHYNLIPHKKIHTNHAPLLCSILKSFRRDLDLSNHGKD 467
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 32.2 bits (73), Expect = 0.12
Identities = 16/58 (27%), Positives = 29/58 (50%), Gaps = 3/58 (5%)
Query: 43 YECDCCTEYFIDRIAYEEHVRLHEGGIICRLCGEKFEKSLMRDHLVTHIPPEHRGKVS 100
Y C C F ++ ++H+R E +C +CG++F + D + H+ +H VS
Sbjct: 74 YVCPLCLMPFSSSVSLKQHIRYTEHSKVCPVCGKEFRNT---DSTLDHVCKKHNICVS 128
>gnl|CDD|200998 pfam00096, zf-C2H2, Zinc finger, C2H2 type. The C2H2 zinc finger
is the classical zinc finger domain. The two conserved
cysteines and histidines co-ordinate a zinc ion. The
following pattern describes the zinc finger.
#-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can
be any amino acid, and numbers in brackets indicate the
number of residues. The positions marked # are those
that are important for the stable fold of the zinc
finger. The final position can be either his or cys. The
C2H2 zinc finger is composed of two short beta strands
followed by an alpha helix. The amino terminal part of
the helix binds the major groove in DNA binding zinc
fingers. The accepted consensus binding sequence for Sp1
is usually defined by the asymmetric hexanucleotide core
GGGCGG but this sequence does not include, among others,
the GAG (=CTC) repeat that constitutes a high-affinity
site for Sp1 binding to the wt1 promoter.
Length = 22
Score = 29.6 bits (67), Expect = 0.15
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 181 QCNVCDKKYSRLSDYKIHMNMH 202
+C C K +SR S+ K H+ H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 27.7 bits (62), Expect = 0.71
Identities = 12/21 (57%), Positives = 12/21 (57%)
Query: 155 CDRCDKRFSLLQNLKRHLAIH 175
C C K FS NLKRHL H
Sbjct: 2 CPDCGKSFSRKSNLKRHLRTH 22
Score = 25.4 bits (56), Expect = 3.6
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 208 QCHICLKCTSRKNYLKRHIIM 228
+C C K SRK+ LKRH+
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRT 21
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 28.2 bits (63), Expect = 0.45
Identities = 8/23 (34%), Positives = 11/23 (47%)
Query: 180 YQCNVCDKKYSRLSDYKIHMNMH 202
Y+C C K + S + HM H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 26.3 bits (58), Expect = 2.2
Identities = 8/23 (34%), Positives = 10/23 (43%)
Query: 153 YACDRCDKRFSLLQNLKRHLAIH 175
Y C C K F L+ H+ H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
>gnl|CDD|233830 TIGR02350, prok_dnaK, chaperone protein DnaK. Members of this
family are the chaperone DnaK, of the DnaK-DnaJ-GrpE
chaperone system. All members of the seed alignment were
taken from completely sequenced bacterial or archaeal
genomes and (except for Mycoplasma sequence) found
clustered with other genes of this systems. This model
excludes DnaK homologs that are not DnaK itself, such as
the heat shock cognate protein HscA (TIGR01991).
However, it is not designed to distinguish among DnaK
paralogs in eukaryotes. Note that a number of dnaK genes
have shadow ORFs in the same reverse (relative to dnaK)
reading frame, a few of which have been assigned
glutamate dehydrogenase activity. The significance of
this observation is unclear; lengths of such shadow ORFs
are highly variable as if the presumptive protein
product is not conserved [Protein fate, Protein folding
and stabilization].
Length = 595
Score = 31.5 bits (72), Expect = 0.57
Identities = 12/54 (22%), Positives = 22/54 (40%), Gaps = 2/54 (3%)
Query: 234 EGQIGEMEDKVGEKKIGEIEAKVGEGNQGKEGGNQTEVGETSMLSNLSKHTHPL 287
E + E DK+ ++ +IE V E + +G + E+ L + L
Sbjct: 538 EKTLKEAGDKLPAEEKEKIEKAVAELKEALKGEDVEEIKAK--TEELQQALQKL 589
>gnl|CDD|215596 PLN03133, PLN03133, beta-1,3-galactosyltransferase; Provisional.
Length = 636
Score = 30.9 bits (70), Expect = 1.0
Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 6/52 (11%)
Query: 255 KVGEGNQGKE--GGNQTEVGETSMLSNLSKHTHPLVCPSSNGREETQYFPFR 304
KV + +Q + G + V TS+ SN S+ + P+ S + +YFPF+
Sbjct: 254 KVDDLDQCNKMVGRDDKRVLSTSLHSNGSRRS-PM---SQEATKARRYFPFK 301
>gnl|CDD|219995 pfam08737, Rgp1, Rgp1. Rgp1 forms heterodimer with Ric1
(pfam07064) which associates with Golgi membranes and
functions as a guanyl-nucleotide exchange factor.
Length = 402
Score = 30.8 bits (70), Expect = 1.1
Identities = 16/70 (22%), Positives = 25/70 (35%), Gaps = 4/70 (5%)
Query: 220 NYLKRHIIMMHTKFEGQIGEMEDKVGEKKIGEIEAKVGEGNQGKEGGNQTEVGETSMLSN 279
+KR + G + + E ++ VG G G T E+S L
Sbjct: 27 EEVKRKGVWGGNG----SGNVGSEGDETDSSGLDKLVGGGALGGSADLLTSGSESSGLGE 82
Query: 280 LSKHTHPLVC 289
LS+ PL+
Sbjct: 83 LSEKGVPLLS 92
>gnl|CDD|221755 pfam12756, zf-C2H2_2, C2H2 type zinc-finger (2 copies). This
family contains two copies of a C2H2-like zinc finger
domain.
Length = 100
Score = 28.4 bits (64), Expect = 1.8
Identities = 12/39 (30%), Positives = 22/39 (56%), Gaps = 2/39 (5%)
Query: 8 LKDKVVPQ-KCPLCERLYKSVYRMKEHM-KKQHKGQLYE 44
L++K+ +C C + +KS+ +++HM K H YE
Sbjct: 43 LREKIHEGNECLYCGKQFKSLEALRQHMRDKGHCKIPYE 81
>gnl|CDD|237042 PRK12291, PRK12291, apolipoprotein N-acyltransferase; Reviewed.
Length = 418
Score = 29.6 bits (67), Expect = 2.1
Identities = 12/45 (26%), Positives = 23/45 (51%), Gaps = 7/45 (15%)
Query: 187 KKYSRLSDYKIHMNMHNGFKYQCHICLKCTSRKNYLK--RHIIMM 229
K S+ SD+ + +G K++ IC + TS + Y + +I +
Sbjct: 328 SKASKFSDFTL-----DGVKFRNAICYEATSEELYEGNPKIVIAI 367
>gnl|CDD|204841 pfam12171, zf-C2H2_jaz, Zinc-finger double-stranded RNA-binding.
This domain family is found in archaea and eukaryotes,
and is approximately 30 amino acids in length. The
mammalian members of this group occur multiple times
along the protein, joined by flexible linkers, and are
referred to as JAZ - dsRNA-binding ZF protein -
zinc-fingers. The JAZ proteins are expressed in all
tissues tested and localise in the nucleus,
particularly the nucleolus. JAZ preferentially binds to
double-stranded (ds) RNA or RNA/DNA hybrids rather than
DNA. In addition to binding double-stranded RNA, these
zinc-fingers are required for nucleolar localisation.
Length = 27
Score = 26.0 bits (58), Expect = 2.6
Identities = 9/24 (37%), Positives = 16/24 (66%), Gaps = 1/24 (4%)
Query: 17 CPLCERLYKSVYRMKEHMK-KQHK 39
C C++ +KS ++ H+K K+HK
Sbjct: 4 CVACDKYFKSENALENHLKSKKHK 27
>gnl|CDD|233324 TIGR01236, D1pyr5carbox1, delta-1-pyrroline-5-carboxylate
dehydrogenase, group 1. This model represents one of
two related branches of delta-1-pyrroline-5-carboxylate
dehydrogenase. The two branches are not as closely
related to each other as some aldehyde dehydrogenases
are to this branch, and separate models are built for
this reason. The enzyme is the second of two in the
degradation of proline to glutamate [Energy metabolism,
Amino acids and amines].
Length = 532
Score = 29.4 bits (66), Expect = 3.0
Identities = 10/32 (31%), Positives = 14/32 (43%), Gaps = 3/32 (9%)
Query: 15 QKCPLCERLY--KSVY-RMKEHMKKQHKGQLY 43
QKC C RLY S++ R K + +
Sbjct: 315 QKCSACSRLYVPHSLWPRFKGRLLAELSRVKV 346
>gnl|CDD|206065 pfam13894, zf-C2H2_4, C2H2-type zinc finger. This family contains
a number of divergent C2H2 type zinc fingers.
Length = 24
Score = 25.7 bits (56), Expect = 3.2
Identities = 7/23 (30%), Positives = 12/23 (52%)
Query: 180 YQCNVCDKKYSRLSDYKIHMNMH 202
++C +C K +S K H+ H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
Score = 25.3 bits (55), Expect = 5.7
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 16 KCPLCERLYKSVYRMKEHMKKQH 38
KCPLC + + S +K H++K H
Sbjct: 2 KCPLCGKSFSSKDALKRHLRKHH 24
Score = 24.9 bits (54), Expect = 6.4
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 207 YQCHICLKCTSRKNYLKRHIIMMH 230
++C +C K S K+ LKRH+ H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKHH 24
Score = 24.5 bits (53), Expect = 7.9
Identities = 11/23 (47%), Positives = 12/23 (52%)
Query: 153 YACDRCDKRFSLLQNLKRHLAIH 175
+ C C K FS LKRHL H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 28.9 bits (64), Expect = 3.5
Identities = 12/30 (40%), Positives = 17/30 (56%), Gaps = 2/30 (6%)
Query: 14 PQKCPL--CERLYKSVYRMKEHMKKQHKGQ 41
P KCP+ C + YK+ +K HM H+ Q
Sbjct: 349 PYKCPVEGCNKKYKNQNGLKYHMLHGHQNQ 378
Score = 28.1 bits (62), Expect = 5.9
Identities = 23/83 (27%), Positives = 30/83 (36%), Gaps = 22/83 (26%)
Query: 170 RHLAIHERIAYQCNV--CDKKYSRLSDYKIHM---------------NMHNGFK-----Y 207
R L + + Y+C V C+KKY + K HM N F Y
Sbjct: 340 RMLKVKDGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPY 399
Query: 208 QCHICLKCTSRKNYLKRHIIMMH 230
+C +C K N LK H H
Sbjct: 400 RCEVCDKRYKNLNGLKYHRKHSH 422
Score = 28.1 bits (62), Expect = 7.6
Identities = 22/77 (28%), Positives = 32/77 (41%), Gaps = 23/77 (29%)
Query: 144 LKHRGDKVFYACD--RCDKRFSLLQNLKRHL-------AIHERIA-------------YQ 181
LK + K Y C C+K++ LK H+ +HE + Y+
Sbjct: 342 LKVKDGKP-YKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYR 400
Query: 182 CNVCDKKYSRLSDYKIH 198
C VCDK+Y L+ K H
Sbjct: 401 CEVCDKRYKNLNGLKYH 417
>gnl|CDD|143441 cd07123, ALDH_F4-17_P5CDH, Delta(1)-pyrroline-5-carboxylate
dehydrogenase, ALDH families 4 and 17.
Delta(1)-pyrroline-5-carboxylate dehydrogenase
(EC=1.5.1.12 ), families 4 and 17: a proline catabolic
enzyme of the aldehyde dehydrogenase (ALDH) protein
superfamily. Delta(1)-pyrroline-5-carboxylate
dehydrogenase (P5CDH), also known as ALDH4A1 in humans,
is a mitochondrial homodimer involved in proline
degradation and catalyzes the NAD + -dependent
conversion of P5C to glutamate. This is a necessary step
in the pathway interconnecting the urea and
tricarboxylic acid cycles. The preferred substrate is
glutamic gamma-semialdehyde, other substrates include
succinic, glutaric and adipic semialdehydes. Also
included in this CD is the Aldh17 Drosophila
melanogaster (Q9VUC0) P5CDH and similar sequences.
Length = 522
Score = 28.7 bits (65), Expect = 4.2
Identities = 9/28 (32%), Positives = 16/28 (57%), Gaps = 3/28 (10%)
Query: 15 QKCPLCERLY--KSVY-RMKEHMKKQHK 39
QKC R Y +S++ +KE + ++ K
Sbjct: 316 QKCSAASRAYVPESLWPEVKERLLEELK 343
>gnl|CDD|234715 PRK00290, dnaK, molecular chaperone DnaK; Provisional.
Length = 627
Score = 28.1 bits (64), Expect = 6.7
Identities = 10/34 (29%), Positives = 18/34 (52%)
Query: 234 EGQIGEMEDKVGEKKIGEIEAKVGEGNQGKEGGN 267
E + E+ DKV + +IEA + E + +G +
Sbjct: 540 EKTLKELGDKVPADEKEKIEAAIKELKEALKGED 573
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 24.7 bits (54), Expect = 7.4
Identities = 11/26 (42%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 167 NLKRHLAIHERI-AYQCNVCDKKYSR 191
NL+RH+ H Y+C VC K +S
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
>gnl|CDD|221727 pfam12706, Lactamase_B_2, Beta-lactamase superfamily domain. This
family is part of the beta-lactamase superfamily and is
related to pfam00753.
Length = 197
Score = 27.1 bits (60), Expect = 9.4
Identities = 16/103 (15%), Positives = 34/103 (33%), Gaps = 15/103 (14%)
Query: 129 ADTFCPRSNMLRHYLLKHRGDKVFYACDRCDKRFSLLQNLKR-HLAIHERIAYQCNVCDK 187
R + + ++ G K++Y+ D LL +K L I + D+
Sbjct: 109 VQHGSGRYLLREGFRIETPGKKIYYSGD-TGYIPDLLAEIKGADLLILD---ATFYDDDE 164
Query: 188 KYSRLSDYKIHMNMHNGFKYQCHICLKCTSRKNYLKRHIIMMH 230
+ + + HM + L + +I++H
Sbjct: 165 EPRKTARRMGHMTPEEALEA--AKDLGA--------KKLILIH 197
>gnl|CDD|225102 COG2191, COG2191, Formylmethanofuran dehydrogenase subunit E
[Energy production and conversion].
Length = 206
Score = 27.4 bits (61), Expect = 9.4
Identities = 10/34 (29%), Positives = 13/34 (38%), Gaps = 5/34 (14%)
Query: 44 ECDCCTEYFIDRIAYEEHVRLHEGGIICRLCGEK 77
C C E F E + G +C+ C EK
Sbjct: 174 RCSKCGELF-----MEPRAVVLNGKPVCKPCAEK 202
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
0.323 0.138 0.434
Gapped
Lambda K H
0.267 0.0804 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,583,165
Number of extensions: 1428143
Number of successful extensions: 1349
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1338
Number of HSP's successfully gapped: 62
Length of query: 319
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 222
Effective length of database: 6,635,264
Effective search space: 1473028608
Effective search space used: 1473028608
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 59 (26.4 bits)