RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14231
(75 letters)
>gnl|CDD|238345 cd00632, Prefoldin_beta, Prefoldin beta; Prefoldin is a hexameric
molecular chaperone complex, composed of two
evolutionarily related subunits (alpha and beta), which
are found in both eukaryotes and archaea. Prefoldin
binds and stabilizes newly synthesized polypeptides
allowing them to fold correctly. The hexameric
structure consists of a double beta barrel assembly with
six protruding coiled-coils. The alpha prefoldin
subunits have two beta hairpin structures while the beta
prefoldin subunits (this CD) have only one hairpin that
is most similar to the second hairpin of the alpha
subunit. The prefoldin hexamer consists of two alpha and
four beta subunits and is assembled from the beta
hairpins of all six subunits. The alpha subunits
initially dimerize providing a structural nucleus for
the assembly of the beta subunits. In archaea, there is
usually only one gene for each subunit while in
eukaryotes there two or more paralogous genes encoding
each subunit adding heterogeneity to the structure of
the hexamer.
Length = 105
Score = 41.6 bits (98), Expect = 2e-06
Identities = 24/61 (39%), Positives = 37/61 (60%)
Query: 3 DGEVYKLIGPILVKQEMEEAKQNVKKRIDYISAELKRHDDTIATLDTKQDTHRENLTKLQ 62
D EVYKL+G +LVKQE EEA+ +K+R++ I +KR + L K +E + + Q
Sbjct: 45 DAEVYKLVGNVLVKQEKEEARTELKERLETIELRIKRLERQEEDLQEKLKELQEKIQQAQ 104
Query: 63 Q 63
+
Sbjct: 105 K 105
>gnl|CDD|202045 pfam01920, Prefoldin_2, Prefoldin subunit. This family includes
prefoldin subunits that are not detected by pfam02996.
Length = 106
Score = 37.6 bits (88), Expect = 5e-05
Identities = 23/63 (36%), Positives = 39/63 (61%)
Query: 3 DGEVYKLIGPILVKQEMEEAKQNVKKRIDYISAELKRHDDTIATLDTKQDTHRENLTKLQ 62
D +VYKLIG +LVKQ+ EE K+ +++R + + E+K + + L+ + + +E L KL
Sbjct: 44 DTKVYKLIGDVLVKQDKEEVKEELEERKETLEKEIKTLEKQLEKLEKELEELKEELYKLF 103
Query: 63 QQF 65
Q
Sbjct: 104 GQQ 106
>gnl|CDD|224300 COG1382, GimC, Prefoldin, chaperonin cofactor [Posttranslational
modification, protein turnover, chaperones].
Length = 119
Score = 31.9 bits (73), Expect = 0.009
Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 7/70 (10%)
Query: 3 DGEVYKLIGPILVKQEMEEAKQNVKKRIDYISAELKRHDDTIATLDTKQDTHRENLTKLQ 62
D VYK +G +LVK EEA +++R + + +K TL+ +++ +E L +LQ
Sbjct: 52 DAPVYKKVGNLLVKVSKEEAVDELEERKETLELRIK-------TLEKQEEKLQERLEELQ 104
Query: 63 QQFQQEQAAK 72
+ Q+
Sbjct: 105 SEIQKALGDA 114
>gnl|CDD|238453 cd00890, Prefoldin, Prefoldin is a hexameric molecular chaperone
complex, found in both eukaryotes and archaea, that
binds and stabilizes newly synthesized polypeptides
allowing them to fold correctly. The complex contains
two alpha and four beta subunits, the two subunits being
evolutionarily related. In archaea, there is usually
only one gene for each subunit while in eukaryotes there
two or more paralogous genes encoding each subunit
adding heterogeneity to the structure of the hexamer.
The structure of the complex consists of a double beta
barrel assembly with six protruding coiled-coils.
Length = 129
Score = 31.5 bits (72), Expect = 0.013
Identities = 16/63 (25%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 2 KDGEVYKLIG-PILVKQEMEEAKQNVKKRIDYISAELKRHDDTIATLDTKQDTHRENLTK 60
D +V +G + V++ +EEA + +KKR++ + ++++ + + L + +E L +
Sbjct: 67 DDDKVLVDLGTGVYVEKSLEEAIEFLKKRLETLEKQIEKLEKQLEKLQDQITELQEELQQ 126
Query: 61 LQQ 63
LQQ
Sbjct: 127 LQQ 129
>gnl|CDD|234172 TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family.
Members of this protein family are homologs of ClpB, an
ATPase associated with chaperone-related functions.
These ClpB homologs, designated ClpV1, are a key
component of the bacterial pathogenicity-associated type
VI secretion system [Protein fate, Protein and peptide
secretion and trafficking, Cellular processes,
Pathogenesis].
Length = 852
Score = 31.8 bits (73), Expect = 0.017
Identities = 14/61 (22%), Positives = 27/61 (44%), Gaps = 10/61 (16%)
Query: 21 EAKQNVKKRIDYISAELKR----------HDDTIATLDTKQDTHRENLTKLQQQFQQEQA 70
A +++++RI + EL HD+ +A L + L L+ ++QQE+
Sbjct: 419 AALEDLRRRIAALELELDALEREAALGADHDERLAELRAELAALEAELAALEARWQQEKE 478
Query: 71 A 71
Sbjct: 479 L 479
>gnl|CDD|216038 pfam00639, Rotamase, PPIC-type PPIASE domain. Rotamases increase
the rate of protein folding by catalyzing the
interconversion of cis-proline and trans-proline.
Length = 94
Score = 25.7 bits (57), Expect = 1.6
Identities = 10/35 (28%), Positives = 17/35 (48%)
Query: 13 ILVKQEMEEAKQNVKKRIDYISAELKRHDDTIATL 47
IL+K + K + + I +L+ +DT A L
Sbjct: 2 ILIKPPESADRAAAKAKAEEILEQLQSGEDTFAEL 36
>gnl|CDD|182611 PRK10642, PRK10642, proline/glycine betaine transporter;
Provisional.
Length = 490
Score = 26.2 bits (58), Expect = 1.7
Identities = 16/60 (26%), Positives = 26/60 (43%), Gaps = 4/60 (6%)
Query: 1 MKDGEVYKLIGPILVKQEMEEAKQNVKKRIDYISAELKRHDDTIATLDTKQDTHRENLTK 60
MK+ L G +++EAK+ + + D I ++ D IA L K R L +
Sbjct: 429 MKETANRPLKGATPAASDIQEAKEILVEHYDNIEQKIDDIDQEIAELQAK----RTRLVQ 484
>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 = 26.2 bits (58), Expect = 1.7
Identities = 11/55 (20%), Positives = 31/55 (56%)
Query: 16 KQEMEEAKQNVKKRIDYISAELKRHDDTIATLDTKQDTHRENLTKLQQQFQQEQA 70
+E+ KQ +++R+ + +L+ + + L++K D E L +L+++ ++ +
Sbjct: 297 ISRLEQQKQILRERLANLERQLEELEAQLEELESKLDELAEELAELEEKLEELKE 351
>gnl|CDD|235248 PRK04192, PRK04192, V-type ATP synthase subunit A; Provisional.
Length = 586
Score = 26.3 bits (59), Expect = 1.7
Identities = 7/25 (28%), Positives = 15/25 (60%)
Query: 1 MKDGEVYKLIGPILVKQEMEEAKQN 25
M G++ ++ GP++V + M A+
Sbjct: 2 MTKGKIVRVSGPLVVAEGMGGARMY 26
>gnl|CDD|131391 TIGR02338, gimC_beta, prefoldin, beta subunit, archaeal.
Chaperonins are cytosolic, ATP-dependent molecular
chaperones, with a conserved toroidal architecture, that
assist in the folding of nascent and/or denatured
polypeptide chains. The group I chaperonin system
consists of GroEL and GroES, and is found (usually) in
bacteria and organelles of bacterial origin. The group
II chaperonin system, called the thermosome in Archaea
and TRiC or CCT in the Eukaryota, is structurally
similar but only distantly related. Prefoldin, also
called GimC, is a complex in Archaea and Eukaryota, that
works with group II chaperonins. Members of this protein
family are the archaeal clade of the beta class of
prefoldin subunit. Closely related, but outside the
scope of this family are the eukaryotic beta-class
prefoldin subunits, Gim-1,3,4 and 6. The alpha class
prefoldin subunits are more distantly related.
Length = 110
Score = 25.4 bits (56), Expect = 2.2
Identities = 22/66 (33%), Positives = 38/66 (57%), Gaps = 7/66 (10%)
Query: 3 DGEVYKLIGPILVKQEMEEAKQNVKKRIDYISAELKRHDDTIATLDTKQDTHRENLTKLQ 62
D VYK +G +LVK + EEA Q +K++ + + +K TL +++ RE L +LQ
Sbjct: 49 DTPVYKSVGNLLVKTDKEEAIQELKEKKETLELRVK-------TLQRQEERLREQLKELQ 101
Query: 63 QQFQQE 68
++ Q+
Sbjct: 102 EKIQEA 107
>gnl|CDD|177331 PHA02004, PHA02004, capsid protein.
Length = 332
Score = 25.6 bits (56), Expect = 2.9
Identities = 9/47 (19%), Positives = 20/47 (42%), Gaps = 3/47 (6%)
Query: 32 YISAELKRHDDTIATLDTKQDTHRENLTKLQQQFQQE---QAAKMRA 75
Y+ + D+ + D +++ + +L ++F Q Q K A
Sbjct: 93 YLRHQFDHQDEWTQSFDMRKEVAELDGQELARKFDQACLIQLIKAAA 139
>gnl|CDD|215756 pfam00155, Aminotran_1_2, Aminotransferase class I and II.
Length = 357
Score = 25.4 bits (56), Expect = 3.3
Identities = 13/31 (41%), Positives = 20/31 (64%)
Query: 9 LIGPILVKQEMEEAKQNVKKRIDYISAELKR 39
L P+LV E+EE +Q +K+R DY+ L+
Sbjct: 258 LSDPLLVASELEEMRQRIKERRDYLRDGLEA 288
>gnl|CDD|187643 cd08939, KDSR-like_SDR_c, 3-ketodihydrosphingosine reductase
(KDSR) and related proteins, classical (c) SDR. These
proteins include members identified as KDSR, ribitol
type dehydrogenase, and others. The group shows strong
conservation of the active site tetrad and glycine rich
NAD-binding motif of the classical SDRs. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold (alpha/beta folding pattern with a
central beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 239
Score = 24.5 bits (54), Expect = 5.2
Identities = 7/38 (18%), Positives = 17/38 (44%)
Query: 15 VKQEMEEAKQNVKKRIDYISAELKRHDDTIATLDTKQD 52
+E+E +++ YISA+L +++ +
Sbjct: 41 AVEEIEAEANASGQKVSYISADLSDYEEVEQAFAQAVE 78
>gnl|CDD|234701 PRK00252, alaS, alanyl-tRNA synthetase; Reviewed.
Length = 865
Score = 24.3 bits (54), Expect = 6.4
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 2/33 (6%)
Query: 7 YKLIGPILVKQEMEEAKQNVKKRIDYISAELKR 39
YKL+ V EM +A +K++ D I LK
Sbjct: 318 YKLVPV--VIDEMGDAYPELKEKQDLIEKVLKA 348
>gnl|CDD|217789 pfam03915, AIP3, Actin interacting protein 3.
Length = 424
Score = 24.6 bits (54), Expect = 6.6
Identities = 18/53 (33%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 19 MEEAKQNVKKRIDYISAELKRHDDTI-ATLDTKQDTHRENLTKLQQQFQQEQA 70
E VKK ID EL ++ LD +Q T + L++LQQ +E A
Sbjct: 72 NVEELDEVKKHIDDSLGELSEKIKSLKQALDDQQSTILQRLSELQQNTAKEVA 124
>gnl|CDD|224644 COG1730, GIM5, Predicted prefoldin, molecular chaperone implicated
in de novo protein folding [Posttranslational
modification, protein turnover, chaperones].
Length = 145
Score = 23.9 bits (52), Expect = 8.3
Identities = 12/58 (20%), Positives = 28/58 (48%)
Query: 13 ILVKQEMEEAKQNVKKRIDYISAELKRHDDTIATLDTKQDTHRENLTKLQQQFQQEQA 70
++ +EA + +KKRI+ + +++ +A L + + + +LQQ+ Q
Sbjct: 86 YYAEKSADEAIEFLKKRIEELEKAIEKLQQALAELAQRIEQLEQEAQQLQQKQAAAQK 143
>gnl|CDD|225638 COG3096, MukB, Uncharacterized protein involved in chromosome
partitioning [Cell division and chromosome
partitioning].
Length = 1480
Score = 24.1 bits (52), Expect = 8.6
Identities = 10/48 (20%), Positives = 20/48 (41%)
Query: 23 KQNVKKRIDYISAELKRHDDTIATLDTKQDTHRENLTKLQQQFQQEQA 70
+Q + + A + + I +L RE L+Q+ +Q Q+
Sbjct: 545 RQGKNLDAEELEALHQELEALIESLSDSVSNAREQRMALRQEQEQLQS 592
>gnl|CDD|236333 PRK08691, PRK08691, DNA polymerase III subunits gamma and tau;
Validated.
Length = 709
Score = 24.3 bits (52), Expect = 9.2
Identities = 15/52 (28%), Positives = 23/52 (44%), Gaps = 3/52 (5%)
Query: 27 KKRIDYISAELKR---HDDTIATLDTKQDTHRENLTKLQQQFQQEQAAKMRA 75
KKR+D I L + T+ T D + + RE ++ Q E K +A
Sbjct: 627 KKRLDKIRDTLAQAYGLQLTLQTQDWRDEAGRETPAMQDKRVQAEDRQKAQA 678
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
0.312 0.127 0.332
Gapped
Lambda K H
0.267 0.0788 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,558,537
Number of extensions: 268338
Number of successful extensions: 646
Number of sequences better than 10.0: 1
Number of HSP's gapped: 631
Number of HSP's successfully gapped: 109
Length of query: 75
Length of database: 10,937,602
Length adjustment: 45
Effective length of query: 30
Effective length of database: 8,941,672
Effective search space: 268250160
Effective search space used: 268250160
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (24.1 bits)