RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13022
(93 letters)
>gnl|CDD|238219 cd00371, HMA, Heavy-metal-associated domain (HMA) is a conserved
domain of approximately 30 amino acid residues found in
a number of proteins that transport or detoxify heavy
metals, for example, the CPx-type heavy metal ATPases
and copper chaperones. HMA domain contains two cysteine
residues that are important in binding and transfer of
metal ions, such as copper, cadmium, cobalt and zinc.
In the case of copper, stoichiometry of binding is one
Cu+ ion per binding domain. Repeats of the HMA domain
in copper chaperone has been associated with
Menkes/Wilson disease due to binding of multiple copper
ions.
Length = 63
Score = 44.1 bits (105), Expect = 1e-07
Identities = 18/43 (41%), Positives = 27/43 (62%), Gaps = 1/43 (2%)
Query: 20 IGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDMGFD 62
+ GV+S++V L +A + Y+P VSP+EL EAI D G+
Sbjct: 20 LEKLPGVESVEVDLETGKATVEYDPE-VSPEELLEAIEDAGYK 61
>gnl|CDD|215902 pfam00403, HMA, Heavy-metal-associated domain.
Length = 62
Score = 33.7 bits (78), Expect = 0.001
Identities = 11/38 (28%), Positives = 21/38 (55%)
Query: 25 GVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDMGFD 62
GV S+ V L + +T +P + ++L +AI G++
Sbjct: 25 GVSSVSVDLETGKVTVTGDPDPLKLEKLKKAIEKAGYE 62
>gnl|CDD|225328 COG2608, CopZ, Copper chaperone [Inorganic ion transport and
metabolism].
Length = 71
Score = 32.7 bits (75), Expect = 0.004
Identities = 13/41 (31%), Positives = 21/41 (51%)
Query: 25 GVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDMGFDTKV 65
GV S+ V L A +T++ V + + EAI D G+ +
Sbjct: 29 GVASVDVDLEKGTATVTFDSNKVDIEAIIEAIEDAGYKVEE 69
>gnl|CDD|188014 TIGR00003, TIGR00003, copper ion binding protein. This model
describes an apparently copper-specific subfamily of
the metal-binding domain HMA (pfam00403). Closely
related sequences outside this model include mercury
resistance proteins and repeated domains of eukaryotic
eukaryotic copper transport proteins. Members of this
family are strictly prokaryotic. The model identifies
both small proteins consisting of just this domain and
N-terminal regions of cation (probably copper)
transporting ATPases [Transport and binding proteins,
Cations and iron carrying compounds].
Length = 66
Score = 32.5 bits (74), Expect = 0.005
Identities = 15/43 (34%), Positives = 25/43 (58%)
Query: 20 IGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDMGFD 62
+G GV +KV L ++ V+ ++ VS E+ EAI D G++
Sbjct: 22 VGEIEGVSKVKVQLEKEKVVVEFDAPNVSATEICEAILDAGYE 64
>gnl|CDD|131107 TIGR02052, MerP, mercuric transport protein periplasmic
component. This model represents the periplasmic
mercury (II) binding protein of the bacterial mercury
detoxification system which passes mercuric ion to the
MerT transporter for subsequent reduction to Hg(0) by
the mercuric reductase MerA. MerP contains a
distinctive GMTCXXC motif associated with metal
binding. MerP is related to a larger family of metal
binding proteins (pfam00403) [Cellular processes,
Detoxification].
Length = 92
Score = 30.4 bits (68), Expect = 0.043
Identities = 14/43 (32%), Positives = 24/43 (55%)
Query: 25 GVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDMGFDTKVTQ 67
GV +V+ K AV+T++ + K L+EA D G+ + + Q
Sbjct: 50 GVSKAEVTFKTKLAVVTFDDEKTNVKALTEATTDAGYPSSLKQ 92
>gnl|CDD|236172 PRK08173, PRK08173, DNA topoisomerase III; Validated.
Length = 862
Score = 31.2 bits (71), Expect = 0.044
Identities = 16/36 (44%), Positives = 22/36 (61%), Gaps = 8/36 (22%)
Query: 27 DSIKVSLADKEAVITYNPTLVSPKELSEA---IYDM 59
D+ K+S D A+I PTL +PK LSE +YD+
Sbjct: 377 DNSKIS--DHFAII---PTLQAPKSLSEPEQKLYDL 407
>gnl|CDD|225127 COG2217, ZntA, Cation transport ATPase [Inorganic ion transport
and metabolism].
Length = 713
Score = 27.6 bits (62), Expect = 0.91
Identities = 13/45 (28%), Positives = 25/45 (55%), Gaps = 1/45 (2%)
Query: 25 GVDSIKVSLADKEAVITYNPTLVS-PKELSEAIYDMGFDTKVTQV 68
GV+ +V+LA + A + Y+P V P ++ A+ G+ ++T
Sbjct: 28 GVEEARVNLATERATVVYDPEEVDLPADIVAAVEKAGYSARLTAA 72
>gnl|CDD|139961 PRK13901, ruvA, Holliday junction DNA helicase RuvA; Provisional.
Length = 196
Score = 26.3 bits (58), Expect = 2.0
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 50 KELSEAIYDMGFDTKV 65
KEL ++I +MGFD K+
Sbjct: 145 KELEQSIVNMGFDRKL 160
>gnl|CDD|235387 PRK05283, PRK05283, deoxyribose-phosphate aldolase; Provisional.
Length = 257
Score = 26.1 bits (58), Expect = 2.8
Identities = 25/78 (32%), Positives = 33/78 (42%), Gaps = 10/78 (12%)
Query: 16 KSSMIGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDMGFDTKVTQVDGKPYVP 75
K+S I + G D IK S K V N TL + + + E I DMG V + P
Sbjct: 151 KASEIAIKAGADFIKTSTG-KVPV---NATLEAARIMLEVIRDMGVAKTVG------FKP 200
Query: 76 ETNVNTSADGLAFKQGAD 93
V T+ D + AD
Sbjct: 201 AGGVRTAEDAAQYLALAD 218
>gnl|CDD|204101 pfam08936, CsoSCA, Carboxysome Shell Carbonic Anhydrase.
Carboxysome Shell Carbonic Anhydrase is a bacterial
carbonic anhydrase localised in the carboxysome, where
it converts bicarbonate ions to carbon dioxide for use
in carbon fixation. It contains three domains, these
being: (1) an N-terminal domain composed primarily of
four alpha-helices; (2) a catalytic domain containing a
tightly bound zinc ion and (3) a C-terminal domain with
weak structural similarity to the catalytic domain.
Length = 459
Score = 25.7 bits (57), Expect = 4.5
Identities = 16/65 (24%), Positives = 25/65 (38%), Gaps = 11/65 (16%)
Query: 19 MIGARTGVDSIKVSLADK----------EAVITYNPTL-VSPKELSEAIYDMGFDTKVTQ 67
+IG T D+I+V + D + Y TL +S ++ AI + Q
Sbjct: 241 LIGLDTDTDAIRVHVPDADGEVDLDRWVDTADLYRETLGLSAEQARAAIAEAVAADGWAQ 300
Query: 68 VDGKP 72
G P
Sbjct: 301 GPGAP 305
>gnl|CDD|107339 cd06344, PBP1_ABC_ligand_binding_like_9, Type I periplasmic
ligand-binding domain of uncharacterized ABC (ATPase
Binding Cassette)-type active transport systems that are
predicted to be involved in uptake of amino acids,
peptides, or inorganic ions. This subgroup includes the
type I periplasmic ligand-binding domain of
uncharacterized ABC (ATPase Binding Cassette)-type
active transport systems that are predicted to be
involved in uptake of amino acids, peptides, or
inorganic ions. Members of this group are
sequence-similar to members of the family of ABC-type
hydrophobic amino acid transporters, such as
leucine/isoleucine/valine binding protein (LIVBP);
however their ligand specificity has not been determined
experimentally.
Length = 332
Score = 25.3 bits (56), Expect = 5.1
Identities = 12/61 (19%), Positives = 23/61 (37%), Gaps = 5/61 (8%)
Query: 22 ARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDMGFDTKVTQVDGKPYVPETNVNT 81
AR +K K+ I YN T + L + F + + + G V ++++
Sbjct: 121 ARALAKYLKKKNKIKKVAIFYNSTSPYSQSLKQE-----FTSALLERGGGIVVTPCDLSS 175
Query: 82 S 82
Sbjct: 176 P 176
>gnl|CDD|227493 COG5164, SPT5, Transcription elongation factor [Transcription].
Length = 607
Score = 25.4 bits (55), Expect = 5.4
Identities = 10/45 (22%), Positives = 16/45 (35%)
Query: 12 KSSSKSSMIGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAI 56
K ++ + +S+KV L +T N EL I
Sbjct: 303 KIEGNVCIVATKDFTESLKVDLDKMNPPVTVNLQNPKTNELERKI 347
>gnl|CDD|177543 PHA03146, PHA03146, helicase-primase primase subunit;
Provisional.
Length = 1075
Score = 25.3 bits (55), Expect = 5.4
Identities = 12/36 (33%), Positives = 20/36 (55%)
Query: 27 DSIKVSLADKEAVITYNPTLVSPKELSEAIYDMGFD 62
+I+V A ITY+ L++ +E SE Y + +D
Sbjct: 8 PTIRVLYATDGCAITYSLMLLTGQEPSEGAYVVSYD 43
>gnl|CDD|185734 cd08993, GH43_DUF377, Glycosyl hydrolase family 43 containing a
domain of unknown function. This subfamily has
sequences similar to the glycosyl hydrolase family 43
(GH43) and contains uncharacterized proteins. GH43
proteins are inverting enzymes (i.e. they invert the
stereochemistry of the anomeric carbon atom of the
substrate) that have an aspartate as the catalytic
general base, a glutamate as the catalytic general acid
and another aspartate that is responsible for pKa
modulation and orienting the catalytic acid. Many of
the GH43 enzymes display both
alpha-L-arabinofuranosidase and beta-D-xylosidase
activity using aryl-glycosides as substrates. A common
structural feature of GH43 enzymes is a 5-bladed
beta-propeller domain that contains the catalytic acid
and catalytic base. A long V-shaped groove, partially
enclosed at one end, forms a single extended
substrate-binding surface across the face of the
propeller.
Length = 268
Score = 25.0 bits (55), Expect = 7.3
Identities = 10/35 (28%), Positives = 15/35 (42%)
Query: 55 AIYDMGFDTKVTQVDGKPYVPETNVNTSADGLAFK 89
+YD G + + G V + S DGL F+
Sbjct: 5 VVYDNGEFYLLYRAAGNDGVIRLGLARSRDGLHFE 39
>gnl|CDD|100037 cd06061, PurM-like1, AIR synthase (PurM) related protein,
subgroup 1 of unknown function. The family of PurM
related proteins includes Hydrogen expression/formation
protein HypE, AIR synthases, FGAM synthase and
Selenophosphate synthetase (SelD). They all contain two
conserved domains and seem to dimerize. The N-terminal
domain forms the dimer interface and is a putative ATP
binding domain.
Length = 298
Score = 24.5 bits (54), Expect = 9.5
Identities = 12/58 (20%), Positives = 23/58 (39%), Gaps = 8/58 (13%)
Query: 4 EVFLPLLDKSSSKSSMIGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDMGF 61
+ L L + ++G G D+ V K V++ +P ++ A D G+
Sbjct: 12 RLILKNL-GADRDEVLVGPGGGEDAAVVDFGGKVLVVSTDP-------ITGAGKDAGW 61
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
0.310 0.129 0.350
Gapped
Lambda K H
0.267 0.0710 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,447,946
Number of extensions: 352292
Number of successful extensions: 248
Number of sequences better than 10.0: 1
Number of HSP's gapped: 247
Number of HSP's successfully gapped: 21
Length of query: 93
Length of database: 10,937,602
Length adjustment: 60
Effective length of query: 33
Effective length of database: 8,276,362
Effective search space: 273119946
Effective search space used: 273119946
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 (21.7 bits)
S2: 53 (24.2 bits)