RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1410
(246 letters)
>gnl|CDD|239148 cd02685, MIT_C, MIT_C; domain found C-terminal to MIT (contained
within Microtubule Interacting and Trafficking
molecules) domains, as well as in some bacterial
proteins. The function of this domain is unknown.
Length = 148
Score = 178 bits (453), Expect = 5e-57
Identities = 67/154 (43%), Positives = 93/154 (60%), Gaps = 10/154 (6%)
Query: 90 NEKGVTYEKLFGRFLDENVEQIDVTDPYIHNKHQCYNFLQFCELAIKNCKNVKRINLLTT 149
N G +Y++LFG +LD+ V +I V DPYI N HQ NFL+FCEL +K +K I+L+T
Sbjct: 1 NATGFSYDRLFGPYLDDGVTEITVEDPYIRNFHQIRNFLRFCELVVKPPCELKYIHLVTG 60
Query: 150 -YADRPQHSNKTARVKQEENLKQLQESLRKMKITLNINYSNTLHDREIVLSNDWVIKIGR 208
D + +Q E L+++++SL + +S+T+HDREI N W+IKIGR
Sbjct: 61 EDEDNGK--------QQIEALEEIKQSLASHGVEFTWEFSDTIHDREIRTDNGWIIKIGR 112
Query: 209 GLDIFCHV-PEFSIGFTDLSLRPCKETVVNIFHR 241
GLD F +FS+G D RPCK T V+IFH
Sbjct: 113 GLDYFKPPEGKFSLGNRDQDFRPCKATEVDIFHT 146
>gnl|CDD|239146 cd02683, MIT_1, MIT: domain contained within Microtubule
Interacting and Trafficking molecules. This sub-family
of MIT domains is found in proteins with unknown
function, co-occuring with an as yet undescribed
domain. The molecular function of the MIT domain is
unclear.
Length = 77
Score = 72.5 bits (178), Expect = 7e-17
Identities = 30/77 (38%), Positives = 53/77 (68%)
Query: 3 SSIELAQFLLIRAVELDERGRWTESLTFYQDGVTELLKHVRGLSNKGDQQKIRDKIETYI 62
S A+ +L RAVELD+ GR+ E+L YQ+G+ L++ ++G ++ ++ +R KI Y+
Sbjct: 1 SLELAAKEVLKRAVELDQEGRFQEALVCYQEGIDLLMQVLKGTKDEAKKKNLRQKISEYM 60
Query: 63 NRAEVLKGKLDEKKKMG 79
+RAE +K +LD++K+ G
Sbjct: 61 DRAEAIKKRLDQEKEDG 77
>gnl|CDD|146707 pfam04212, MIT, MIT (microtubule interacting and transport)
domain. The MIT domain forms an asymmetric three-helix
bundle and binds ESCRT-III (endosomal sorting complexes
required for transport) substrates.
Length = 69
Score = 60.3 bits (147), Expect = 2e-12
Identities = 24/69 (34%), Positives = 41/69 (59%)
Query: 4 SIELAQFLLIRAVELDERGRWTESLTFYQDGVTELLKHVRGLSNKGDQQKIRDKIETYIN 63
+E A L+ +AVE DE G + E+L Y++ + LL+ ++ + ++ +R KI Y++
Sbjct: 1 YLEKALELVKKAVEADEAGNYEEALELYKEAIEYLLQALKYEPDPKRREALRQKIAEYLD 60
Query: 64 RAEVLKGKL 72
RAE LK L
Sbjct: 61 RAEELKELL 69
>gnl|CDD|239121 cd02656, MIT, MIT: domain contained within Microtubule
Interacting and Trafficking molecules. The MIT domain
is found in sorting nexins, the nuclear thiol protease
PalBH, the AAA protein spastin and archaebacterial
proteins with similar domain architecture, vacuolar
sorting proteins and others. The molecular function of
the MIT domain is unclear.
Length = 75
Score = 58.5 bits (142), Expect = 1e-11
Identities = 22/75 (29%), Positives = 46/75 (61%)
Query: 3 SSIELAQFLLIRAVELDERGRWTESLTFYQDGVTELLKHVRGLSNKGDQQKIRDKIETYI 62
++ A+ L+ +AV+ DE G + E+L Y++ + LL+ ++ ++ +R K++ Y+
Sbjct: 1 ELLQQAKELIKQAVKEDEDGNYEEALELYKEALDYLLQALKAEKEPKLRKLLRKKVKEYL 60
Query: 63 NRAEVLKGKLDEKKK 77
+RAE LK L ++K+
Sbjct: 61 DRAEFLKELLKKQKQ 75
>gnl|CDD|197854 smart00745, MIT, Microtubule Interacting and Trafficking molecule
domain.
Length = 77
Score = 53.1 bits (128), Expect = 1e-09
Identities = 20/73 (27%), Positives = 42/73 (57%)
Query: 3 SSIELAQFLLIRAVELDERGRWTESLTFYQDGVTELLKHVRGLSNKGDQQKIRDKIETYI 62
+ A+ L+ +A++ DE G + E+L Y+ + LL+ ++ S+ ++ ++ K Y+
Sbjct: 3 DYLSKAKELISKALKADEAGNYEEALELYKKAIEYLLEGIKVESDSKRREALKAKAAEYL 62
Query: 63 NRAEVLKGKLDEK 75
+RAE +K L E+
Sbjct: 63 DRAEEIKKSLLER 75
>gnl|CDD|239141 cd02678, MIT_VPS4, MIT: domain contained within Microtubule
Interacting and Trafficking molecules. This sub-family
of MIT domains is found in intracellular protein
transport proteins of the AAA-ATPase family. The
molecular function of the MIT domain is unclear.
Length = 75
Score = 46.1 bits (110), Expect = 4e-07
Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 4/73 (5%)
Query: 5 IELAQFLLIRAVELDERGRWTESLTFYQDGVTELLKHVRGLSNKGDQQKIRDKIETYINR 64
IEL + +A+E D G + E+L YQ + + ++ N ++ IR K Y++R
Sbjct: 7 IELVK----KAIEEDNAGNYEEALRLYQHALEYFMHALKYEKNPKSKESIRAKCTEYLDR 62
Query: 65 AEVLKGKLDEKKK 77
AE LK L +K+K
Sbjct: 63 AEKLKEYLAKKEK 75
>gnl|CDD|239147 cd02684, MIT_2, MIT: domain contained within Microtubule
Interacting and Trafficking molecules. This sub-family
of MIT domains is found in proteins with an n-terminal
serine/threonine kinase domain. The molecular function
of the MIT domain is unclear.
Length = 75
Score = 44.8 bits (106), Expect = 1e-06
Identities = 19/74 (25%), Positives = 40/74 (54%)
Query: 4 SIELAQFLLIRAVELDERGRWTESLTFYQDGVTELLKHVRGLSNKGDQQKIRDKIETYIN 63
S+E A L+++AV+ D+RG +L+ Y + + + ++ ++ +R K+ Y++
Sbjct: 2 SLEKAIALVVQAVKKDQRGDAAAALSLYCSALQYFVPALHYETDAQRKEALRQKVLQYVS 61
Query: 64 RAEVLKGKLDEKKK 77
RAE LK + +
Sbjct: 62 RAEELKALIASDTQ 75
>gnl|CDD|239144 cd02681, MIT_calpain7_1, MIT: domain contained within Microtubule
Interacting and Trafficking molecules. This sub-family
of MIT domains is found in the nuclear thiol protease
PalBH. The molecular function of the MIT domain is
unclear.
Length = 76
Score = 33.7 bits (77), Expect = 0.009
Identities = 16/56 (28%), Positives = 33/56 (58%), Gaps = 3/56 (5%)
Query: 15 AVELDERGRWTESLTFYQDGVTELLKHVRGLSNKGDQ--QKIRDKIETYINRAEVL 68
AV+ D+ GR++E++ +Y++ +LL + D + I++K Y++RA+ L
Sbjct: 13 AVQRDQEGRYSEAVFYYKEA-AQLLIYAEMAGTLNDSHLKTIQEKSNEYLDRAQAL 67
>gnl|CDD|239140 cd02677, MIT_SNX15, MIT: domain contained within Microtubule
Interacting and Trafficking molecules. This MIT domain
sub-family is found in sorting nexin 15 and related
proteins. The molecular function of the MIT domain is
unclear.
Length = 75
Score = 33.1 bits (76), Expect = 0.020
Identities = 23/64 (35%), Positives = 37/64 (57%)
Query: 3 SSIELAQFLLIRAVELDERGRWTESLTFYQDGVTELLKHVRGLSNKGDQQKIRDKIETYI 62
+E A L+ A+E +E G + + FY+ GV LLK V+G S+ ++ ++ KI Y+
Sbjct: 1 DYLEQAAELIRLALEKEEEGDYEAAFEFYRAGVDLLLKGVQGDSSPERREAVKRKIAEYL 60
Query: 63 NRAE 66
RAE
Sbjct: 61 KRAE 64
>gnl|CDD|239143 cd02680, MIT_calpain7_2, MIT: domain contained within Microtubule
Interacting and Trafficking molecules. This sub-family
of MIT domains is found in the nuclear thiol protease
PalBH. The molecular function of the MIT domain is
unclear.
Length = 75
Score = 32.7 bits (74), Expect = 0.024
Identities = 18/65 (27%), Positives = 33/65 (50%)
Query: 5 IELAQFLLIRAVELDERGRWTESLTFYQDGVTELLKHVRGLSNKGDQQKIRDKIETYINR 64
+E A FL+ +A + DE+G E++ Y + V + ++ Q K++ ++R
Sbjct: 3 LERAHFLVTQAFDEDEKGNAEEAIELYTEAVELCINTSNETMDQALQTKLKQLARQALDR 62
Query: 65 AEVLK 69
AE LK
Sbjct: 63 AEALK 67
>gnl|CDD|213237 cd03270, ABC_UvrA_I, ATP-binding cassette domain I of the excision
repair protein UvrA. Nucleotide excision repair in
eubacteria is a process that repairs DNA damage by the
removal of a 12-13-mer oligonucleotide containing the
lesion. Recognition and cleavage of the damaged DNA is a
multistep ATP-dependent reaction that requires the UvrA,
UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases,
with UvrA having two ATP binding sites, which have the
characteristic signature of the family of ABC proteins,
and UvrB having one ATP binding site that is
structurally related to that of helicases.
Length = 226
Score = 29.9 bits (68), Expect = 1.1
Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 10/49 (20%)
Query: 165 QEENLKQLQESLRKMKITLNINYSNTL----HDREIVLSNDWVIKIGRG 209
+N + L E+L++++ + NT+ HD + + + D VI IG G
Sbjct: 172 PRDNDR-LIETLKRLR-----DLGNTVLVVEHDEDTIRAADHVIDIGPG 214
>gnl|CDD|233055 TIGR00617, rpa1, replication factor-a protein 1 (rpa1). All
proteins in this family for which functions are known
are part of a multiprotein complex made up of homologs
of RPA1, RPA2 and RPA3 that bind ssDNA and function in
the recognition of DNA damage for nucleotide excision
repairThis family is based on the phylogenomic analysis
of JA Eisen (1999, Ph.D. Thesis, Stanford University)
[DNA metabolism, DNA replication, recombination, and
repair].
Length = 608
Score = 29.3 bits (66), Expect = 2.0
Identities = 10/44 (22%), Positives = 18/44 (40%), Gaps = 3/44 (6%)
Query: 184 NINYSNTLHDREIVLSNDWVIKIGRGLDIFCHVPEFSIGFTDLS 227
N ++N +D E+ L D VI+ +P+ F +
Sbjct: 262 NKQFTNLGNDYEMTLDRDTVIEECEDET---AIPKIQFNFVKID 302
>gnl|CDD|185691 cd02182, GH16_Strep_laminarinase_like, Streptomyces
laminarinase-like, member of glycosyl hydrolase family
16. Proteins similar to Streptomyces sioyaensis
beta-1,3-glucanase (laminarinase) present in
Actinomycetales as well as Peziomycotina. Laminarinases
belong to glycosyl hydrolase family 16 and hydrolyze the
glycosidic bond of the 1,3-beta-linked glucan, a major
component of fungal and plant cell walls and the
structural and storage polysaccharides (laminarin) of
marine macro-algae. Members of the GH16 family have a
conserved jelly roll fold with an active site channel.
Length = 259
Score = 28.8 bits (65), Expect = 2.4
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 13 IRAVELDERGRWTESLTFYQDGV 35
AVE+D ES+ +Y DGV
Sbjct: 176 TYAVEIDRTNGDAESIRWYLDGV 198
>gnl|CDD|233062 TIGR00630, uvra, excinuclease ABC, A subunit. This family is a
member of the ABC transporter superfamily of proteins of
which all members for which functions are known except
the UvrA proteins are involved in the transport of
material through membranes. UvrA orthologs are involved
in the recognition of DNA damage as a step in nucleotide
excision repair. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 925
Score = 29.2 bits (66), Expect = 2.7
Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 10/53 (18%)
Query: 165 QEENLKQLQESLRKMKITLNINYSNTL----HDREIVLSNDWVIKIGRGLDIF 213
Q +N + L +L++++ + NTL HD + + + D+VI IG G
Sbjct: 523 QRDNRR-LINTLKRLR-----DLGNTLIVVEHDEDTIRAADYVIDIGPGAGEH 569
>gnl|CDD|221623 pfam12531, DUF3731, DNA-K related protein. This domain family is
found in bacteria, and is approximately 250 amino acids
in length. There are two conserved sequence motifs: RPG
and WRR. The proteins in this family are frequently
annotated as DNA-K related proteins however there is
little accompanying literature to confirm this.
Length = 249
Score = 28.4 bits (64), Expect = 3.0
Identities = 13/45 (28%), Positives = 22/45 (48%), Gaps = 1/45 (2%)
Query: 44 GLSNKGDQQKIRDKIETYINRAEVLKGKLDEKKKMGNYHEQIEIA 88
GL N+G QQ++ D + Y+ KL + +Y E + +A
Sbjct: 62 GL-NEGQQQQLLDDLAPYLQPGAQRNLKLPKGPTPQSYDEMVRLA 105
>gnl|CDD|234734 PRK00349, uvrA, excinuclease ABC subunit A; Reviewed.
Length = 943
Score = 28.1 bits (64), Expect = 4.9
Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 10/49 (20%)
Query: 165 QEENLKQLQESLRKMKITLNINYSNTL----HDREIVLSNDWVIKIGRG 209
Q +N + L E+L+ ++ + NTL HD + + + D+++ IG G
Sbjct: 524 QRDNDR-LIETLKHLR-----DLGNTLIVVEHDEDTIRAADYIVDIGPG 566
>gnl|CDD|187851 cd09720, Cas1_II, CRISPR/Cas system-associated protein Cas1.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Cas1 is the most universal CRISPR system protein thought
to be involved in spacer intergration. Cas1 is
metal-dependent deoxyribonuclease, also binds RNA; Shown
to possess a unique fold consisting of a N-terminal
beta-strand domain and a C-terminal alpha-helical
domain.
Length = 275
Score = 28.0 bits (63), Expect = 5.0
Identities = 16/59 (27%), Positives = 31/59 (52%), Gaps = 11/59 (18%)
Query: 51 QQKIRDKIETYINRAEVLK--GKLDEKKKMGNYHEQIEIA--NNEKG----VTYEKLFG 101
Q+ I+ KI +N+A VL+ G ++ +K+ N ++E N + + ++ LFG
Sbjct: 104 QKIIKQKI---LNQAFVLEKLGIFEDAEKLKNLANKVESGDKTNREAHAAKLYFKTLFG 159
>gnl|CDD|188475 TIGR03960, rSAM_fuse_unch, radical SAM family uncharacterized
protein. This model describes a radical SAM protein, or
protein region, regularly found paired with or fused to
a region described by TIGR03936. PSI-BLAST analysis of
TIGR03936 suggests a relationship to the tRNA
pseudouridine synthase TruA, suggesting that this system
may act in RNA modification [Unknown function, Enzymes
of unknown specificity].
Length = 605
Score = 28.0 bits (63), Expect = 5.6
Identities = 7/28 (25%), Positives = 15/28 (53%)
Query: 56 DKIETYINRAEVLKGKLDEKKKMGNYHE 83
D +E Y+ + + L K+ + N+H+
Sbjct: 463 DTMEEYLRKQKHLLDKIKSRSIKYNWHD 490
>gnl|CDD|227195 COG4858, COG4858, Uncharacterized membrane-bound protein conserved
in bacteria [Function unknown].
Length = 226
Score = 27.1 bits (60), Expect = 7.1
Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 6/57 (10%)
Query: 50 DQQKIRDKIETYINRAE---VLKGKLDEKKKMGNYH--EQIEIANNEKGVTYEKLFG 101
Q++ K + Y++ + GK DE+ K+ QI + +KG+T KL G
Sbjct: 12 LLQELTKKNQEYVHEVTKQLIGDGKSDEEIKIILEEMIPQI-LEEQKKGITARKLLG 67
>gnl|CDD|213205 cd03238, ABC_UvrA, ATP-binding cassette domain of the excision
repair protein UvrA. Nucleotide excision repair in
eubacteria is a process that repairs DNA damage by the
removal of a 12-13-mer oligonucleotide containing the
lesion. Recognition and cleavage of the damaged DNA is a
multistep ATP-dependent reaction that requires the UvrA,
UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases,
with UvrA having two ATP binding sites, which have the
characteristic signature of the family of ABC proteins,
and UvrB having one ATP binding site that is
structurally related to that of helicases.
Length = 176
Score = 26.9 bits (60), Expect = 8.1
Identities = 13/52 (25%), Positives = 27/52 (51%), Gaps = 9/52 (17%)
Query: 166 EENLKQLQESLRKMKITLNINYSNTL----HDREIVLSNDWVIKIGRGLDIF 213
++++ QL E ++ + I+ NT+ H+ +++ S DW+I G G
Sbjct: 122 QQDINQLLEVIKGL-----IDLGNTVILIEHNLDVLSSADWIIDFGPGSGKS 168
>gnl|CDD|225104 COG2193, Bfr, Bacterioferritin (cytochrome b1) [Inorganic ion
transport and metabolism].
Length = 157
Score = 26.5 bits (59), Expect = 8.3
Identities = 11/48 (22%), Positives = 16/48 (33%), Gaps = 1/48 (2%)
Query: 66 EVLKGKLD-EKKKMGNYHEQIEIANNEKGVTYEKLFGRFLDENVEQID 112
E+L+ L E + E I + L L + E ID
Sbjct: 85 EMLEADLALEYEARDALKEAIAYCEEVQDYVSRDLLEEILADEEEHID 132
>gnl|CDD|227056 COG4712, COG4712, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 234
Score = 26.9 bits (59), Expect = 9.2
Identities = 15/71 (21%), Positives = 24/71 (33%), Gaps = 20/71 (28%)
Query: 139 KNVKRINLLTTYADRPQHS---NKTARVKQEE----------------NLKQLQESLRKM 179
+N KR+ LL +A P S N+ + Q E ++ + +
Sbjct: 133 ENKKRVPLLPKWA-FPVKSINYNQEREINQLEIVDNNVRYKLGTDISTDIDKATVVIPLD 191
Query: 180 KITLNINYSNT 190
K SNT
Sbjct: 192 KKATGKPNSNT 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
0.319 0.136 0.394
Gapped
Lambda K H
0.267 0.0730 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,300,298
Number of extensions: 1164915
Number of successful extensions: 1337
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1330
Number of HSP's successfully gapped: 52
Length of query: 246
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 152
Effective length of database: 6,768,326
Effective search space: 1028785552
Effective search space used: 1028785552
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: 58 (26.1 bits)