RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15948
(196 letters)
>gnl|CDD|146145 pfam03357, Snf7, Snf7. This family of proteins are involved in
protein sorting and transport from the endosome to the
vacuole/lysosome in eukaryotic cells. Vacuoles/lysosomes
play an important role in the degradation of both lipids
and cellular proteins. In order to perform this
degradative function, vacuoles/lysosomes contain
numerous hydrolases which have been transported in the
form of inactive precursors via the biosynthetic pathway
and are proteolytically activated upon delivery to the
vacuole/lysosome. The delivery of transmembrane
proteins, such as activated cell surface receptors to
the lumen of the vacuole/lysosome, either for
degradation/downregulation, or in the case of
hydrolases, for proper localisation, requires the
formation of multivesicular bodies (MVBs). These late
endosomal structures are formed by invaginating and
budding of the limiting membrane into the lumen of the
compartment. During this process, a subset of the
endosomal membrane proteins is sorted into the forming
vesicles. Mature MVBs fuse with the vacuole/lysosome,
thereby releasing cargo containing vesicles into its
hydrolytic lumen for degradation. Endosomal proteins
that are not sorted into the intralumenal MVB vesicles
are either recycled back to the plasma membrane or Golgi
complex, or remain in the limiting membrane of the MVB
and are thereby transported to the limiting membrane of
the vacuole/lysosome as a consequence of fusion.
Therefore, the MVB sorting pathway plays a critical role
in the decision between recycling and degradation of
membrane proteins. A few archaeal sequences are also
present within this family.
Length = 169
Score = 105 bits (265), Expect = 3e-29
Identities = 49/166 (29%), Positives = 86/166 (51%), Gaps = 2/166 (1%)
Query: 4 HLFNLKFAAKELERNSKRCEKEEKAEKLKTKKAIQKGNLEVARIHAENAIRQKNQSINYL 63
+ +L+ A +EL++ + EK+ K + + KK +KGN + A I + R + Q
Sbjct: 2 AILSLRKAIRELDKKQESLEKKIKKLEAEIKKLAKKGNKDAALILLKQKKRYEKQLDQLD 61
Query: 64 RMSARVDAVASRVQTALTTRKVTQSMSGVVKAMDAAMKSMNLEKISGLMDKFEEQFEDLD 123
A ++ V ++ A T ++V +M G KAM A K+M+++KI LMD+ E+Q E D
Sbjct: 62 GQLANLEQVRMAIENAKTNQEVLNAMKGGAKAMKAMNKNMDIDKIDDLMDEIEDQMEKAD 121
Query: 124 VQSSYMENTMSQSVTTSVPQNDVDSLMKQVADEAGLELTMALPSGP 169
S + +T+ + ++D+ + + DE G E + LPS P
Sbjct: 122 EISEMLSDTLDD--ADEEDEEELDAELDALLDEIGDEELVELPSAP 165
>gnl|CDD|227778 COG5491, VPS24, Conserved protein implicated in secretion [Cell
motility and secretion].
Length = 204
Score = 62.1 bits (151), Expect = 4e-12
Identities = 45/157 (28%), Positives = 65/157 (41%), Gaps = 11/157 (7%)
Query: 12 AKELERNSKRCEKEEKAEKLKTKKAIQKGNLEVARIHAENAIRQKNQSINYLRMSARVDA 71
LER +K+ +E K E K + + + A N R + + +R+DA
Sbjct: 2 RSSLERQAKKLVRELKQEAKKGQVLLNE-----IAKKAPNRRRLAEELYKLRKARSRLDA 56
Query: 72 VASRVQTALTTRKVTQSMSGVVKAMDAAMKSMN-LEKISGLMDKFEEQFEDLDVQSS--- 127
SR+Q+ T M V M A MN LE I +M FE QF L++
Sbjct: 57 SISRLQSLDTMLFEKVVMRQVSGDMAKAAMYMNELESIRRIMQLFETQFLALELVQLRLE 116
Query: 128 YMENTMSQSVTTSV--PQNDVDSLMKQVADEAGLELT 162
M+ M V V ++D L+ +V E GLEL
Sbjct: 117 TMDELMDVVVGDPVLEDLEELDELVNKVLPEIGLELD 153
>gnl|CDD|235185 PRK03980, PRK03980, flap endonuclease-1; Provisional.
Length = 292
Score = 30.9 bits (71), Expect = 0.33
Identities = 17/46 (36%), Positives = 30/46 (65%), Gaps = 4/46 (8%)
Query: 9 KFAAKELERNSKRCEKEEKAEKLKTKKAIQKGNLEVARIHAENAIR 54
+ A+E+E R E E+AE+ K ++A ++G+LE AR +A+ + R
Sbjct: 38 ELKAEEIEE---RREVREEAEE-KYEEAKEEGDLEEARKYAQRSSR 79
>gnl|CDD|179314 PRK01641, leuD, isopropylmalate isomerase small subunit;
Provisional.
Length = 200
Score = 29.7 bits (68), Expect = 0.60
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 141 VPQNDVDSLMKQVADEAGLELTMALPS 167
+P+ DVD L K V G ELT+ L +
Sbjct: 121 LPEEDVDELFKLVEANPGAELTVDLEA 147
>gnl|CDD|234306 TIGR03674, fen_arch, flap structure-specific endonuclease.
Endonuclease that cleaves the 5'-overhanging flap
structure that is generated by displacement synthesis
when DNA polymerase encounters the 5'-end of a
downstream Okazaki fragment. Has 5'-endo-/exonuclease
and 5'-pseudo-Y-endonuclease activities. Cleaves the
junction between single and double-stranded regions of
flap DNA.
Length = 338
Score = 29.9 bits (68), Expect = 0.71
Identities = 17/41 (41%), Positives = 28/41 (68%), Gaps = 4/41 (9%)
Query: 9 KFAAKELERNSKRCEKEEKAEKLKTKKAIQKGNLEVARIHA 49
+ A+ LE +R E E+AE+ K ++A++KG+LE AR +A
Sbjct: 85 ELKAETLE---ERREIREEAEE-KWEEALEKGDLEEARKYA 121
>gnl|CDD|224822 COG1910, COG1910, Periplasmic molybdate-binding protein/domain
[Inorganic ion transport and metabolism].
Length = 223
Score = 29.6 bits (67), Expect = 0.79
Identities = 24/120 (20%), Positives = 49/120 (40%), Gaps = 8/120 (6%)
Query: 36 AIQKGNLEVARIH-AENAIRQKNQSI--NYLRMSARVDAVASRVQTALTTRKVTQSMSGV 92
AI++G ++A IH +N N YL A + R Q + + +++S +
Sbjct: 33 AIKRGEADIAGIHLLDNESGTYNIPYVKKYLPGEAVLIRGYLREQGLMVQKGNPKNISSL 92
Query: 93 VKAMDAAMKSMNLEKISGLMDKFEEQFEDLDVQSSYM-----ENTMSQSVTTSVPQNDVD 147
+ ++ +N + SG +E +L++ + E T +V ++V D
Sbjct: 93 EDLLRKDLRFVNRNRGSGTRILLDELLGELNILPDSIKGYSDEATTHDAVASAVASGRAD 152
>gnl|CDD|240317 PTZ00217, PTZ00217, flap endonuclease-1; Provisional.
Length = 393
Score = 30.0 bits (68), Expect = 0.82
Identities = 18/58 (31%), Positives = 32/58 (55%), Gaps = 8/58 (13%)
Query: 12 AKELERNSKRCEKEEKAEKLKTKKAIQKGNLEVARIHAENAIR----QKNQSINYLRM 65
+ ELE KR E+ E+AE + +KAI++G+ E + ++ +R Q + LR+
Sbjct: 96 SGELE---KRRERREEAE-EELEKAIEEGDDEEIKKQSKRTVRVTKEQNEDAKKLLRL 149
>gnl|CDD|132290 TIGR03246, arg_catab_astC, succinylornithine transaminase family.
Members of the seed alignment for this protein family
are the enzyme succinylornithine transaminase (EC
2.6.1.81), which catalyzes the third of five steps in
arginine succinyltransferase (AST) pathway, an
ammonia-releasing pathway of arginine degradation. All
seed alignment sequences are found within arginine
succinyltransferase operons, and all proteins that score
above 820.0 bits should function as succinylornithine
transaminase. However, a number of sequences extremely
closely related in sequence, found in different genomic
contexts, are likely to act in different biological
processes and may act on different substrates. This
model is desigated subfamily rather than equivalog,
pending further consideration, for this reason [Energy
metabolism, Amino acids and amines].
Length = 397
Score = 28.9 bits (65), Expect = 1.7
Identities = 13/45 (28%), Positives = 24/45 (53%)
Query: 151 KQVADEAGLELTMALPSGPDSIAASSQVSQEQDELSQRLARLRQA 195
KQ + A E +AL +GP+ + + + D++ + LAR +A
Sbjct: 348 KQFVNAAAEEGVIALIAGPNVVRFAPSLVISDDDIDEGLARFERA 392
>gnl|CDD|240425 PTZ00464, PTZ00464, SNF-7-like protein; Provisional.
Length = 211
Score = 28.2 bits (63), Expect = 2.1
Identities = 23/101 (22%), Positives = 45/101 (44%), Gaps = 7/101 (6%)
Query: 28 AEKLKTKKAIQKGNLEVARIHAENAIR---QK----NQSINYLRMSARVDAVASRVQTAL 80
AE +K K+ IQ+ H + A++ QK NQ ++ +D + ++
Sbjct: 39 AELMKLKEQIQRTRGMTQSRHKQRAMQLLQQKRMYQNQQDMMMQQQFNMDQLQFTTESVK 98
Query: 81 TTRKVTQSMSGVVKAMDAAMKSMNLEKISGLMDKFEEQFED 121
T+ +M K + K +N++K+ L D+ + +ED
Sbjct: 99 DTKVQVDAMKQAAKTLKKQFKKLNVDKVEDLQDELADLYED 139
>gnl|CDD|183699 PRK12720, PRK12720, secretion system apparatus protein SsaV;
Provisional.
Length = 675
Score = 28.9 bits (65), Expect = 2.1
Identities = 23/79 (29%), Positives = 39/79 (49%), Gaps = 8/79 (10%)
Query: 37 IQKGNLEVARIHAE---NAIRQKNQSINYLRMSARVDAVASRVQTALTTRKVTQSMSGVV 93
I KG+ VA + A + + K SI+ + +DA +R R+ Q S ++
Sbjct: 131 ITKGSERVAEVSARFSLDGMPGKQMSIDGDMRAGVIDADEARRL-----RQHVQKESRLL 185
Query: 94 KAMDAAMKSMNLEKISGLM 112
AMD AMK + + I+G++
Sbjct: 186 GAMDGAMKFVKGDAIAGII 204
>gnl|CDD|239154 cd02753, MopB_Formate-Dh-H, Formate dehydrogenase H (Formate-Dh-H)
catalyzes the reversible oxidation of formate to CO2
with the release of a proton and two electrons. It is a
component of the anaerobic formate hydrogen lyase
complex. The E. coli formate dehydrogenase H (Fdh-H) is
a monomer composed of a single polypeptide chain with a
Mo active site region and a [4Fe-4S] center. Members of
the MopB_Formate-Dh-H CD belong to the
molybdopterin_binding (MopB) superfamily of proteins.
Length = 512
Score = 28.3 bits (64), Expect = 2.8
Identities = 12/26 (46%), Positives = 19/26 (73%), Gaps = 2/26 (7%)
Query: 168 GPDSIA--ASSQVSQEQDELSQRLAR 191
GPD+IA S++ + E++ L Q+LAR
Sbjct: 90 GPDAIAFFGSAKCTNEENYLFQKLAR 115
>gnl|CDD|146478 pfam03866, HAP, Hydrophobic abundant protein (HAP). Expression of
HAP is thought to be developmentally regulated and
possibly involved in spherule cell wall formation.
Length = 167
Score = 27.6 bits (61), Expect = 3.3
Identities = 19/97 (19%), Positives = 43/97 (44%), Gaps = 5/97 (5%)
Query: 80 LTTRKVTQSMSGVVKAMDAAMKSMNLEKISGLMDKFEEQFEDLDVQSSYMENTMSQSVTT 139
+T V + + G V + A + ++ L+ + G + F D D +E ++ +
Sbjct: 65 ITLSGVLEIVIGTVLGLVATLAALALDLVGGSVGGICNDFLDFDAILELIEESLHSLLAQ 124
Query: 140 SVPQNDVDSLMKQVADEAGLELTMALPSGPDSIAASS 176
++ V+++ L L +AL + D+IA ++
Sbjct: 125 ALLAGLVNAIFA-----LPLALLVALSALTDAIARAA 156
>gnl|CDD|235350 PRK05134, PRK05134, bifunctional 3-demethylubiquinone-9
3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol
methylase; Provisional.
Length = 233
Score = 27.8 bits (63), Expect = 3.3
Identities = 10/27 (37%), Positives = 16/27 (59%), Gaps = 4/27 (14%)
Query: 41 NLEVARIHAENAIRQKNQSINYLRMSA 67
N+EVAR+HA + I+Y + +A
Sbjct: 82 NIEVARLHAL----ESGLKIDYRQTTA 104
>gnl|CDD|213359 cd12825, EcCorA-like, Escherichia coli Mg2+ transporter CorA_like
subfamily. A bacterial subfamily of the Escherichia
coli CorA-Salmonella typhimurium
ZntB_like(EcCorA_ZntB-like) family of the MIT
superfamily of essential membrane proteins involved in
transporting divalent cations (uptake or efflux) across
membranes. This subfamily includes the Mg2+ transporters
Escherichia coli, Salmonella typhimurium, and
Helicobacter pylori CorAs (which can also transport
Co2+, and Ni2+). Structures of the intracellular domain
of Vibrio parahaemolyticus and Salmonella typhimurium
ZntB form funnel-shaped homopentamers, the tip of the
funnel is formed from two C-terminal transmembrane (TM)
helices from each monomer, and the large opening of the
funnel from the N-terminal cytoplasmic domains. The GMN
signature motif of the MIT superfamily occurs just after
TM1, mutation within this motif is known to abolish Mg2+
transport through Salmonella typhimurium CorA, and
Mrs2p. Natural variants such as GVN and GIN, such as
occur in some ZntB family proteins, may be associated
with the transport of different divalent cations, such
as zinc and cadmium. The functional diversity of MIT
transporters may also be due to minor structural
differences regulating gating, substrate selection, and
transport.
Length = 287
Score = 28.1 bits (63), Expect = 3.4
Identities = 9/35 (25%), Positives = 17/35 (48%)
Query: 117 EQFEDLDVQSSYMENTMSQSVTTSVPQNDVDSLMK 151
E ED+++ S Y E+ +T S P + ++
Sbjct: 27 EHLEDIEISSRYWEDDSQLFITLSFPNQTKEDTIE 61
>gnl|CDD|222496 pfam14014, DUF4230, Protein of unknown function (DUF4230). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are typically between 203 and 228 amino
acids in length.
Length = 154
Score = 27.2 bits (61), Expect = 3.7
Identities = 13/30 (43%), Positives = 20/30 (66%)
Query: 26 EKAEKLKTKKAIQKGNLEVARIHAENAIRQ 55
++A+K K A++ G LE AR +AE A+ Q
Sbjct: 110 KEAKKKIEKAALESGLLERARENAEKALEQ 139
>gnl|CDD|130652 TIGR01591, Fdh-alpha, formate dehydrogenase, alpha subunit,
archaeal-type. This model describes a subset of formate
dehydrogenase alpha chains found mainly archaea but also
in alpha and gamma proteobacteria and a small number of
gram positive bacteria. The alpha chain contains domains
for molybdopterin dinucleotide binding and molybdopterin
oxidoreductase (pfam01568 and pfam00384, respectively).
The holo-enzyme also contains beta and gamma subunits.
The enzyme catalyzes the oxidation of formate (produced
from pyruvate during anaerobic growth) to carbon dioxide
with the concomitant release of two electrons and two
protons. The enzyme's purpose is to allow growth on
formate in some circumstances and, in the case of FdhH
in gamma proteobacteria, to pass electrons to
hydrogenase (by which process acid is neutralized). This
model is well-defined, with only a single fragmentary
sequence falling between trusted and noise. The alpha
subunit of a version of nitrate reductase is closely
related.
Length = 671
Score = 27.8 bits (62), Expect = 4.4
Identities = 13/26 (50%), Positives = 18/26 (69%), Gaps = 2/26 (7%)
Query: 168 GPDSIA--ASSQVSQEQDELSQRLAR 191
GPDSI SS+ + E++ L Q+LAR
Sbjct: 89 GPDSIGFIGSSRGTNEENYLLQKLAR 114
>gnl|CDD|185600 PTZ00410, PTZ00410, NAD-dependent SIR2; Provisional.
Length = 349
Score = 27.5 bits (61), Expect = 4.4
Identities = 11/46 (23%), Positives = 18/46 (39%)
Query: 103 MNLEKISGLMDKFEEQFEDLDVQSSYMENTMSQSVTTSVPQNDVDS 148
NLE++ GLM +F S + S S ++ + S
Sbjct: 237 FNLERVGGLMFRFPTDPLTTFHADSVAKEGRSSSSSSRSSSDSSTS 282
>gnl|CDD|214753 smart00636, Glyco_18, Glyco_18 domain.
Length = 334
Score = 27.3 bits (61), Expect = 5.1
Identities = 12/27 (44%), Positives = 17/27 (62%)
Query: 149 LMKQVADEAGLELTMALPSGPDSIAAS 175
L K+ A+ G LT+A+P+GPD I
Sbjct: 139 LDKEGAEGKGYLLTIAVPAGPDKIDKG 165
>gnl|CDD|183486 PRK12381, PRK12381, bifunctional succinylornithine
transaminase/acetylornithine transaminase; Provisional.
Length = 406
Score = 27.4 bits (61), Expect = 5.6
Identities = 12/45 (26%), Positives = 25/45 (55%)
Query: 151 KQVADEAGLELTMALPSGPDSIAASSQVSQEQDELSQRLARLRQA 195
KQ++ EA M L +GP+ + + ++ ++E++ L R +A
Sbjct: 352 KQISQEAAKAGVMVLIAGPNVVRFAPALNISEEEITTGLDRFARA 396
>gnl|CDD|183031 PRK11194, PRK11194, ribosomal RNA large subunit methyltransferase
N; Provisional.
Length = 372
Score = 27.0 bits (60), Expect = 6.7
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 79 ALTTRKVTQSMSGVVKAMD 97
L+ R+VT S SGVV A+D
Sbjct: 190 GLSKRRVTLSTSGVVPALD 208
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
0.308 0.120 0.301
Gapped
Lambda K H
0.267 0.0738 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,048,655
Number of extensions: 792529
Number of successful extensions: 1196
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1178
Number of HSP's successfully gapped: 92
Length of query: 196
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 104
Effective length of database: 6,857,034
Effective search space: 713131536
Effective search space used: 713131536
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 56 (25.3 bits)