RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13590
(90 letters)
>gnl|CDD|233147 TIGR00840, b_cpa1, sodium/hydrogen exchanger 3. The Monovalent
Cation:Proton Antiporter-1 (CPA1) Family (TC 2.A.36)The
CPA1 family is a large family of proteins derived from
Gram-positive and Gram-negative bacteria, blue green
bacteria, yeast, plants and animals.Transporters from
eukaryotes have been functionally characterized, and all
of these catalyze Na+:H+ exchange. Their primary
physiological functions may be in(1) cytoplasmic pH
regulation, extruding the H+ generated during
metabolism, and (2) salt tolerance (in plants), due to
Na+ uptake into vacuoles.This model is specific for the
eukaryotic members members of this family [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 559
Score = 96.4 bits (240), Expect = 5e-25
Identities = 41/88 (46%), Positives = 60/88 (68%)
Query: 1 MTPRLNQIFPESCLLIFVGVVIGVLLFLTTNIHIHPLTPDTFFLYMLPPIILDAGYFMPN 60
+T ++ + PES LLI G+++G ++ + +I L FFLY+LPPI+LDAGYFMP
Sbjct: 27 LTHKVIRAVPESVLLIVYGLLVGGIIKASPHIDPPTLDSSYFFLYLLPPIVLDAGYFMPQ 86
Query: 61 RLFFDHLGTILLFAVIGTIFNTLSIACI 88
R FF++LG+IL+FAV+GT+ N I
Sbjct: 87 RNFFENLGSILIFAVVGTLINAFVIGLS 114
>gnl|CDD|216235 pfam00999, Na_H_Exchanger, Sodium/hydrogen exchanger family.
Na/H antiporters are key transporters in maintaining
the pH of actively metabolising cells. The molecular
mechanisms of antiport are unclear. These antiporters
contain 10-12 transmembrane regions (M) at the
amino-terminus and a large cytoplasmic region at the
carboxyl terminus. The transmembrane regions M3-M12
share identity with other members of the family. The M6
and M7 regions are highly conserved. Thus, this is
thought to be the region that is involved in the
transport of sodium and hydrogen ions. The cytoplasmic
region has little similarity throughout the family.
Length = 370
Score = 45.3 bits (108), Expect = 4e-07
Identities = 17/75 (22%), Positives = 30/75 (40%), Gaps = 3/75 (4%)
Query: 9 FPESCLLIFVGVVIGVLLFLTTNIHIHPLTPDTFFLYMLPPIILDAGYFMPNRLFFDHLG 68
P LI G+++G + L + LP ++ AG + R +
Sbjct: 20 LPPVVGLILAGILLGPSGL---GLVEPDLDLEVLAELGLPLLLFLAGLELDLRELRKNGK 76
Query: 69 TILLFAVIGTIFNTL 83
+ILL A++G + L
Sbjct: 77 SILLLALLGVLIPFL 91
>gnl|CDD|129911 TIGR00831, a_cpa1, Na+/H+ antiporter, bacterial form. The
Monovalent Cation:Proton Antiporter-1 (CPA1) Family (TC
2.A.36) The CPA1 family is a large family of proteins
derived from Gram-positive and Gram-negative bacteria,
blue green bacteria, yeast, plants and animals.
Transporters from eukaryotes have been functionally
characterized, and all of these catalyze Na+:H+
exchange. Their primary physiological functions may be
in (1) cytoplasmic pH regulation, extruding the H+
generated during metabolism, and (2) salt tolerance (in
plants), due to Na+ uptake into vacuoles. This model is
specific for the bacterial members of this family
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 525
Score = 39.5 bits (92), Expect = 6e-05
Identities = 15/66 (22%), Positives = 29/66 (43%)
Query: 20 VVIGVLLFLTTNIHIHPLTPDTFFLYMLPPIILDAGYFMPNRLFFDHLGTILLFAVIGTI 79
++ G+LL L + PL + LPP++ +A R ++ I L A + +
Sbjct: 29 ILAGLLLGLAGLLPEVPLDREIVLFLFLPPLLFEAAMNTDLRELRENFRPIALIAFLLVV 88
Query: 80 FNTLSI 85
T+ +
Sbjct: 89 VTTVVV 94
>gnl|CDD|223104 COG0025, NhaP, NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic
ion transport and metabolism].
Length = 429
Score = 33.8 bits (78), Expect = 0.005
Identities = 17/79 (21%), Positives = 33/79 (41%), Gaps = 1/79 (1%)
Query: 10 PESCLLIFVGVVIGVLLFLTTNIHIHPLTPDTFFLYMLPPIILDAGYFMPNRLFFDHLGT 69
PE LL+ +G++ G + + L P+ F + L ++ G + R +
Sbjct: 31 PEIPLLLLLGLLGGPPGLNLISPDLE-LDPELFLVLFLAILLFAGGLELDLRELRRVWRS 89
Query: 70 ILLFAVIGTIFNTLSIACI 88
IL+ A+ + L I +
Sbjct: 90 ILVLALPLVLITALGIGLL 108
>gnl|CDD|225628 COG3086, RseC, Positive regulator of sigma E activity [Signal
transduction mechanisms].
Length = 150
Score = 28.5 bits (64), Expect = 0.32
Identities = 12/45 (26%), Positives = 17/45 (37%), Gaps = 1/45 (2%)
Query: 42 FFLYMLPPIILDAGYFMPNRLFFDHLGTILLFAVIGTIFNTLSIA 86
+Y+ P + L G + LFF L I A +G L
Sbjct: 79 LLVYIFPLVGLFLGAILAQYLFFSELIVI-FGAFLGLALGFLLAR 122
>gnl|CDD|217463 pfam03264, Cytochrom_NNT, NapC/NirT cytochrome c family,
N-terminal region. Within the NapC/NirT family of
cytochrome c proteins, some members, such as NapC and
NirT, bind four haem groups, while others, such as
TorC, bind five haems. This family aligns the common
N-terminal region that contains four haem-binding
C-X(2)-CH motifs.
Length = 174
Score = 28.0 bits (63), Expect = 0.41
Identities = 8/30 (26%), Positives = 15/30 (50%), Gaps = 1/30 (3%)
Query: 14 LLIFVGVVIGVLLFLTTNIHIHPLTPDTFF 43
+L+ VG ++GV+ + N + T F
Sbjct: 10 VLLLVGFLLGVVFWGGFNTALE-ATNTEEF 38
>gnl|CDD|233781 TIGR02212, lolCE, lipoprotein releasing system, transmembrane
protein, LolC/E family. This model describes the LolC
protein, and its paralog LolE found in some species.
These proteins are homologous to permease proteins of
ABC transporters. In some species, two paralogs occur,
designated LolC and LolE. In others, a single form is
found and tends to be designated LolC [Protein fate,
Protein and peptide secretion and trafficking].
Length = 411
Score = 27.6 bits (62), Expect = 0.87
Identities = 18/71 (25%), Positives = 31/71 (43%), Gaps = 16/71 (22%)
Query: 19 GVVIGVLL---------FLTTNIHIHPLTPDTFFLYMLPPIILDAGYFMPNRLFFDHLGT 69
GV++GVLL F+ I + D +FL LP + P + + T
Sbjct: 331 GVILGVLLALNLTTIINFIEWLIGVKFFNADIYFLDFLPSKLD------PLDVLLI-IVT 383
Query: 70 ILLFAVIGTIF 80
LL +++ T++
Sbjct: 384 ALLLSLLATLY 394
>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family. Emg1 and Nop14 are novel
proteins whose interaction is required for the
maturation of the 18S rRNA and for 40S ribosome
production.
Length = 809
Score = 27.3 bits (61), Expect = 1.1
Identities = 7/19 (36%), Positives = 12/19 (63%)
Query: 64 FDHLGTILLFAVIGTIFNT 82
LG ++L ++GT+F T
Sbjct: 506 KPGLGDLVLLKLVGTLFPT 524
>gnl|CDD|225550 COG3005, TorC, Nitrate/TMAO reductases, membrane-bound tetraheme
cytochrome c subunit [Energy production and
conversion].
Length = 190
Score = 27.0 bits (60), Expect = 1.3
Identities = 9/30 (30%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 14 LLIFVGVVIGVLLFLTTNIHIHPLTPDTFF 43
L+ +G V+G+L + N+ + LT F
Sbjct: 19 TLLLIGFVVGILFWGGFNVGLE-LTNTEEF 47
>gnl|CDD|168145 PRK05639, PRK05639, 4-aminobutyrate aminotransferase; Provisional.
Length = 457
Score = 26.8 bits (59), Expect = 1.4
Identities = 15/48 (31%), Positives = 20/48 (41%)
Query: 24 VLLFLTTNIHIHPLTPDTFFLYMLPPIILDAGYFMPNRLFFDHLGTIL 71
L +L + H + PD PI DAG +P FF L +L
Sbjct: 205 FLDYLENYVFSHVVPPDEVAALFAEPIQGDAGIVVPPENFFKELKKLL 252
>gnl|CDD|226957 COG4591, LolE, ABC-type transport system, involved in lipoprotein
release, permease component [Cell envelope biogenesis,
outer membrane].
Length = 408
Score = 26.5 bits (59), Expect = 1.9
Identities = 13/74 (17%), Positives = 38/74 (51%), Gaps = 6/74 (8%)
Query: 11 ESCLLIFVGVVIGVLLFLTTNIHIHPLTPDTFFLYMLPPIILDAG-YFMPNRLFFDHLGT 69
+ ++ +G ++GV+L + +++ ++ +++ P + G +P L +
Sbjct: 322 QGLIIGLIGALLGVILGVLLALNL-----NSIIIFIEPLLGHTFGISTLPIELSLLDVVL 376
Query: 70 ILLFAVIGTIFNTL 83
+L+FA++ ++ TL
Sbjct: 377 VLVFALLLSLLATL 390
>gnl|CDD|202942 pfam04246, RseC_MucC, Positive regulator of sigma(E), RseC/MucC.
This bacterial family of integral membrane proteins
represents a positive regulator of the sigma(E)
transcription factor, namely RseC/MucC. The sigma(E)
transcription factor is up-regulated by cell envelope
protein misfolding, and regulates the expression of
genes that are collectively termed ECF (devoted to
Extra-Cellular Functions). In Pseudomonas aeruginosa,
de-repression of sigma(E) is associated with the
alginate-overproducing phenotype characteristic of
chronic respiratory tract colonisation in cystic
fibrosis patients. The mechanism by which RseC/MucC
positively regulates the sigma(E) transcription factor
is unknown. RseC is also thought to have a role in
thiamine biosynthesis in Salmonella typhimurium. In
addition, this family also includes an N-terminal part
of RnfF, a Rhodobacter capsulatus protein, of unknown
function, that is essential for nitrogen fixation. This
protein also contains an ApbE domain pfam02424, which is
itself involved in thiamine biosynthesis.
Length = 135
Score = 25.7 bits (57), Expect = 2.5
Identities = 10/38 (26%), Positives = 16/38 (42%), Gaps = 1/38 (2%)
Query: 42 FFLYMLPPIILDAGYFMPNRLFFDHLGTILLFAVIGTI 79
+Y+LP + L G + L L I L ++G
Sbjct: 72 LLVYLLPLLGLLLGALLGQALGLSELLAI-LGGLLGLA 108
>gnl|CDD|184078 PRK13481, PRK13481, glycosyltransferase; Provisional.
Length = 232
Score = 25.9 bits (57), Expect = 2.6
Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 12/79 (15%)
Query: 14 LLIFVGVVIGVLLFLTTNIHIHPL---TPDTFFLYM--LPPIILDAGYFMPNRLFFDHLG 68
+LI + + IG++ FL+T ++ L + F+ +P + A M + F+ H G
Sbjct: 15 ILIIIALFIGIMYFLSTRDNVDELRKIENKSSFVSADNMPEYVKGAFISMEDERFYKHHG 74
Query: 69 TILLFAVIGT---IFNTLS 84
F + GT +F+T+S
Sbjct: 75 ----FDLKGTTRALFSTIS 89
>gnl|CDD|227244 COG4907, COG4907, Predicted membrane protein [Function unknown].
Length = 595
Score = 25.3 bits (55), Expect = 4.8
Identities = 7/27 (25%), Positives = 12/27 (44%)
Query: 3 PRLNQIFPESCLLIFVGVVIGVLLFLT 29
L+ F L V +G++LF +
Sbjct: 443 GLLSTAFNTVNTLFIFFVPLGIILFFS 469
>gnl|CDD|130809 TIGR01748, rhaA, L-rhamnose isomerase. This enzyme interconverts
L-rhamnose and L-rhamnulose. In some species, including
E. coli, this is the first step in rhamnose catabolism.
Sequential steps are catalyzed by rhamnulose kinase
(rhaB), then rhamnulose-1-phosphate aldolase (rhaD) to
yield glycerone phosphate and (S)-lactaldehyde.
Characterization of this family is based on members in
E. coli and Salmonella [Energy metabolism, Sugars].
Length = 414
Score = 25.2 bits (55), Expect = 4.9
Identities = 7/24 (29%), Positives = 15/24 (62%)
Query: 50 IILDAGYFMPNRLFFDHLGTILLF 73
+ LDAG+F P + + + + +L+
Sbjct: 252 LCLDAGHFHPTEVISNKISSAMLY 275
>gnl|CDD|217792 pfam03918, CcmH, Cytochrome C biogenesis protein. Members of this
family include NrfF, CcmH, CycL, Ccl2.
Length = 144
Score = 24.5 bits (54), Expect = 7.5
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 36 PLTPDTFFLYMLPPIILDAG 55
PLT T L++ P ++L G
Sbjct: 93 PLTGATLLLWLGPLLLLLLG 112
>gnl|CDD|238880 cd01842, SGNH_hydrolase_like_5, SGNH_hydrolase subfamily. SGNH
hydrolases are a diverse family of lipases and
esterases. The tertiary fold of the enzyme is
substantially different from that of the alpha/beta
hydrolase family and unique among all known hydrolases;
its active site closely resembles the Ser-His-Asp(Glu)
triad found in other serine hydrolases.
Length = 183
Score = 24.8 bits (54), Expect = 8.2
Identities = 4/14 (28%), Positives = 10/14 (71%)
Query: 4 RLNQIFPESCLLIF 17
+L+ + P CL+++
Sbjct: 84 KLDSVLPIECLIVW 97
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
0.337 0.154 0.487
Gapped
Lambda K H
0.267 0.0765 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,981,443
Number of extensions: 449113
Number of successful extensions: 1335
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1324
Number of HSP's successfully gapped: 109
Length of query: 90
Length of database: 10,937,602
Length adjustment: 58
Effective length of query: 32
Effective length of database: 8,365,070
Effective search space: 267682240
Effective search space used: 267682240
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 39 (21.7 bits)
S2: 53 (24.1 bits)