RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5829
(147 letters)
>gnl|CDD|185519 PTZ00219, PTZ00219, Sec61 alpha subunit; Provisional.
Length = 474
Score = 170 bits (433), Expect = 7e-52
Identities = 70/111 (63%), Positives = 85/111 (76%), Gaps = 2/111 (1%)
Query: 24 MLATVLVFAIVIYFQGFRVDLPIKSARYRGQYSSYPIKLFYTSNIPIILQSALVSNLYVI 83
+LATVLVF +VIYFQGFRVDLP+KS + RGQ SYPIKLFYTSNIPIILQ+ALVSNLY
Sbjct: 248 LLATVLVFLVVIYFQGFRVDLPLKSQKVRGQQQSYPIKLFYTSNIPIILQTALVSNLYFF 307
Query: 84 SQMLAVKFHGNIFVNLLGEWADVGGGGPARAYPIGGLCYYLSPPENLGHFL 134
SQ+L +F N +NLLG+W +V G ++ P+GGL YYLSPP + +
Sbjct: 308 SQILYRRFKNNFLINLLGQWQEVEYSG--QSVPVGGLAYYLSPPNSFSDII 356
>gnl|CDD|236293 PRK08568, PRK08568, preprotein translocase subunit SecY; Reviewed.
Length = 462
Score = 86.8 bits (216), Expect = 8e-21
Identities = 38/114 (33%), Positives = 61/114 (53%), Gaps = 11/114 (9%)
Query: 25 LATVLVFAIVIYFQGFRVDLPIKSARYRGQYSSYPIKLFYTSNIPIILQSALVSNLYVIS 84
+ T+++F IV+Y + RV++P+ R RG YP+K Y S +P+IL AL +N+ +
Sbjct: 238 ITTIVIFLIVVYLESMRVEIPLSHGRVRGARGRYPLKFIYVSVLPVILVRALQANIQLFG 297
Query: 85 QMLAVKFHGNIFVNLLGEWADVGGGGPARAYPIGGLCYYLSPPENLGHFLLLLL 138
Q+L + + +LG + G PI GL YYLSPP + ++ L
Sbjct: 298 QLLQ-----RLGIPILGTYDSSGAS------PISGLAYYLSPPHSPYDWIQDPL 340
>gnl|CDD|233214 TIGR00967, 3a0501s007, preprotein translocase, SecY subunit.
Members of this protein family are the SecY component of
the SecYEG translocon, or protein translocation pore,
which is driven by the ATPase SecA. This model does not
discriminate bacterial from archaeal forms [Protein
fate, Protein and peptide secretion and trafficking].
Length = 410
Score = 81.6 bits (202), Expect = 4e-19
Identities = 33/81 (40%), Positives = 49/81 (60%), Gaps = 5/81 (6%)
Query: 25 LATVLVFAIVIYFQGFRVDLPIKSARYRG-----QYSSYPIKLFYTSNIPIILQSALVSN 79
+AT++VFA+V++ Q R +PI+SA+ +G Q + P+KL Y IP+I SAL+SN
Sbjct: 206 IATIIVFAVVVFVQQARRKIPIQSAKRQGGRRGSQSTYLPLKLNYAGVIPVIFASALLSN 265
Query: 80 LYVISQMLAVKFHGNIFVNLL 100
ISQ L G F+N +
Sbjct: 266 PATISQFLNSNQGGAWFLNPI 286
>gnl|CDD|215869 pfam00344, SecY, SecY translocase.
Length = 340
Score = 79.1 bits (196), Expect = 2e-18
Identities = 40/124 (32%), Positives = 59/124 (47%), Gaps = 27/124 (21%)
Query: 21 AVMMLATVLVFAIVIYFQGFRVDLPIKSAR-----YRGQYSSYPIKLFYTSNIPIILQSA 75
+++LAT+ V +V+Y Q R +PI+ A+ RGQ S PIKL Y IPII S+
Sbjct: 149 LLLLLATLAVILLVVYLQEARRRIPIQYAKRVVGGGRGQSSYLPIKLNYAGVIPIIFASS 208
Query: 76 LVSNLYVISQMLAVKFHGNIFVNLLGEWADVGGGGPARAYPIGGLCYYLSPPENLGHFLL 135
L++N I+Q L F +P+ GL YYL P + + L
Sbjct: 209 LLANPQTIAQFLGSSFPL---------------------WPVSGLAYYL-PIGSPVYILF 246
Query: 136 LLLL 139
++L
Sbjct: 247 YIVL 250
>gnl|CDD|223279 COG0201, SecY, Preprotein translocase subunit SecY [Intracellular
trafficking and secretion].
Length = 436
Score = 66.5 bits (163), Expect = 1e-13
Identities = 25/66 (37%), Positives = 38/66 (57%), Gaps = 3/66 (4%)
Query: 25 LATVLVFAIVIYFQGFRVDLPIKSAR---YRGQYSSYPIKLFYTSNIPIILQSALVSNLY 81
L T+ + +V+Y + R +PI+ A+ YRGQ S P+KL Y IP+I S+L+
Sbjct: 224 LLTLAIIFLVVYVEQARRRIPIQYAKRQSYRGQSSYLPLKLNYAGVIPVIFASSLLLFPS 283
Query: 82 VISQML 87
I+Q L
Sbjct: 284 TIAQFL 289
>gnl|CDD|236412 PRK09204, secY, preprotein translocase subunit SecY; Reviewed.
Length = 426
Score = 28.9 bits (66), Expect = 0.87
Identities = 17/68 (25%), Positives = 34/68 (50%), Gaps = 9/68 (13%)
Query: 19 KMAVMMLATVLVFAIVIYF-QGFRVDLPIKSAR-------YRGQYSSYPIKLFYTSNIPI 70
++++ + V A V++ Q R +P++ A+ Y GQ S P+K+ IP+
Sbjct: 215 VFLLLIVLFLAVIAFVVFVEQAQR-RIPVQYAKRQVGRKMYGGQSSYLPLKVNMAGVIPV 273
Query: 71 ILQSALVS 78
I S+++
Sbjct: 274 IFASSILL 281
>gnl|CDD|227634 COG5324, COG5324, Uncharacterized conserved protein [Function
unknown].
Length = 758
Score = 28.8 bits (64), Expect = 1.2
Identities = 20/78 (25%), Positives = 34/78 (43%), Gaps = 7/78 (8%)
Query: 33 IVI--YFQGFRVD-LPIKSARYRGQYSSYPIKLFYTSNIPIILQSALVSNLYVISQMLAV 89
IVI Y + F + I Y +Y++ P ++ N II S L + ++S +
Sbjct: 77 IVIRGYDKFFNYGEVNITLWDYLYKYATGPYRVTKKYNGCIIFISVLNDGVVLVSSKHSS 136
Query: 90 KFHGNIFVNLLGEWADVG 107
+ +IF + AD G
Sbjct: 137 GKYKDIFQSH----ADKG 150
>gnl|CDD|183828 PRK12907, secY, preprotein translocase subunit SecY; Reviewed.
Length = 434
Score = 28.4 bits (63), Expect = 1.5
Identities = 21/77 (27%), Positives = 38/77 (49%), Gaps = 8/77 (10%)
Query: 19 KMAVMMLATVLVFAIVIYFQGFRVDLPIKSAR-------YRGQYSSY-PIKLFYTSNIPI 70
KM ++ L + + VIY Q +PI+ A+ Y+G +++ P+K+ IP+
Sbjct: 216 KMLLIGLVILAIVVGVIYIQQAVRKIPIQYAKAVSGNNQYQGAKNTHLPLKVNSAGVIPV 275
Query: 71 ILQSALVSNLYVISQML 87
I SA + I+Q+
Sbjct: 276 IFASAFLMTPRTIAQLF 292
>gnl|CDD|191703 pfam07219, HemY_N, HemY protein N-terminus. This family
represents the N-terminus (approximately 150 residues)
of bacterial HemY porphyrin biosynthesis proteins. This
is a membrane protein involved in a late step of
protoheme IX synthesis.
Length = 108
Score = 26.5 bits (59), Expect = 3.8
Identities = 6/35 (17%), Positives = 16/35 (45%)
Query: 21 AVMMLATVLVFAIVIYFQGFRVDLPIKSARYRGQY 55
+++L + V ++ + + LP + RY +
Sbjct: 20 VILLLLVLAVLFLLEWLLRLIIRLPRRVRRYFRRR 54
>gnl|CDD|239786 cd04253, AAK_UMPK-PyrH-Pf, AAK_UMPK-PyrH-Pf: UMP kinase (UMPK)-Pf,
the mostly archaeal uridine monophosphate kinase
(uridylate kinase) enzymes that catalyze UMP
phosphorylation and play a key role in pyrimidine
nucleotide biosynthesis; regulation of this process is
via feed-back control and via gene repression of
carbamoyl phosphate synthetase (the first enzyme of the
pyrimidine biosynthesis pathway). The UMP kinase of
Pyrococcus furiosus (Pf) is known to function as a
homohexamer, with GTP and UTP being allosteric
effectors. Like other related enzymes (carbamate kinase,
aspartokinase, and N-acetylglutamate kinase) the E. coli
and most bacterial UMPKs have a conserved, N-terminal,
lysine residue proposed to function in the catalysis of
the phosphoryl group transfer, whereas most archaeal
UMPKs (this CD) appear to lack this residue and the
Pyrococcus furiosus structure has an additional Mg ion
bound to the ATP molecule which is proposed to function
as the catalysis instead. Members of this CD belong to
the Amino Acid Kinase Superfamily (AAK).
Length = 221
Score = 26.8 bits (60), Expect = 3.8
Identities = 10/27 (37%), Positives = 14/27 (51%), Gaps = 7/27 (25%)
Query: 96 FVNLLGEWAD-------VGGGGPARAY 115
+ N+L + +D VGGG AR Y
Sbjct: 23 YANVLRKISDGHKVAVVVGGGRLAREY 49
>gnl|CDD|235668 PRK06007, fliF, flagellar MS-ring protein; Reviewed.
Length = 542
Score = 26.8 bits (60), Expect = 5.0
Identities = 6/32 (18%), Positives = 10/32 (31%), Gaps = 3/32 (9%)
Query: 8 RSKFLSSLQNSKM---AVMMLATVLVFAIVIY 36
K LQ ++ A V A ++
Sbjct: 9 MEKLKEFLQKLSKKRKIALIGAGAAVVAAIVA 40
>gnl|CDD|237117 PRK12493, PRK12493, magnesium chelatase subunit H; Provisional.
Length = 1310
Score = 26.1 bits (58), Expect = 8.5
Identities = 12/25 (48%), Positives = 17/25 (68%), Gaps = 1/25 (4%)
Query: 122 YYL-SPPENLGHFLLLLLLRFVNKP 145
Y+L PENL +FLL+L+ R+V
Sbjct: 182 YWLGGSPENLENFLLMLIDRYVPGY 206
>gnl|CDD|233832 TIGR02353, NRPS_term_dom, non-ribosomal peptide synthetase terminal
domain of unknown function. This domain is found
exclusively in non-ribosomal peptide synthetases and
always as the final domain in the polypeptide. This
domain is roughly 700 amino acids in size and is found
in polypeptides roughly twice that size.
Length = 695
Score = 26.3 bits (58), Expect = 9.1
Identities = 15/48 (31%), Positives = 20/48 (41%), Gaps = 2/48 (4%)
Query: 77 VSNLYVISQMLA-VKFHGNIFVNLLGEWADVGGGGPARAYPIGGLCYY 123
VS LY+ + L G + + +W VG P YPI G Y
Sbjct: 35 VSWLYLRAVALVFAVPVGRLGFAIAAKWLLVGRWKPGT-YPIWGSTYL 81
>gnl|CDD|233023 TIGR00557, pdxA, 4-hydroxythreonine-4-phosphate dehydrogenase.
This model represents PdxA, an NAD+-dependent
4-hydroxythreonine 4-phosphate dehydrogenase (EC
1.1.1.262) active in pyridoxal phosphate biosynthesis
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Pyridoxine].
Length = 320
Score = 25.9 bits (58), Expect = 9.7
Identities = 9/17 (52%), Positives = 10/17 (58%)
Query: 11 FLSSLQNSKMAVMMLAT 27
FL+ L K VMMLA
Sbjct: 134 FLAELTGVKDVVMMLAG 150
>gnl|CDD|183033 PRK11197, lldD, L-lactate dehydrogenase; Provisional.
Length = 381
Score = 25.8 bits (57), Expect = 10.0
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 40 FRVDLPIKSARYRGQYS 56
F VD+P+ ARYR +S
Sbjct: 154 FTVDMPVPGARYRDAHS 170
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
0.329 0.144 0.444
Gapped
Lambda K H
0.267 0.0664 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,435,028
Number of extensions: 669907
Number of successful extensions: 974
Number of sequences better than 10.0: 1
Number of HSP's gapped: 965
Number of HSP's successfully gapped: 44
Length of query: 147
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 59
Effective length of database: 7,034,450
Effective search space: 415032550
Effective search space used: 415032550
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 54 (24.7 bits)