RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780561|ref|YP_003064974.1| thiamine transporter substrate
binding subunit [Candidatus Liberibacter asiaticus str. psy62]
(338 letters)
>gnl|CDD|33896 COG4143, TbpA, ABC-type thiamine transport system, periplasmic
component [Coenzyme metabolism].
Length = 336
Score = 381 bits (981), Expect = e-106
Identities = 166/340 (48%), Positives = 227/340 (66%), Gaps = 7/340 (2%)
Query: 1 MKKFARIVVGIMMITGVISYCTLDGLPAKPVLTVYTYNSFVADEGAGPKIKQAFERKCNC 60
M++ R ++G + V + A P LTVYTY+SF ++ G GPK+K+AFE + C
Sbjct: 1 MRRLLRALIG--LALLVSAALGAQA--ATPTLTVYTYDSFASEWGPGPKVKKAFEAEYGC 56
Query: 61 ELKLIGLSDGVALLNKLRMEGENSAADIVLGFDNNLIDLARKTGLFAKSNIDASQLKLPI 120
++ + L DGV LLN+L +EG+N AD+V+G DNNL+ AR+TGLFA +DAS + +P
Sbjct: 57 KVNFVALGDGVELLNRLILEGKNPKADVVVGLDNNLLARARETGLFAPYGVDASDVPVPE 116
Query: 121 KWDDDIF-VPYDYGYLAFIYDKRQITQPPKNFDELINSTKPWKIIYQDPRTSTLGLGLLL 179
W D F +PYDYGY AF+YDK ++ PPK+ +L+ KIIYQDPRTS+ GLG LL
Sbjct: 117 GWKIDTFALPYDYGYFAFVYDKTKLKNPPKSLKDLVEPEYAGKIIYQDPRTSSPGLGFLL 176
Query: 180 WIQKIYG-DNSAQVWKKIATKTATVTKGWTESYGFFLKGESDFVLSYSTSPGFYLLNYGQ 238
W +YG D + + W K+A TVTKGW+E+YG F KGE+ VLSY+TSP +++ +
Sbjct: 177 WTISVYGEDGAPEAWAKLADNGVTVTKGWSEAYGAFTKGEAPLVLSYTTSPAYHVYPEKK 236
Query: 239 DDYVAALFSEGHYLQIEVAAQLVRSKQPQLAQEFMQFMISPSFQRILPTTNWMYPVV-DI 297
D Y AALF EGHYLQ+E AA L +K P+LA +F+QFM+SP FQ +PTTNWMYP V ++
Sbjct: 237 DRYAAALFPEGHYLQVEGAAVLKGAKNPELADKFLQFMLSPEFQDAIPTTNWMYPAVKNV 296
Query: 298 SMPDVYQAIRIPQKSLRFNAEETTRYRNQWISSWQNAVSR 337
+P V+ A+ P K++ + +E R WIS WQ AVSR
Sbjct: 297 PLPAVFDALVKPAKTVSLSPKEVAANRKAWISEWQRAVSR 336
>gnl|CDD|32025 COG1840, AfuA, ABC-type Fe3+ transport system, periplasmic
component [Inorganic ion transport and metabolism].
Length = 299
Score = 77.4 bits (190), Expect = 5e-15
Identities = 61/300 (20%), Positives = 110/300 (36%), Gaps = 18/300 (6%)
Query: 50 IKQAFERKCNCELKLIGLSDGVALLNKLRMEGENSAADIVLGFDNNLIDLARKTGLFAKS 109
+ +AFE+K +++ + G L + +G AAD++ G +D ++ GL
Sbjct: 1 LIKAFEKKPGIKVEFVDAGSGELLARIIAEKGNPQAADVLWGGAPVSLDQLKEAGLLQPY 60
Query: 110 NID-ASQLKLPIKWDDDIFVPYDYGYLAFIY----DKRQITQPPKNFDELINSTKP-WK- 162
++ D + G L F +K + PK++ +L KP +K
Sbjct: 61 KSPELDEIPAWAPDPDGAYGGGYVGPLVFAVNTDYNKDLLKPVPKSWADL---AKPEYKG 117
Query: 163 -IIYQDPRTSTLGLGLLLWIQKIYGDNSAQVWKKIATKTATVTKGWT-ESYGFFLKGESD 220
+ DP +S LL +Q + K +A AT T G + GE+
Sbjct: 118 KVQMADPTSSGTAYAALLALQAYGEEKGWAYLKGLAANLATYTGGSSSVVAKVVAGGEAA 177
Query: 221 FVLSYSTSPGFYLLNYGQDDYVAALF-SEGHYLQIEVAAQLVRSKQPQLAQEFMQFMISP 279
L G Y + + V ++ EG + A L ++K P+ A+ F+ F++S
Sbjct: 178 VGLGN-LYYGAYAKDKAKGAPVEVVYPEEGTGVNPSGVALLKKAKNPEAAKLFIDFLLSK 236
Query: 280 SFQRILPTTNWMYPVVDISMPDVYQAIRIPQKSLRFNAE----ETTRYRNQWISSWQNAV 335
Q IL + + + A + + E R ++ W V
Sbjct: 237 EGQEILAKKGYSPEIPVNPKAEDSPAALDFADLIALDFETLGKLLEAEREKFAEKWVKEV 296
>gnl|CDD|31031 COG0687, PotD, Spermidine/putrescine-binding periplasmic protein
[Amino acid transport and metabolism].
Length = 363
Score = 66.3 bits (161), Expect = 1e-11
Identities = 57/366 (15%), Positives = 111/366 (30%), Gaps = 36/366 (9%)
Query: 1 MKKFARIVVGIMMITGVISYCTLDGLPAKP-VLTVYTYNSFVADEGAGPKIKQAFERKCN 59
MKK +R + + + A+ L VY + ++ + + FE++
Sbjct: 2 MKKLSRRSFLALAALALAALAGAAAAAAEGKTLNVYNWGGYIDPA-----LLKPFEKETG 56
Query: 60 CELKLIGLSDGVALLNKLRMEGENSAADIVLGFDNNLIDLARKTGLFAK---------SN 110
++ +L KL+ G D+V+ + K GL N
Sbjct: 57 IKVVYDTFDSNEEMLAKLKAGGGG--YDVVV-PSGYFVARLIKEGLLQPLDKSKLPNWKN 113
Query: 111 IDASQLKLPIKWDDDIF-VPYDYGYLAFIYDKRQIT--QPPKNFDELIN-----STKPWK 162
+D L P + + VPY +G Y+ ++ PP ++ +L + K
Sbjct: 114 LDPEFLNPPKFDPGNKYSVPYFWGTTGIAYNTDKVKDAPPPTSWADLFDPEKFPGLKGKG 173
Query: 163 IIYQDPRTSTLGLGLLLWIQKIYGDNSAQVWKKIAT--KTATVTKGWTESYGF---FLKG 217
+ D G L L + + + K K V W + + G
Sbjct: 174 VALLDDDREVFGAALALLGKSPNTTDPEDLKKAFDLLDKLKPVNVYWFDGSQYVQLLANG 233
Query: 218 ESDFVLSYSTSPGFYLLNYGQDDYVAALFSEGHYLQIEVAAQLVRSKQPQLAQEFMQFMI 277
E + +S + EG L + A +K A +F+ F++
Sbjct: 234 EVVLAMGWSGDAAAAKAAKNGAPIEFVIPKEGSILWFDNLAIPKGAKNVDAAYKFINFLL 293
Query: 278 SPSFQRILPTTNWMYPVVDISMPDVYQAIR-----IPQKSLRFNAEETTRYRNQWISSWQ 332
P L P + + + I+ P + + + +
Sbjct: 294 DPEVAAKLAEFVGYAPPNKAARKLLPKEIKDDPAIYPTAEILKKLFGQKDLGPEALRLYT 353
Query: 333 NAVSRL 338
A +
Sbjct: 354 KAWQEI 359
>gnl|CDD|31839 COG1653, UgpB, ABC-type sugar transport system, periplasmic
component [Carbohydrate transport and metabolism].
Length = 433
Score = 45.0 bits (105), Expect = 3e-05
Identities = 51/274 (18%), Positives = 91/274 (33%), Gaps = 29/274 (10%)
Query: 1 MKKFARIVVGIMMITGVISYCTLDGLPAKPV-LTVYTYNSFVADEGAGPKIKQAFERK-C 58
+KK +++++ ++ ++ C A V +T + + + A ++ + FE++
Sbjct: 1 LKKISKLLLLLLAAALGLAACGSAAASAAGVTITFWHSWTGGEEADALEELIKEFEKENP 60
Query: 59 NCELKLIGLSDGVALLNKLRMEGENSAADIVLGFDNNLIDLARKTGLFA------KSNID 112
++K++ + L L A D+V L A+ GL +D
Sbjct: 61 GIKVKVVNVPGDDYLQKLLTALASGDAPDVVQLDPEWLAAFAKAGGLLEDLTDLINPKLD 120
Query: 113 ASQLKLPI----KWDDDIF-VPYDYGYLAFIY-----DKRQITQPPKNFDELINSTKPWK 162
S + +D ++ VP++ A Y K + PPK +DEL+ + K K
Sbjct: 121 LSDFPPALLDTTTYDGKLYGVPFNSSTPALFYNKDLFKKAGLKPPPKTWDELLAAAKKLK 180
Query: 163 IIYQDP-----RTSTLGLGLLLWIQKIYGDNSAQVWKKIATKTATVTKGWTESYGFFLKG 217
D G L G K + E+ F
Sbjct: 181 EKGGDVYGIAGGGGWQGEDLFFTFALFLGGAGGGFLDKDGGEAFLNDPEAVEALEFLKDL 240
Query: 218 ESDFVLSYSTSPGFYLLNYGQDDYVAALFSEGHY 251
+L S YG DD A F G
Sbjct: 241 YKKGLLPKGAS------GYGWDDAGALAFGSGKV 268
>gnl|CDD|144951 pfam01547, SBP_bac_1, Bacterial extracellular solute-binding
protein. This family also includes the bacterial
extracellular solute-binding protein family POTD/POTF.
Length = 260
Score = 43.6 bits (102), Expect = 7e-05
Identities = 36/257 (14%), Positives = 78/257 (30%), Gaps = 30/257 (11%)
Query: 48 PKIKQAFERKC-NCELKLIGLSDGVALLNKLR--MEGENSAADIVLGFDNNLIDLARKTG 104
+ FE++ ++++ + G +L KL + + AD+ D+ L LA+
Sbjct: 11 QALVAEFEKEHPGIKVEVESVGSG-SLAQKLTTAIAAGDGPADVFASADDWLAKLAKAGL 69
Query: 105 LFAKSNIDASQLKLPIKWDDDI-------FVPYDYGYLAFIYDKRQITQPPKNFDELINS 157
L +D + WD+ + A+ D L +
Sbjct: 70 LL---PLDDYVKNYLVTWDELLEAAKKLKEKGKTPIGGAYGGDASGTLGYFTLAL-LASL 125
Query: 158 TKPWKIIYQDPRTSTLGLGLLLWIQKIYGDNSAQVWKKIATKTATVTKGWTESYGFFLKG 217
P + + + +++ +Y K E+ F +G
Sbjct: 126 GGPLFDKDGGALDNPEAVTAITYVEDLYAIVLLLKKLKNPG---VAGADGREALALFEQG 182
Query: 218 ESDFVLSYSTSPGFYLLN------------YGQDDYVAALFSEGHYLQIEVAAQLVRSKQ 265
++ + + G Y + ++ A SK
Sbjct: 183 KAAMAIVGGGAASANKPGLKVAFAAPAPDPKGDIGYAPLPAGKATFVGGYGLAIPKGSKN 242
Query: 266 PQLAQEFMQFMISPSFQ 282
+ A++F+ F++SP Q
Sbjct: 243 KEAAKKFLDFLLSPEAQ 259
>gnl|CDD|33890 COG4134, COG4134, ABC-type uncharacterized transport system,
periplasmic component [General function prediction
only].
Length = 384
Score = 40.8 bits (95), Expect = 5e-04
Identities = 38/182 (20%), Positives = 60/182 (32%), Gaps = 30/182 (16%)
Query: 127 FVPYDYGYLAFIYDKRQITQPPKNFDELINSTK--PWKIIYQDPRTSTLGLGLLLWIQ-K 183
P+ L FIYD+ ++ Q P++F+EL+ K P + Y P G L +
Sbjct: 144 ESPWGGNQLVFIYDRDKVPQVPQSFEELLVWAKANPKRFGYPRPPNGGTGTAFLKQLLIM 203
Query: 184 IYGDNSAQVWKKIATKTATVTKGWTESYGFFLKGESDFVLSYSTSPG--FYLLNYGQ--- 238
+ GD +A + A AT K W + + L ++ P LLN G
Sbjct: 204 LTGDAAAL---QQAVDPATFAKVWAPLWQY-LDELHPYIWRTGKGPADMLQLLNDGTLYL 259
Query: 239 ------------------DDYVAALFSEGHYLQIEVAAQLVRSKQPQLAQEFMQFMISPS 280
+ +G A + A F++SP
Sbjct: 260 TLTFPDHASSAIATGDLPASARSFALEKGMVGNGHFMAIPANANAKAAALVLANFLLSPE 319
Query: 281 FQ 282
Q
Sbjct: 320 AQ 321
>gnl|CDD|31069 COG0725, ModA, ABC-type molybdate transport system, periplasmic
component [Inorganic ion transport and metabolism].
Length = 258
Score = 36.8 bits (85), Expect = 0.007
Identities = 28/113 (24%), Positives = 42/113 (37%), Gaps = 22/113 (19%)
Query: 173 LGLGLLLWIQKIYGDNSAQVWKKIATKTATVTKGWTESYGFFLKGESDFVLSYSTSPGFY 232
LGL L + + N Q + T GE+D Y +
Sbjct: 159 LGLWYTLKDKLVLATNVRQALAYVET------------------GEADAGFVYVS----D 196
Query: 233 LLNYGQDDYVAALFSEGHYLQIEVAAQLVRSKQPQLAQEFMQFMISPSFQRIL 285
L + V + H + A L +K P+LA+EF+ F++SP Q IL
Sbjct: 197 ALLSKKVKIVGVFPEDLHSPIVYPIAVLKNAKNPELAKEFVDFLLSPEAQEIL 249
>gnl|CDD|32365 COG2182, MalE, Maltose-binding periplasmic proteins/domains
[Carbohydrate transport and metabolism].
Length = 420
Score = 33.0 bits (75), Expect = 0.11
Identities = 26/120 (21%), Positives = 43/120 (35%), Gaps = 11/120 (9%)
Query: 49 KIKQAFERKCNCELKLIGLSDGVALLNKLRMEG-ENSAADIVLGFDNNLIDLARKTGLFA 107
+ FE++ ++K I D LL K + DI + + + LA + GL
Sbjct: 58 EAAAKFEKETGIKVK-IVEEDYDDLLEKFLLAAPAGQGPDIFVWAHDRIGGLA-EAGLLL 115
Query: 108 --KSNIDASQLKLPIKWDDDIF------VPYDYGYLAFIYDKRQITQPPKNFDELINSTK 159
P + +P LA Y+K + +PPK ++EL K
Sbjct: 116 EIDPYATKYTDFYPAALVAATYKGKLYGLPQAVETLALYYNKDLVPEPPKTWEELEALAK 175
>gnl|CDD|143439 cd07121, ALDH_EutE, Ethanolamine utilization protein EutE-like.
Coenzyme A acylating aldehyde dehydrogenase (ACDH), an
NAD+ and CoA-dependent acetaldehyde dehydrogenase,
acetylating (EC=1.2.1.10), converts acetaldehyde into
acetyl-CoA. This CD is limited to such monofunctional
enzymes as the Ethanolamine utilization protein, EutE,
in Salmonella typhimurium. Mutations in eutE abolish
the ability to utilize ethanolamine as a carbon source.
Length = 429
Score = 30.7 bits (70), Expect = 0.55
Identities = 16/38 (42%), Positives = 21/38 (55%), Gaps = 4/38 (10%)
Query: 82 ENSAADIVLG--FDNNLIDLARKTGLFAKSNIDASQLK 117
E +A DIV G FDNNL +A K + A ++ A L
Sbjct: 222 EKAARDIVQGASFDNNLPCIAEKE-VIAVDSV-ADYLI 257
>gnl|CDD|28914 cd00032, CASc, Caspase, interleukin-1 beta converting enzyme (ICE)
homologues; Cysteine-dependent aspartate-directed
proteases that mediate programmed cell death
(apoptosis). Caspases are synthesized as inactive
zymogens and activated by proteolysis of the peptide
backbone adjacent to an aspartate. The resulting two
subunits associate to form an (alpha)2(beta)2-tetramer
which is the active enzyme. Activation of caspases can
be mediated by other caspase homologs..
Length = 243
Score = 29.1 bits (65), Expect = 2.0
Identities = 8/15 (53%), Positives = 13/15 (86%)
Query: 218 ESDFVLSYSTSPGFY 232
E+DF+++YST PG+
Sbjct: 163 EADFLVAYSTVPGYV 177
>gnl|CDD|38877 KOG3673, KOG3673, KOG3673, FtsJ-like RNA methyltransferase [RNA
processing and modification].
Length = 845
Score = 27.7 bits (61), Expect = 4.4
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 3/39 (7%)
Query: 205 KGW-TESYGFFLKGESDFVLS--YSTSPGFYLLNYGQDD 240
K W + +GF L G++DF L + S F+ YG D
Sbjct: 289 KFWNAKGFGFTLAGKNDFKLEKFTAASQEFFETFYGTKD 327
>gnl|CDD|37754 KOG2543, KOG2543, KOG2543, Origin recognition complex, subunit 5
[Replication, recombination and repair].
Length = 438
Score = 27.2 bits (60), Expect = 7.4
Identities = 14/57 (24%), Positives = 22/57 (38%), Gaps = 3/57 (5%)
Query: 221 FVLSYSTSPGFYLLNYGQDDYVAALFSEGHYLQIEVAAQLVRSKQPQLAQEF-MQFM 276
+LS + YL+N G + V F + Y E L R + + QF+
Sbjct: 152 IILSAPSCEKQYLINTGTLEIVVLHFPQ--YSVEETQVILSRDNPGKRKLDVYAQFL 206
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.321 0.137 0.414
Gapped
Lambda K H
0.267 0.0646 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,232,348
Number of extensions: 222872
Number of successful extensions: 461
Number of sequences better than 10.0: 1
Number of HSP's gapped: 456
Number of HSP's successfully gapped: 17
Length of query: 338
Length of database: 6,263,737
Length adjustment: 94
Effective length of query: 244
Effective length of database: 4,232,491
Effective search space: 1032727804
Effective search space used: 1032727804
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 (26.3 bits)