Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_078427103.1 BK574_RS00955 ABC transporter ATP-binding protein
Query= uniprot:D8IZC7 (521 letters) >NCBI__GCF_002019605.1:WP_078427103.1 Length = 509 Score = 286 bits (732), Expect = 1e-81 Identities = 171/499 (34%), Positives = 274/499 (54%), Gaps = 15/499 (3%) Query: 6 LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILL 65 +++M+ IRK F +A ++ L ++ GEIHAL+GENGAGKSTLM VL G++ P++GEIL+ Sbjct: 4 VIEMKDIRKEFPGIVANDNVTLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGEILV 63 Query: 66 DGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTD 125 G+PV + DP + GI +++Q + +V N+ +G E T G I+ + Sbjct: 64 KGKPVKITDPNVANRLGIGMVHQHFMLVEKFTVTENIILGKE-PTAGGKINIKKAAKAVE 122 Query: 126 AVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNV 185 + +Q G +S+ QQ+VEI + L + I+I DEPTAAL+ +E +L + Sbjct: 123 TISKQYGLAVDPYAKIQDISVGMQQRVEILKTLYRGAEILIFDEPTAALTPQEITELIQI 182 Query: 186 VRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSLS 245 +++L EG +II I+H++ E+ + DR TV+R G +G + E + + MMVGR ++ Sbjct: 183 MKKLVSEGKSIILITHKLKEIMEVCDRCTVIRRGRGIGTVDISESTPDSLAAMMVGREVN 242 Query: 246 EFYQHQRIAPADAAQLPTVMQVRALAGGKIRPAS------FDVRAGEVLGFAGLVGAGRT 299 + P DA V+Q++ L R + +V AGE+LG AG+ G G+T Sbjct: 243 FSVEKDPAQPKDA-----VLQIKDLVVKDSRDITAVNDLHLEVHAGEILGVAGVDGNGQT 297 Query: 300 ELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANAT 359 EL + G +GG+I L G+ + PR AG+ ++P+DR GL L V N Sbjct: 298 ELIEAITGLRKPTGGNIQLNGQDITGLTPRKITGAGVGHIPQDRHKHGLVLDFTVGENIV 357 Query: 360 MNV--ASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLE 417 + ++ G++ + A I+ +V+ T LSGGNQQK ++AR ++ Sbjct: 358 LQTYYQKPYSTSGVLNFNEIYKKANELIEDYDVRTPSEHTLARALSGGNQQKAIIAREVD 417 Query: 418 IAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREG 477 +P +LI +PTRG+D+ A I+ + + +G AV++IS EL EV+ + DR+ V+ EG Sbjct: 418 RSPDLLIAAQPTRGLDVGAIESIHHRLVKERDKGKAVLLISLELDEVLNVSDRIAVIYEG 477 Query: 478 MITGELAGAAITQENIMRL 496 I + A T EN + L Sbjct: 478 KIVA-IVDADKTNENELGL 495 Score = 90.5 bits (223), Expect = 1e-22 Identities = 59/224 (26%), Positives = 106/224 (47%), Gaps = 6/224 (2%) Query: 279 SFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAY 338 + V+ GE+ G GAG++ L +LFG G+IL++G+PV I P A R GI Sbjct: 24 TLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGEILVKGKPVKITDPNVANRLGIGM 83 Query: 339 VPEDRKGQGLFLQMAVAANATMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETP 398 V Q L + + T G + + ++ + V P Sbjct: 84 VH-----QHFMLVEKFTVTENIILGKEPTAGGKINIKKAAKAVETISKQYGLAV-DPYAK 137 Query: 399 VGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVIS 458 + +S G QQ+V + + L ++LI DEPT + +E+ Q++ +L S+G ++++I+ Sbjct: 138 IQDISVGMQQRVEILKTLYRGAEILIFDEPTAALTPQEITELIQIMKKLVSEGKSIILIT 197 Query: 459 SELPEVIGICDRVLVMREGMITGELAGAAITQENIMRLATDTNV 502 +L E++ +CDR V+R G G + + T +++ + V Sbjct: 198 HKLKEIMEVCDRCTVIRRGRGIGTVDISESTPDSLAAMMVGREV 241 Score = 79.7 bits (195), Expect = 2e-19 Identities = 56/230 (24%), Positives = 114/230 (49%), Gaps = 7/230 (3%) Query: 21 ALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALRDPGASRA 80 A++D+HL + GEI + G +G G++ L++ ++G+ P G I L+G+ + P Sbjct: 272 AVNDLHLEVHAGEILGVAGVDGNGQTELIEAITGLRKPTGGNIQLNGQDITGLTPRKITG 331 Query: 81 AGINLIYQEL---AVAPNISVAANVFMGSELR---TRLGLIDHAAMRSRTDAVLRQLGAG 134 AG+ I Q+ + + +V N+ + + + + G+++ + + + ++ Sbjct: 332 AGVGHIPQDRHKHGLVLDFTVGENIVLQTYYQKPYSTSGVLNFNEIYKKANELIEDYDVR 391 Query: 135 FGASD-LAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLRDEG 193 + LA LS QQ+ IAR + ++I +PT L E + + + + RD+G Sbjct: 392 TPSEHTLARALSGGNQQKAIIAREVDRSPDLLIAAQPTRGLDVGAIESIHHRLVKERDKG 451 Query: 194 LAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRS 243 A++ IS + EV ++DR+ V+ +G V + D+ + + +M G S Sbjct: 452 KAVLLISLELDEVLNVSDRIAVIYEGKIVAIVDADKTNENELGLLMAGGS 501 Lambda K H 0.320 0.135 0.378 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 628 Number of extensions: 35 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 4 Number of HSP's successfully gapped: 3 Length of query: 521 Length of database: 509 Length adjustment: 35 Effective length of query: 486 Effective length of database: 474 Effective search space: 230364 Effective search space used: 230364 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: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory