Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate SMc02337 SMc02337 ABC transporter ATP-binding protein
Query= uniprot:Q9WXX0 (520 letters) >FitnessBrowser__Smeli:SMc02337 Length = 501 Score = 398 bits (1023), Expect = e-115 Identities = 215/497 (43%), Positives = 310/497 (62%), Gaps = 13/497 (2%) Query: 14 ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILV 73 ++ GI K F GV A+ VDF++ E+ +L+GENGAGKSTL+++L G +KP +G + + Sbjct: 4 LVSLSGISKNFSGVQALKGVDFDLRAGEVHALVGENGAGKSTLMRVLAGEMKPTSGTVSI 63 Query: 74 NGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYM 133 +GE ++ P A +GISVIHQEL L ++TVAENIFL L V+ + Sbjct: 64 HGETMQHSGPRGAAGRGISVIHQELALAPDLTVAENIFLG---------RLPRIVNHRRL 114 Query: 134 YTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETE 193 + E+L+ +G P LT A +Q+VEI KAL RII DEPT+ L + E Sbjct: 115 RKAASEILERLGFDIDPAIHAGRLTVAHQQVVEIAKALSNRARIIVFDEPTAVLANTDAE 174 Query: 194 RLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMV 253 RL II L++ G V++SHRL+EV +SDRI VM+DG + L+ DVD +I MV Sbjct: 175 RLLAIIRELRAGGTGAVYISHRLNEVFDLSDRITVMKDGSHVETLETSATDVDAVIARMV 234 Query: 254 GREVE-FFPHGIETRPGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTETML 312 GR++ FP PGE+ + VRN+ KV++VSF VR GEV+G GLVG+GRTE Sbjct: 235 GRQMSALFPSKAGRVPGEVVVRVRNVSRGRKVRDVSFSVRAGEVVGLGGLVGSGRTEVAR 294 Query: 313 LVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLPSL 372 LVFG ++ +SG + +NG+ + + +P +A++ IGL+PEDRK QG++L ++ N L + Sbjct: 295 LVFGADKMDSGTVELNGKPLHLSSPREAVRARIGLVPEDRKQQGVILDAPIRINTTLAKI 354 Query: 373 KKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNADI 432 + ISR G LD KE +++ + +K S+ +LSGGNQQKV LAKW + D+ Sbjct: 355 RSISRLGF-LDAGKERQVAVALGAEMRLKASSVDAPVSSLSGGNQQKVALAKWFHADCDL 413 Query: 433 LIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEITAV 492 LI DEPTRG+DVGAK EI+ +I +LA GKA+++ISSE E+ + DR++VM EG I Sbjct: 414 LILDEPTRGVDVGAKGEIYNLINDLAKAGKAILVISSEHQELFGICDRVLVMAEGAIVGE 473 Query: 493 LDNREKRVTQEEIMYYA 509 L E + T+++++ A Sbjct: 474 L--TESKFTEQQLLTLA 488 Score = 75.9 bits (185), Expect = 3e-18 Identities = 55/233 (23%), Positives = 114/233 (48%), Gaps = 14/233 (6%) Query: 30 VDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVNGERVEFHSPVDAFKK 89 V +V F V E+V L G G+G++ + +++ G K D+G + +NG+ + SP +A + Sbjct: 266 VRDVSFSVRAGEVVGLGGLVGSGRTEVARLVFGADKMDSGTVELNGKPLHLSSPREAVRA 325 Query: 90 GISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSR--VDENYMYTRSKELLDLIGAK 147 I ++ ++ V + + + R++S +D + +++ +GA+ Sbjct: 326 RIGLVPEDRK---QQGVILDAPIRINTTLAKIRSISRLGFLDAG----KERQVAVALGAE 378 Query: 148 F-----SPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETERLFEIIEML 202 S DA V +L+ +Q V + K + ++ +DEPT + V ++ +I L Sbjct: 379 MRLKASSVDAPVSSLSGGNQQKVALAKWFHADCDLLILDEPTRGVDVGAKGEIYNLINDL 438 Query: 203 KSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMVGR 255 G +++ +S E+ I DR++VM +G +GEL + +F ++ + + R Sbjct: 439 AKAGKAILVISSEHQELFGICDRVLVMAEGAIVGELTESKFTEQQLLTLAMTR 491 Lambda K H 0.319 0.138 0.381 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: 667 Number of extensions: 35 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 520 Length of database: 501 Length adjustment: 34 Effective length of query: 486 Effective length of database: 467 Effective search space: 226962 Effective search space used: 226962 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 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 2021. 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