Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate SMc02337 SMc02337 ABC transporter ATP-binding protein
Query= uniprot:D8J111 (520 letters) >FitnessBrowser__Smeli:SMc02337 Length = 501 Score = 428 bits (1101), Expect = e-124 Identities = 220/495 (44%), Positives = 324/495 (65%), Gaps = 5/495 (1%) Query: 22 VIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILL 81 +++L + K F GV AL F+L AGEVHAL+GENGAGKSTLM++L+G + SG + + Sbjct: 4 LVSLSGISKNFSGVQALKGVDFDLRAGEVHALVGENGAGKSTLMRVLAGEMKPTSGTVSI 63 Query: 82 DGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQA 141 G+ ++ + PR A GI +IHQEL L L+ A+NIF+GR PR ++ L + A Sbjct: 64 HGETMQHSGPRGAAGRGISVIHQELALAPDLTVAENIFLGRLPR-----IVNHRRLRKAA 118 Query: 142 AAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFR 201 + I R+ D+DP+ G LTVA QQ+VEIAKALS +R+++ DEPTA L N + L Sbjct: 119 SEILERLGFDIDPAIHAGRLTVAHQQVVEIAKALSNRARIIVFDEPTAVLANTDAERLLA 178 Query: 202 IIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRAL 261 IIR+L+A G G VYISH+++E+ ++DR++VM+DG ++ T+ T +D +I+ MVGR + Sbjct: 179 IIRELRAGGTGAVYISHRLNEVFDLSDRITVMKDGSHVETLETSATDVDAVIARMVGRQM 238 Query: 262 DGEQRIPPDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFG 321 +VV+ VR ++RGR +RDVSF++R GE++G GL+G+GRTEVAR +FG Sbjct: 239 SALFPSKAGRVPGEVVVRVRNVSRGRKVRDVSFSVRAGEVVGLGGLVGSGRTEVARLVFG 298 Query: 322 ADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFT 381 AD +++G + ++G + SP +AV IG + EDRK G+ + ++ N L+ + + Sbjct: 299 ADKMDSGTVELNGKPLHLSSPREAVRARIGLVPEDRKQQGVILDAPIRINTTLAKIRSIS 358 Query: 382 RVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDE 441 R+GF+D R+ A ++ +K SV+ LSGGNQQK+ +AKW DCD+L DE Sbjct: 359 RLGFLDAGKERQVAVALGAEMRLKASSVDAPVSSLSGGNQQKVALAKWFHADCDLLILDE 418 Query: 442 PTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARAD 501 PTRG+DVGAK EIY L++ LA+ GKAI++ISSE E+ + RVLVM EG I GEL + Sbjct: 419 PTRGVDVGAKGEIYNLINDLAKAGKAILVISSEHQELFGICDRVLVMAEGAIVGELTESK 478 Query: 502 ATQEKIMQLATQRES 516 T+++++ LA R + Sbjct: 479 FTEQQLLTLAMTRSA 493 Lambda K H 0.320 0.135 0.372 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: 691 Number of extensions: 28 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 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 (21.8 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