Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate SM_b21344 SM_b21344 sugar uptake ABC transporter ATP-binding protein
Query= uniprot:B2T9V9 (510 letters) >FitnessBrowser__Smeli:SM_b21344 Length = 497 Score = 300 bits (769), Expect = 6e-86 Identities = 176/474 (37%), Positives = 268/474 (56%), Gaps = 5/474 (1%) Query: 20 VTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFSGAAAP 79 + K F AL S+ V E ALVG+NGAGKSTL+ ILTG + D G V F+G Sbjct: 8 ICKSFNGIPALRAASLEVGEAEVMALVGQNGAGKSTLIKILTGAYRRDEGAVVFAGEGVS 67 Query: 80 SIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGVIDWQAMRRDARALLDHWK 139 ++ +A +YQ + SVAEN++++R+P R G+ID +AMR A A+L + Sbjct: 68 FSMPAESQARGIATIYQEINLAPQRSVAENIYLSREPRRFGLIDRRAMRDGAAAVLRAFN 127 Query: 140 IDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRISELQRE 199 +++ D S RQ+V IARA++ AR +I+DEPT+ LD E+ LF I L+R Sbjct: 128 LEIDVDQPVAGFSAATRQMVAIARAVTQKARLVIMDEPTSSLDEREVGILFDTIRTLKRG 187 Query: 200 GVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTGERGGLAVADAA 259 GV+ +FI H L+E+Y IC VT++RD + + +A ++ +P+ L+ M G+ LA +A Sbjct: 188 GVSVVFIGHRLEELYRICDRVTIMRDGKTVATAAMADMPKLALVRHMLGKE--LAAFEAI 245 Query: 260 ARGA-LPADTAVALELKEL-TGADYEGVSFTVKRGEVVGLTGATSSGRTSVAEAIAGLRA 317 A+ A A V L ++ G VS TV+ GE+ GL G SGRT A I G Sbjct: 246 AKDADEGAQRPVRLSVRNAGAGVRVRDVSLTVREGEISGLAGLLGSGRTETANLIFGADR 305 Query: 318 AKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENASMTIARVLGKFG 377 +RG I +G ++A GIG V +DR +G++ S+ EN ++ + L + G Sbjct: 306 LQRGEIRYNGEARAYRQPADAIADGIGLVAEDRKVDGIIPDMSIRENMTLALLPKLARAG 365 Query: 378 IAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALATNPNVLVLIDPTA 437 I A+++ ++ I AL I P+ + LSGGNQQKV++ R L T+P +L++ +PT Sbjct: 366 IVDRARQDEIVERYITALAIKCTSPDQPIKELSGGNQQKVLLGRWLCTDPKLLIVDEPTR 425 Query: 438 GVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRTCDRVLVMFRGRVAAEFP 490 G+D+ +K +L ++ R+ +EG VL++S EL++ L DRV V+ G A P Sbjct: 426 GIDIGAKSEILRLLRRLADEGLGVLMISSELEELLAAADRVTVLSDGTSVAVLP 479 Score = 82.8 bits (203), Expect = 3e-20 Identities = 69/230 (30%), Positives = 108/230 (46%), Gaps = 17/230 (7%) Query: 25 GSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFSGAAAPSIADR 84 G+ + DVS+ V GE L G G+G++ +++ G + GE+R++G A Sbjct: 265 GAGVRVRDVSLTVREGEISGLAGLLGSGRTETANLIFGADRLQRGEIRYNGEARAYRQPA 324 Query: 85 DAWRERVACVYQHST---IIRDLSVAENLFINRQP--LRGGVIDWQAMRRDARALLDHWK 139 DA + + V + II D+S+ EN+ + P R G++D + Sbjct: 325 DAIADGIGLVAEDRKVDGIIPDMSIRENMTLALLPKLARAGIVDRARQDEIVERYITALA 384 Query: 140 IDVRE-DARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLD---GDEIKRLFRRISE 195 I D +LS +Q V + R L + +I+DEPT +D EI RL RR+++ Sbjct: 385 IKCTSPDQPIKELSGGNQQKVLLGRWLCTDPKLLIVDEPTRGIDIGAKSEILRLLRRLAD 444 Query: 196 LQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEA 245 EG+ L IS L+E+ VTVL D V+ LPR++L EA Sbjct: 445 ---EGLGVLMISSELEELLAAADRVTVLSD-----GTSVAVLPRKELSEA 486 Lambda K H 0.318 0.134 0.377 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: 616 Number of extensions: 36 Number of successful extensions: 6 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: 510 Length of database: 497 Length adjustment: 34 Effective length of query: 476 Effective length of database: 463 Effective search space: 220388 Effective search space used: 220388 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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