Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate 3609044 Dshi_2433 ABC transporter related (RefSeq)
Query= uniprot:B2T9V9 (510 letters) >FitnessBrowser__Dino:3609044 Length = 510 Score = 280 bits (716), Expect = 9e-80 Identities = 165/472 (34%), Positives = 260/472 (55%), Gaps = 8/472 (1%) Query: 20 VTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFSGAAAP 79 +TK F AL+DVS+ + PG+ AL+G NGAGKST+V ILTG+ +PD G + G P Sbjct: 26 ITKTFPGVKALSDVSLSLYPGKVTALIGENGAGKSTVVKILTGIYQPDGGRILVDGQPVP 85 Query: 80 SIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRG--GVIDWQAMRRDARALLDH 137 + A V ++Q + + +LSVAEN+F+ P RG G+IDW+ +ARALL Sbjct: 86 FSTPQAAADHGVTAIHQETVLFDELSVAENIFLGHAP-RGAFGLIDWKKTTENARALLTS 144 Query: 138 WKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRISELQ 197 ++ D + DL + + LV IARALS AR +I+DEPTA L EI+ L+ + L+ Sbjct: 145 IGAELDPDHKLKDLGIANKHLVAIARALSIEARVVIMDEPTAALSHKEIEELYELVESLK 204 Query: 198 REGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTGERGGLAVAD 257 +G LFISH E++ I TV RD + I ++ + L++ M G Sbjct: 205 AQGKAILFISHKFDEIFRIADNYTVFRDGQLIGDGAIADVTEADLVKMMVGRDVSQIFPQ 264 Query: 258 AAARGALPADTAVALELKELTGADYEGVSFTVKRGEVVGLTGATSSGRTSVAEAIAGLRA 317 A DT + ++ +++ +SFT++ GE++G G +GR+ +++ G+ Sbjct: 265 RAPN---VGDTVLTVQ-GYAHPTEFDDISFTLREGEILGFYGLVGAGRSEFMQSLFGITR 320 Query: 318 AKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENASMTIARVLGKFG 377 G++ + GA ++ HGI VP+DR +G +L + +N ++ + + G Sbjct: 321 PSAGSVEIGGARAEISSPADAVDHGIVYVPEDRGKQGAILDLPIFQNVTLPSLGRISRKG 380 Query: 378 IAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALATNPNVLVLIDPTA 437 A++ A ++ + L + A + V LSGGNQQKVV+A+ LAT P V++L +PT Sbjct: 381 FLRLAEEFALAREYTERLDLRAASLDTHVGNLSGGNQQKVVIAKWLATRPRVIILDEPTK 440 Query: 438 GVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRTCDRVLVMFRGRVAAE 488 GVD+ SK A+ + + +G AV++VS E+ + L DRV+VM GR+ AE Sbjct: 441 GVDIGSKAAVHDFMAELAAQGLAVIMVSSEIPEVLGMSDRVIVMREGRIVAE 492 Score = 70.1 bits (170), Expect = 2e-16 Identities = 63/227 (27%), Positives = 102/227 (44%), Gaps = 12/227 (5%) Query: 31 NDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFSGAAAPSIADRDAWRER 90 +D+S + GE G GAG+S + L G+ +P G V GA A + DA Sbjct: 286 DDISFTLREGEILGFYGLVGAGRSEFMQSLFGITRPSAGSVEIGGARAEISSPADAVDHG 345 Query: 91 VACVYQH---STIIRDLSVAENLFINRQPLRGGVIDWQAMR-RDARALLDHW--KIDVRE 144 + V + I DL + +N+ + P G + +R + AL + ++D+R Sbjct: 346 IVYVPEDRGKQGAILDLPIFQNVTL---PSLGRISRKGFLRLAEEFALAREYTERLDLRA 402 Query: 145 ---DARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRISELQREGV 201 D G+LS +Q V IA+ L+ R IILDEPT +D + ++EL +G+ Sbjct: 403 ASLDTHVGNLSGGNQQKVVIAKWLATRPRVIILDEPTKGVDIGSKAAVHDFMAELAAQGL 462 Query: 202 TFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTG 248 + +S + EV + V V+R+ R + L E L+ G Sbjct: 463 AVIMVSSEIPEVLGMSDRVIVMREGRIVAELAGDDLQPETLVRHAAG 509 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: 602 Number of extensions: 33 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: 510 Length of database: 510 Length adjustment: 34 Effective length of query: 476 Effective length of database: 476 Effective search space: 226576 Effective search space used: 226576 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