Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate GFF3594 PS417_18400 sugar ABC transporter ATPase
Query= uniprot:B2T9V9 (510 letters) >FitnessBrowser__WCS417:GFF3594 Length = 517 Score = 260 bits (664), Expect = 9e-74 Identities = 176/506 (34%), Positives = 273/506 (53%), Gaps = 22/506 (4%) Query: 8 LTSSVPVVEALEVTKRFGSTAA---LNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLR 64 ++SS P A+ G T A L+D+++ + GE AL G NGAGKSTL I+ GL Sbjct: 1 MSSSAP--NAVLSVSGIGKTYAQPVLSDITLTLNRGEVLALTGENGAGKSTLSKIIGGLV 58 Query: 65 KPDTGEVRFSGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGVIDW 124 P TG ++F+G + A V V Q ++ L+VAENLF++ P G I Sbjct: 59 TPTTGHMQFNGQDFRPGSRTQAEELGVRMVMQELNLLPTLTVAENLFLDNLPSHCGWISR 118 Query: 125 QAMRRDARALLDHWKID-VREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDG 183 + +R+ A + +D + D G L + +Q+VEIAR L +ILDEPTA L Sbjct: 119 KQLRKAAIEAMAQVGLDAIDPDTLVGSLGIGHQQMVEIARNLIGDCHVLILDEPTAMLTA 178 Query: 184 DEIKRLFRRISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLI 243 E++ LF +I+ LQ GV ++ISH L+E+ + Q + VLRD + + P++ EQL+ Sbjct: 179 REVEMLFEQITRLQARGVAIIYISHRLEELARVAQRIAVLRDGKLVCVEPMANYNSEQLV 238 Query: 244 EAMTGERGGLAVADAAARGALPADTAVALELKELTGAD-YEGVSFTVKRGEVVGLTGATS 302 M G G + D R AL +K LT +D VSF V+ GE+ G++G Sbjct: 239 TLMVGRELGEHI-DLGPRTI----GGPALTVKGLTRSDKVRDVSFEVRAGEIYGISGLIG 293 Query: 303 SGRTSVAEAIAGLRAAKRGTISVDG-----AILPPGDVPASLAHGIGCVPKDRHHEGLVL 357 +GRT + I G A GT+++ +I P D ++ HGI + +DR EGL+L Sbjct: 294 AGRTELLRLIFGADLADSGTVALGSPAQVVSIRSPVD---AVGHGIALITEDRKGEGLLL 350 Query: 358 TQSVAENASMTIARVLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKV 417 TQS++ N ++ + G+ + A ++ IDA+ I + P +VS LSGGNQQKV Sbjct: 351 TQSISANIALGNMPEISGGGVVNSRDETALAKRQIDAMRIRSSSPAQLVSELSGGNQQKV 410 Query: 418 VMARALATNPNVLVLIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDDLR-TCDR 476 V+ R L + +V++ +PT G+DV +K + +++ + +GKA++VVS +L +L CDR Sbjct: 411 VIGRWLERDCSVMLFDEPTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDR 470 Query: 477 VLVMFRGRVAAEFPA-GWQDHDLIAS 501 + V+ GR+ F W +L+A+ Sbjct: 471 IGVLSAGRLIETFERDSWTQDELLAA 496 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: 571 Number of extensions: 39 Number of successful extensions: 9 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: 510 Length of database: 517 Length adjustment: 35 Effective length of query: 475 Effective length of database: 482 Effective search space: 228950 Effective search space used: 228950 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