Align D-gluconate TRAP transporter, large permease component (characterized)
to candidate BPHYT_RS30450 BPHYT_RS30450 ABC transporter permease
Query= reanno::psRCH2:GFF2081 (425 letters) >FitnessBrowser__BFirm:BPHYT_RS30450 Length = 619 Score = 209 bits (531), Expect = 2e-58 Identities = 125/419 (29%), Positives = 211/419 (50%), Gaps = 1/419 (0%) Query: 1 MTVVVFLSSLLGFMTL-GMPIAFALLLTGSVLMWYLDFWDVQLLAQNLQAGADSFPLLAV 59 + +++F L+ L G+PIAF+ L + + ++ + G LL+V Sbjct: 197 LNLLIFFVGLVALGVLSGVPIAFSFGLATFGYLALTTNTPMPVVVGRMDEGMSHLILLSV 256 Query: 60 PFFILAGELMNAGGISRRIIAMAQAYFGHKRGGLGYVAIAASVLLASMSGSALADTAALA 119 P F+ G+L+ G++ +IA + GH RGGL YV + A L++ +SGS AD AA+A Sbjct: 257 PLFVFLGQLIEMTGMAAAMIAFLASLLGHVRGGLSYVLVGAMYLVSGISGSKAADMAAVA 316 Query: 120 TLLLPMMRERGYPLSSSSGLVAAGGIIAPIIPPSMPFVIYGVVTGTSISQLFLAGMVPGL 179 +L P M+ RG L+AA G IPPS+ + G VTG SIS LF GM+PG+ Sbjct: 317 PVLFPEMKARGAKPGDLVALLAATGAQTETIPPSLVLITLGSVTGVSISALFTGGMLPGI 376 Query: 180 IMGMGLIVAWTLIARRIDEPKQEKASAAERRRVLVDGAAALMLPVIIVGGLRGGLFTPTE 239 ++ + L + RR D ++A+ E R LV AL LP +I + G+ T TE Sbjct: 377 VLAITLCIVVQWRYRREDMSSVKRATRGEILRKLVIAFPALALPFVIRAAVVEGIATATE 436 Query: 240 AAVVAAVYALAVSTLLYRELNWAGLVEVLTRASRTTASVMFLCAAATVSAYMITLAQLPD 299 + + YA+ L+YR W L +L + + +++ + AAT A+ +T + Sbjct: 437 VSTIGIAYAVLAGLLIYRRFEWKRLKPMLIDTATLSGAILLIIGAATAMAWALTQSGFSG 496 Query: 300 EIAAMLGPLAQDPKLLMVAIMLLMIAVGMVLDLTPTILILGPVLAPIAIKAGIDPVYFGV 359 ++A LG L + M A + + + +G VL+ P I++ GP++ PIA I V++ + Sbjct: 497 QLAQTLGALPGGAAMFMAASICMFVILGSVLEGIPAIVLFGPLMFPIARAMHIHDVHYAM 556 Query: 360 MFVLIGSIGLITPPVGTVLNVVGGIGRLRMETLVRGVMPFFLIYLVIVGLLIAVPSIIT 418 + +L +GL PP G + R+ + ++ ++ + + + ++ AVP I T Sbjct: 557 VVILSMGVGLFAPPFGVGYYSACAVSRIHPDEGMKPILGYIAALMAGLIIVAAVPWIST 615 Lambda K H 0.328 0.142 0.413 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: 695 Number of extensions: 37 Number of successful extensions: 2 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: 425 Length of database: 619 Length adjustment: 35 Effective length of query: 390 Effective length of database: 584 Effective search space: 227760 Effective search space used: 227760 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (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