Align ABC transporter permease (characterized, see rationale)
to candidate GFF2762 HP15_2706 inner-membrane translocator
Query= uniprot:A0A165KC95 (309 letters) >FitnessBrowser__Marino:GFF2762 Length = 291 Score = 196 bits (497), Expect = 7e-55 Identities = 105/304 (34%), Positives = 172/304 (56%), Gaps = 19/304 (6%) Query: 5 LQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMPGA 64 LQ + G+ +G+ YALIALG+T++Y +INFA GE LMIG + + S M G Sbjct: 6 LQYLFTGITIGATYALIALGFTLIYNASHVINFAQGEFLMIGGMATVSLTAM------GV 59 Query: 65 PGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMIIWK 124 P ++LA ++A ++A L +++ A P + + + +I IG SI ++ +A ++W Sbjct: 60 P----MILAVVLAVILAGILGVALQRFAIAPAKQADVVTLIIITIGASIFIRGIAQVVWG 115 Query: 125 PNYKPYPTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRATAENP 184 Y P E+ GA + + +LG+ A+ + LV T +G+A+ AT+ N Sbjct: 116 KEYHVMQNFSTDQPIEVFGAVLNSQSLWVLGIGAILVVGLVLFFTKTLIGKAILATSMNK 175 Query: 185 RVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAVFGGI 244 A L+G++ MV+ F++ A+L ++AGI+ A T+ + +G + GLK F AA GG+ Sbjct: 176 EAARLVGIRTQMVLMLAFMVSALLGSVAGIVVAPITFTS-YDIGIILGLKGFVAAAIGGL 234 Query: 245 GNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGLLGER 304 G+ GAVVGG+ LG++EA+ +GYI S Y D AF +++++L P GL G + Sbjct: 235 GSGVGAVVGGLSLGIVEAMAAGYI--------SSDYKDAVAFSMILLVLFFMPRGLFGAK 286 Query: 305 VADR 308 V +R Sbjct: 287 VVER 290 Lambda K H 0.327 0.142 0.419 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: 194 Number of extensions: 9 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: 309 Length of database: 291 Length adjustment: 27 Effective length of query: 282 Effective length of database: 264 Effective search space: 74448 Effective search space used: 74448 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: 48 (23.1 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