Align ABC transporter permease; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine ABC transporter permease HisM; SubName: Full=Histidine transport system permease protein; SubName: Full=Histidine/lysine/arginine/ornithine ABC transporter permease HisM (characterized, see rationale)
to candidate GFF136 Psest_0136 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family
Query= uniprot:A0A1N7U128 (237 letters) >FitnessBrowser__psRCH2:GFF136 Length = 229 Score = 166 bits (420), Expect = 4e-46 Identities = 89/211 (42%), Positives = 135/211 (63%), Gaps = 2/211 (0%) Query: 20 LSGVAMTLWLFIISVVLGFFLSIPLALARVSEHVWLRWPVEVYTYLFRGTPLYIQLLICY 79 + G +TL L +SV+ G +++PL +AR S H+ +R Y + FRGTPL +QL + Y Sbjct: 14 IDGAWLTLQLVGVSVIAGLIVAVPLGIARSSRHLAVRALPYGYIFFFRGTPLLVQLFLVY 73 Query: 80 TGLYSLEIVQDNALLNQFFRNALNCTLLAFVLNTCAYTVEIFAGAIRNIPHGEIEAARAY 139 G+ ++V+ +AL + R+ C ++ L+T AY EI GAI+N+PHGEIEAARA Sbjct: 74 YGMAQFDVVRQSALW-PYLRDPYWCAIITMTLHTAAYIAEIIRGAIQNVPHGEIEAARAL 132 Query: 140 GLHGWRLNLFVVVPAALRRALPAYSNEMILMLHATSLAFTATVADILKVARDANAETFLT 199 G+ + L +++P A R LPAYSNE+ILML A++LA T T+ ++ +AR A T+L Sbjct: 133 GMSRSQALLHIILPRATRIGLPAYSNEVILMLKASALASTITLLELTGMARKIAARTYLH 192 Query: 200 FQAFGIAALLYMLLSFALVGLFRLAERRWMR 230 + F A L+Y+L++F L+ F+L E RW+R Sbjct: 193 EEMFLTAGLIYLLIAFILMQGFKLLE-RWLR 222 Lambda K H 0.332 0.143 0.443 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: 193 Number of extensions: 8 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: 237 Length of database: 229 Length adjustment: 23 Effective length of query: 214 Effective length of database: 206 Effective search space: 44084 Effective search space used: 44084 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (22.0 bits) S2: 46 (22.3 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