Align High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M (characterized)
to candidate WP_015927866.1 MNOD_RS05615 ABC transporter
Query= SwissProt::P22729 (425 letters) >NCBI__GCF_000022085.1:WP_015927866.1 Length = 678 Score = 181 bits (460), Expect = 5e-50 Identities = 114/305 (37%), Positives = 174/305 (57%), Gaps = 18/305 (5%) Query: 96 LLVLAVAWPFMV-SRGTVDIATLTMIYIILGLGLNVVVGLSGLLVLGYGGFYAIGAYTFA 154 L++ A+P +V S+ + + T+ IY IL LGL++VVG +G + LG+ G + +GAY A Sbjct: 33 LVLFLAAFPHVVTSQYYIHLLTVIAIYAILILGLDIVVGYTGQVSLGHAGLFGVGAYAAA 92 Query: 155 LLNHYYGLGFWTCLPIAGL-MAAAAGFLLGFPVLRLRGDYLAIVTLGFGEIVRILLLNNT 213 +L + LG W L +AG+ + AA G LL P LR+ G YLA+VTL FG IV+I + T Sbjct: 93 VLFLKFKLGIWVGL-LAGIGVTAAFGLLLAIPALRVSGPYLAMVTLAFGTIVQIFINEMT 151 Query: 214 EITGGPNGISQIPKPTLFGLEFSRTAREGGWDTFSNFFGLKYDPSDRVIFLYLVALLLVV 273 ++T GP GI+ P L+FS + W ++ F YLV L+ Sbjct: 152 DLTNGPLGITLPPARV---LDFSLLGLQAPWGAAGR----------KLEFYYLVCASLLA 198 Query: 274 LSLFVINRLLRMPLGRAWEALREDEIACRSLGLSPRRIKLTAFTISAAFAGFAGTLFAAR 333 ++ V+NR++R P GRA+EALR+ IAC +G+S R K+ AF ISAA AG AG LFA Sbjct: 199 -TILVVNRVVRSPFGRAFEALRDSPIACDCMGVSVYRYKVYAFVISAALAGLAGALFAWS 257 Query: 334 QGFVSPESFTFAESAFVLAIVVLGGMGSQFAVILAAILLVVSRELMRDFNEYSMLMLGGL 393 + +V+P ++ F + L V +GG S+ ++ A ++V+ ++ D +M GG+ Sbjct: 258 ERYVAPNTYGFELTVLFLLAVTMGGRKSRSGPLIGAAIIVMMPNILADI-ALVRIMAGGI 316 Query: 394 MVLMM 398 L + Sbjct: 317 AALAL 321 Lambda K H 0.330 0.145 0.436 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: 502 Number of extensions: 18 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: 678 Length adjustment: 35 Effective length of query: 390 Effective length of database: 643 Effective search space: 250770 Effective search space used: 250770 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 (21.8 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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