Align High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M (characterized)
to candidate WP_012331692.1 M446_RS08490 ABC transporter
Query= SwissProt::P22729 (425 letters) >NCBI__GCF_000019365.1:WP_012331692.1 Length = 679 Score = 185 bits (470), Expect = 3e-51 Identities = 119/305 (39%), Positives = 176/305 (57%), Gaps = 19/305 (6%) Query: 95 ALLVLAVA-WPFMV-SRGTVDIATLTMIYIILGLGLNVVVGLSGLLVLGYGGFYAIGAYT 152 ALL+L +A +P +V S+ + + T+ IY IL LGL++VVG +G + LG+ G + +GAY Sbjct: 32 ALLILGLAAFPHLVGSQYYIHLVTVIAIYAILILGLDIVVGYTGQVSLGHAGLFGVGAYA 91 Query: 153 FALLNHYYGLGFWTCLPIAGL-MAAAAGFLLGFPVLRLRGDYLAIVTLGFGEIVRILLLN 211 A+L + LG W L +AG+ + AA G LL P LR+ G YLA+VTL FG IV+I + Sbjct: 92 AAVLFLKFKLGIWLGL-LAGIGVTAAFGLLLAIPALRVSGPYLAMVTLAFGTIVQIFINE 150 Query: 212 NTEITGGPNGISQIPKPTLFGLEFSRTAREGGWDTFSNFFGLKYDPSDRVIFLYLVALLL 271 T++T GP GI+ P L+FS W R+ F YLV L Sbjct: 151 MTDLTNGPLGITLPPARV---LDFSLLGLSSPWGAAGR----------RLEFYYLVCACL 197 Query: 272 VVLSLFVINRLLRMPLGRAWEALREDEIACRSLGLSPRRIKLTAFTISAAFAGFAGTLFA 331 +L++ V+NR++R P GRA+EALR+ IAC +G+S R K+ AF ISA AG AG LFA Sbjct: 198 -LLTILVVNRVVRSPFGRAFEALRDSPIACDCMGVSVYRYKVYAFVISAGLAGLAGALFA 256 Query: 332 ARQGFVSPESFTFAESAFVLAIVVLGGMGSQFAVILAAILLVVSRELMRDFNEYSMLMLG 391 + +V+P ++ F + L V +GG S+ ++ A ++V+ ++ D E +M G Sbjct: 257 WSERYVAPNTYGFELTVLFLLAVTMGGRKSRSGPLIGAAIVVMMPNILADI-ELVRMMAG 315 Query: 392 GLMVL 396 G+ L Sbjct: 316 GIAAL 320 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: 507 Number of extensions: 20 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: 679 Length adjustment: 35 Effective length of query: 390 Effective length of database: 644 Effective search space: 251160 Effective search space used: 251160 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