Align High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M (characterized)
to candidate Ac3H11_4985 Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)
Query= SwissProt::P22729 (425 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4985 Length = 345 Score = 150 bits (379), Expect = 6e-41 Identities = 107/336 (31%), Positives = 166/336 (49%), Gaps = 39/336 (11%) Query: 89 QKLFLVALLVLAVAWPFMVSRGTVDIATLTMIYIILGLGLNVVVGLSGLLVLGYGGFYAI 148 QK++L L V +PFM S + +A L I + GLN++ G +GL+ LG F + Sbjct: 22 QKVWLAVGAALLVLFPFMASDYWLYLACLVSINVASATGLNILTGYTGLVSLGQAAFMGL 81 Query: 149 GAYTFALLNHYYGLGFWTCLPIAGLMAAAAGFLLGFPVLRLRGDYLAIVTLGFGEIVRIL 208 GAYT A+L G F L G +A G ++G P LR++G YLAI T+ I + Sbjct: 82 GAYTVAVLETKVGTPFVLNLLAGGFVAMLGGIVVGIPSLRVKGLYLAIATIAASFIAHFI 141 Query: 209 LLNNTEITGGPNGISQIPKPTLFGLEFSRTAREGGWDTFSNFFGLKYDPSDRVIFLYLVA 268 N + TGG G+S +P LFG+ + R LY + Sbjct: 142 FA-NWKFTGGTGGLS-VPPAKLFGMALDTSFR-----------------------LYWLI 176 Query: 269 LLLVVLSLFVINRLLRMPLGRAWEALREDEIACRSLGLSPRRIKLTAFTISAAFAGFAGT 328 + + +L L L R +GRA+ A+R+ +I+ LG+ R KL +F +S+ +AG AG Sbjct: 177 VPVTILMLLGAANLFRTRVGRAFIAIRDRDISAEVLGIPLLRYKLLSFGLSSFYAGVAGG 236 Query: 329 LFAARQGFVSPESFTFAESAFVLAIVVLGGMGSQFAVILAAILLVVSRELMR-------D 381 L+A V+PESF S F LA +++GGMGS IL A+ + + EL++ Sbjct: 237 LWAYFFRVVTPESFPLLMSIFFLAAIIVGGMGSILGGILGAVFMTMVPELLKLVVDLMPG 296 Query: 382 FNEYSMLM-------LGGLMVLMMIWRPQGLLPMTR 410 +E ++L+ G L++ +++ P GL + R Sbjct: 297 GSELTVLLSPVRTVIFGLLIIGFLVFEPHGLAEVWR 332 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: 311 Number of extensions: 14 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: 345 Length adjustment: 30 Effective length of query: 395 Effective length of database: 315 Effective search space: 124425 Effective search space used: 124425 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: 50 (23.9 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