Align High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M (characterized)
to candidate AZOBR_RS25635 AZOBR_RS25635 high-affinity branched-chain amino acid ABC transporter (permease protein) (fragment)
Query= SwissProt::P22729 (425 letters) >FitnessBrowser__azobra:AZOBR_RS25635 Length = 328 Score = 203 bits (517), Expect = 5e-57 Identities = 123/318 (38%), Positives = 187/318 (58%), Gaps = 28/318 (8%) Query: 93 LVALLVLAVAWPFMVS---RGTV-DIATLTMIYIILGLGLNVVVGLSGLLVLGYGGFYAI 148 L+ALLV V P +++ RG IA L +I+I+L +++V G++GLL LG+ FY + Sbjct: 6 LLALLVF-VGLPAVLAGFDRGYFYQIANLALIFILLSASMHLVTGVAGLLHLGHAAFYGV 64 Query: 149 GAYTFALLNHYYGLGFWTCLPIAGLMAAAAGFLLGFPVLRLRGDYLAIVTLGFGEIVRIL 208 GAYT ALL+ +GLGF LP++GL+AA FL+ P +RL Y A+ TL G+++ ++ Sbjct: 65 GAYTAALLSTKFGLGFTVTLPLSGLVAALIAFLVALPTMRLVSIYFAVATLAIGQMLYLV 124 Query: 209 LLNNTEITGGPNGISQIPKPTLFGLEFSRTAREGGWDTFSNFFGLKYDPSDRVIFLYLVA 268 +LN E T GPNGI LFG + S R+ Y VA Sbjct: 125 MLNWVEFTKGPNGIIVTKGLELFG----------------------FSLSGRLATYYTVA 162 Query: 269 LLLVVLSLFVINRLLRMPLGRAWEALREDEIACRSLGLSPRRIKLTAFTISAAFAGFAGT 328 +V L + I RL G A ++RED+ ++G+S R+K+ AFT+SA FAG AG+ Sbjct: 163 -TVVALCVLAIGRLSHSYYGNALRSIREDDQCADAMGVSTARLKMEAFTLSAFFAGVAGS 221 Query: 329 LFAARQGFVSPESFTFAESAFVLAIVVLGGMGSQFAVILAAILLVVSRELMRDFNEYSML 388 L+A G++SP F F+ES +LA+VV+GG+GS ++ A+LL++ E +R F ++ + Sbjct: 222 LWAHMTGYISPGDFKFSESILILAMVVVGGLGSLPGAVIGALLLILLPEGLRAFGDFRNI 281 Query: 389 MLGGLMVLMMIWRPQGLL 406 M+G +M L ++ P+GLL Sbjct: 282 MVGLVMFLSILLLPKGLL 299 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: 307 Number of extensions: 11 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: 328 Length adjustment: 30 Effective length of query: 395 Effective length of database: 298 Effective search space: 117710 Effective search space used: 117710 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