Align High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M (characterized)
to candidate WP_068169394.1 HTA01S_RS08705 branched-chain amino acid ABC transporter permease
Query= SwissProt::P22729 (425 letters) >NCBI__GCF_001592305.1:WP_068169394.1 Length = 333 Score = 150 bits (379), Expect = 6e-41 Identities = 105/344 (30%), Positives = 174/344 (50%), Gaps = 30/344 (8%) Query: 72 VSGPKFILPAIDGSTVKQKLFLVALLVLAVAWPFMVSRGT---VDIATLTMIYIILGLGL 128 +S PK L + S Q L + + LA A+P + S + + + MI I + L Sbjct: 1 MSSPKAQLEKLPRSV--QVLLALGAVALA-AFPLVPSDSADFYLQMLSQMMILAIFAMSL 57 Query: 129 NVVVGLSGLLVLGYGGFYAIGAYTFALLNHYYG-LGFWTCLPIAGLMAAAAGFLLGFPVL 187 +++ G+SGL+ LG+ ++ + Y A L + W LP++ L A A ++GF V+ Sbjct: 58 DLLQGVSGLVSLGHAAYFGLAGYALAFLTPADAPISLWWALPVSALGAGLAALVIGFFVV 117 Query: 188 RLRGDYLAIVTLGFGEIVRILLLNNTEITGGPNG--ISQIPKPTLFGLEFSRTAREGGWD 245 R G Y +VT+ F ++V L +N E+ GG +G ++ P TLFG Sbjct: 118 RTHGIYFIMVTMAFAQMVFFLFFDNKEL-GGSDGLYVNFRPDATLFG------------- 163 Query: 246 TFSNFFGLKYDPSDRVIFLYLVALLLVVLSLFVINRLLRMPLGRAWEALREDEIACRSLG 305 + G+ D ++ F Y +LV + F + RLL P GR +R +E R++G Sbjct: 164 ----WAGI--DLENKTTFYYFTLAMLVAVYAF-LRRLLFSPFGRVLAGIRVNEHRMRAVG 216 Query: 306 LSPRRIKLTAFTISAAFAGFAGTLFAARQGFVSPESFTFAESAFVLAIVVLGGMGSQFAV 365 KL AFT++ AG AG L+AA+ GFV+P+ F SA + +V+LGGMG+ Sbjct: 217 YGTFGYKLAAFTLAGTLAGVAGFLWAAQTGFVNPDLMGFHMSAHAIMMVILGGMGNFAGA 276 Query: 366 ILAAILLVVSRELMRDFNEYSMLMLGGLMVLMMIWRPQGLLPMT 409 I+ A +D ++ L++G +VL++++ P+GLL ++ Sbjct: 277 IVGAFAFEYVMHFFKDLTKHWQLLMGSFIVLVVVFAPRGLLGLS 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: 284 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: 425 Length of database: 333 Length adjustment: 30 Effective length of query: 395 Effective length of database: 303 Effective search space: 119685 Effective search space used: 119685 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 Apr 09 2024. 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