Align High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M (characterized)
to candidate BPHYT_RS31745 BPHYT_RS31745 ABC transporter ATP-binding protein
Query= SwissProt::P22729 (425 letters) >FitnessBrowser__BFirm:BPHYT_RS31745 Length = 389 Score = 243 bits (620), Expect = 7e-69 Identities = 155/385 (40%), Positives = 211/385 (54%), Gaps = 52/385 (13%) Query: 80 PAIDGSTVKQKLFLVALLVLAV-AWPFMVSRGT----VDIATLTMIYIILGLGLNVVVGL 134 P +VK+ L + AL + V A P ++ V + M+Y++L LGLN+VVG Sbjct: 12 PLCPERSVKKYLTISALTAIGVTALPLLIGAAAGNYGVRVLDFAMLYVMLALGLNIVVGF 71 Query: 135 SGLLVLGYGGFYAIGAYTFALLN------HYYGLG----------FWTCLPIAGLMAAAA 178 +GLL LGY FYA+GAYT ALL H+ +G +W +P+A ++AA A Sbjct: 72 AGLLDLGYIAFYAVGAYTAALLTSPHLAAHFEWIGHMWPSGFHAPYWFVMPVAMVLAAIA 131 Query: 179 GFLLGFPVLRLRGDYLAIVTLGFGEIVRILLLN---NTEITGGPNGISQIPKPTLFGLEF 235 G LG P LRLRGDYLAIVTLGFGEIVRI + N IT GP GI+ + T+ G Sbjct: 132 GICLGAPTLRLRGDYLAIVTLGFGEIVRIFMNNLDRPVNITNGPQGITGVAPVTVAGFNL 191 Query: 236 SRTAREGGWDTFSNFFGLKYDPSDRVIFLYLVALLLVVLSLFVINRLLRMPLGRAWEALR 295 S T F G ++ V Y V +L +L ++V RL +GRAW A+R Sbjct: 192 SETHA---------FLGFQFTT---VYMYYYVFVLCSLLVVWVCTRLQHSRIGRAWAAIR 239 Query: 296 EDEIACRSLGLSPRRIKLTAFTISAAFAGFAGTLFAARQGFVSPESFTFAESAFVLAIVV 355 EDEIA +++G++ R +KL AF + A+F G +G +FA QGFVSPESFT ES VLA VV Sbjct: 240 EDEIAAKAMGINTRNVKLLAFAMGASFGGLSGAMFAGFQGFVSPESFTLWESVTVLACVV 299 Query: 356 LGGMGSQFAVILAAILLVVSRELMR----------------DFNEYSMLMLGGLMVLMMI 399 LGGMG VI A+LL + E++R D L+ G MV++M+ Sbjct: 300 LGGMGHIPGVIFGAVLLAILPEILRSTMTPLQNAIFGHVIVDTEVIRQLLYGLAMVIIML 359 Query: 400 WRPQGLLPMTRPQLKLKNGAAKGEQ 424 RP+GL P + + ++ A K + Sbjct: 360 RRPEGLWPAPKHEDRIARVAKKNHR 384 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: 360 Number of extensions: 13 Number of successful extensions: 4 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: 389 Length adjustment: 31 Effective length of query: 394 Effective length of database: 358 Effective search space: 141052 Effective search space used: 141052 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