Align High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M (characterized)
to candidate BPHYT_RS04435 BPHYT_RS04435 ABC transporter
Query= SwissProt::P22729 (425 letters) >FitnessBrowser__BFirm:BPHYT_RS04435 Length = 646 Score = 176 bits (445), Expect = 2e-48 Identities = 111/300 (37%), Positives = 171/300 (57%), Gaps = 29/300 (9%) Query: 89 QKLFLVALLVLAVAWPFMVSRGT---VDIATLTMIYIILGLGLNVVVGLSGLLVLGYGGF 145 +KL AL ++A+A F V G + + MIY IL GL++VVG +G + LG+ G Sbjct: 4 KKLVASALALIALA-VFPVLSGNPYYIHLLETIMIYAILLFGLDIVVGYTGQVSLGHAGL 62 Query: 146 YAIGAYTFALLNHYYGLGFWTCLPIAGLMAAAAGFLLGFPVLRLRGDYLAIVTLGFGEIV 205 + +GAYT +L G+ F P+A L+ AA G +L P LR+ G YLA+VTL FG I+ Sbjct: 63 FGVGAYTAGVLFFKLGMPFIVTAPLAILITAAFGAILALPALRVSGPYLAMVTLAFGTIL 122 Query: 206 RILLLNNTEITGGPNGISQIPKPTLFGLEFSRTAREGGWDTFSNFFGLKYDPSDRVIFLY 265 +IL+ +T GP G+ +IPKP+L G P + V + + Sbjct: 123 QILINEMDFLTNGPMGV-KIPKPSLAG-----------------------RPMNEVEYYW 158 Query: 266 LVALLLVVLSLFVINRLLRMPLGRAWEALREDEIACRSLGLSPRRIKLTAFTISAAFAGF 325 LVA LLV SL V++R+LR LGRA+EALR+ IA +G+S R K+ AF ISA FAG Sbjct: 159 LVAALLVA-SLIVVHRVLRSHLGRAFEALRDSPIASDCMGVSVYRYKVYAFVISAGFAGL 217 Query: 326 AGTLFAARQGFVSPESFTFAESAFVLAIVVLGGMGSQFAVILAAILLVVSRELMRDFNEY 385 AG L++ + ++SP ++ F + L +++GG ++ +L + ++V+ +L+ D + + Sbjct: 218 AGCLYSYSEQYISPNTYNFELTILFLLAIIMGGRKTRTGALLGSAIIVLLPKLLDDIDMF 277 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: 472 Number of extensions: 18 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: 646 Length adjustment: 35 Effective length of query: 390 Effective length of database: 611 Effective search space: 238290 Effective search space used: 238290 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 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