Align High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate GFF2761 HP15_2705 inner-membrane translocator
Query= TCDB::P21628 (417 letters) >FitnessBrowser__Marino:GFF2761 Length = 335 Score = 179 bits (453), Expect = 1e-49 Identities = 110/322 (34%), Positives = 174/322 (54%), Gaps = 11/322 (3%) Query: 87 LPSTQRWAVLALVVVAFVWPFFASRGAVDIATLILIYVMLGIGLNIVVGLAGLLDLGYVG 146 + S R V+ +++ + F + ++ T + I +GLN++VG AG + LG+ G Sbjct: 6 MQSRLRGLVILALILVILPAFLGNPFHYELVTQMAIIAATVVGLNLLVGFAGQISLGHAG 65 Query: 147 FYAVGAYTYALLAEYAGFGFWTALPIAGMMAALFGFLLGFPVLRLRGDYLAIVTLGFGEI 206 F+ +GAY + G+ AL + ++ +++G P+LRL+G YL++ TL G I Sbjct: 66 FFGLGAYFTGIATGTYGWSSVPALVVGAIVVGAIAWIVGRPILRLKGHYLSMATLAVGFI 125 Query: 207 IRILLRNMTEITGGPNGIGSIPKPTLFGLTFERRAPEGMQTFHEFFGIAYNTNYKVILLY 266 I I+L N +TGGP+G+ +P +FG + FGI T Y Sbjct: 126 IAIILNNERALTGGPDGM-PVPAFEIFGWELSAFGR------YSLFGI---TIEGFQAWY 175 Query: 267 VVALLLVLLALFVINRLMRMPIGRAWEALREDEVACRALGLNPTIVKLSAFTIGASFAGF 326 + A +++L+A++ L+ PIGRA ++ EVA +G+N K F I A +A Sbjct: 176 IFASVVLLVAVWFALNLIESPIGRALRSVHGSEVAASVVGVNTAKYKSLVFVISAIYASL 235 Query: 327 AGSFFAARQGLVTPESFTFIESAMILAIVVLGGMGSQLGVILAAVVMVLL-QEMRGFNEY 385 GS +A QG +TP +F S + + +VVLGGMGS GVIL AVV+ LL Q + F E Sbjct: 236 MGSLYAHFQGFITPAVASFEFSILFITMVVLGGMGSTFGVILGAVVLKLLPQVLADFQEL 295 Query: 386 RMLIFGLTMIVMMIWRPQGLLP 407 ++FGL +++ MI+ P+GLLP Sbjct: 296 EHVMFGLILMLTMIFMPKGLLP 317 Lambda K H 0.330 0.146 0.439 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: 418 Number of extensions: 18 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: 417 Length of database: 335 Length adjustment: 30 Effective length of query: 387 Effective length of database: 305 Effective search space: 118035 Effective search space used: 118035 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 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