Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate H281DRAFT_06397 H281DRAFT_06397 amino acid/amide ABC transporter membrane protein 1, HAAT family
Query= ecocyc::LIVH-MONOMER (308 letters) >FitnessBrowser__Burk376:H281DRAFT_06397 Length = 286 Score = 157 bits (397), Expect = 3e-43 Identities = 100/299 (33%), Positives = 167/299 (55%), Gaps = 22/299 (7%) Query: 8 FLQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMGID 67 +L Q+ NG+ +G Y L+A+G ++V+G++ +NFAHG YM+G+Y F A M Sbjct: 4 YLLQIVNGIGVGMLYFLLAVGLSIVFGLLRFVNFAHGAFYMLGAY--FCYQAMQWSMSFW 61 Query: 68 TGWLLVAAGFVGAIVIASAYGWSIERVAYRPVRNSKRLIALISAIGMSIFLQNYVSLTEG 127 T ++V + A W +E++ R V + ++ +G+++ +Q L G Sbjct: 62 TALIVVP-------IAVGALAWVVEKLILRHVYAQQHEFHILVTVGLALVVQECAILVWG 114 Query: 128 --SRDVALPSLFNGQWVVGHSENFSASITTMQAVIWIVTFLAMLALTIF--IRYSRMGRA 183 +VA+P + NG + G S + ++++ F A+LA ++ + +R+G A Sbjct: 115 PLGDNVAVPDMLNGVVIWG-------SFVYPKYRLFVIGFTAVLAALLWWVLEGTRLGSA 167 Query: 184 CRACAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAGMKAF 243 RA +E +M SLLGIN RV +L F +GAA AA+AGVL GV +P++G A AF Sbjct: 168 VRAGSESTEMVSLLGINVLRVFSLVFALGAATAALAGVLAAPIRGV-DPFMGIEALGVAF 226 Query: 244 TAAVLGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVMPTGILGR 302 V+GG+G+ GA++GGL++GI +++ S L E ++ + + VLL+ P G+LGR Sbjct: 227 VVVVVGGMGNFLGALVGGLLVGIVQSVMST-LWPEGARLMIYVAMAAVLLLRPNGLLGR 284 Lambda K H 0.328 0.141 0.410 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: 254 Number of extensions: 17 Number of successful extensions: 5 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: 308 Length of database: 286 Length adjustment: 26 Effective length of query: 282 Effective length of database: 260 Effective search space: 73320 Effective search space used: 73320 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: 48 (23.1 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