Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate BPHYT_RS04440 BPHYT_RS04440 ABC transporter permease
Query= ecocyc::LIVH-MONOMER (308 letters) >FitnessBrowser__BFirm:BPHYT_RS04440 Length = 291 Score = 158 bits (399), Expect = 2e-43 Identities = 97/301 (32%), Positives = 160/301 (53%), Gaps = 15/301 (4%) Query: 9 LQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMGIDT 68 LQ +++G+ LG YA+IA GY + + G +NF G+ M+G+ V ++ +G++ Sbjct: 5 LQLIYSGIALGMIYAVIAFGYQLTFATSGTLNFGQGDALMLGALVGLTLVT----LGVNY 60 Query: 69 GWLLVAAGFVGAIVIASAYGWSIERVAYRP-VRNSKRLIALISAIGMSIFLQNYVSLTEG 127 WL++ V G +ER+ RP +R ++S I + I +N G Sbjct: 61 -WLMIPL----VCVFGLLQGAFVERIGVRPAIRIKSEFGWIMSTIALGIIFKNVAENLWG 115 Query: 128 SRDVALPSLFNGQWVVGHSENFSASITTMQAVIWIVTFLAMLALTIFIRYSRMGRACRAC 187 D+ PS + + F A++ M+ ++ + MLA+ F R + G+A A Sbjct: 116 RDDLRFPSPLPEAPL----KVFGANVLPMELLVVGGALVMMLAVEFFNRKTIFGKAVVAT 171 Query: 188 AEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAGMKAFTAAV 247 A D A+L+GINT VI ++ + + AA AGVL+ + +G + G+KAF A+ Sbjct: 172 ANDRDAAALMGINTGLVITFSYALSSLTAAFAGVLIAPLT-LTGATMGAVLGLKAFAVAI 230 Query: 248 LGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVMPTGILGRPEVEK 307 +GG+ S G ++GG+ILGIAE + Y+ST YKDV LL++VL + P G+ G+ ++K Sbjct: 231 IGGLSSGLGIVVGGVILGIAETTTGFYISTGYKDVPGLVLLLIVLALKPAGLFGKTSIKK 290 Query: 308 V 308 V Sbjct: 291 V 291 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: 250 Number of extensions: 16 Number of successful extensions: 3 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: 291 Length adjustment: 27 Effective length of query: 281 Effective length of database: 264 Effective search space: 74184 Effective search space used: 74184 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