Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate AZOBR_RS32415 AZOBR_RS32415 branched-chain amino acid ABC transporter permease
Query= ecocyc::LIVH-MONOMER (308 letters) >FitnessBrowser__azobra:AZOBR_RS32415 Length = 305 Score = 195 bits (495), Expect = 1e-54 Identities = 106/306 (34%), Positives = 184/306 (60%), Gaps = 21/306 (6%) Query: 6 LYFLQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMG 65 ++FLQQ+ NG+++G YAL+AIG+T+++G++ ++NFAHGEVY IG++V M+I A+ Sbjct: 5 VFFLQQVINGLSIGCVYALMAIGFTLIFGVLNVVNFAHGEVYTIGAFVGLMVITAMAPPL 64 Query: 66 IDTGWLLVAAGFVGAIVIASAYGWSIERVAYRPVRN----------SKRLIALISAIGMS 115 + L++A G V + +ER+A+RP R + R L+S++ +S Sbjct: 65 LAVVPLVLAVGAVSGV--------GLERIAFRPFRRFTDEASQKSRAMREATLLSSLAVS 116 Query: 116 IFLQNYVSLTEGSRDVALPSLFNGQWVVGHSENFSASITTMQAVIWIVTFLAMLALTIFI 175 I + + G +PS + Q V AS + VI+ + + + AL + Sbjct: 117 IMTREIMMHIFGGDMQGIPSGYLLQQPVAIGPIMVASGSL---VIFATSAVMLGALQFLL 173 Query: 176 RYSRMGRACRACAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIG 235 ++ G RA + + A +GINTDR I TF +G+ + A AG+L+G + G I+P++G Sbjct: 174 YRTQTGLGIRAVSNNQLGARYVGINTDRTIVTTFAVGSMLGATAGILVGLYDGAISPHMG 233 Query: 236 FMAGMKAFTAAVLGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVM 295 F G+KAF A V+GG+ SIPGA+ L+LG++E++++ +LS+ +KD+++++LL++ L+ Sbjct: 234 FAPGVKAFVAMVMGGLSSIPGAVACALLLGVSESIATEFLSSGWKDLITYSLLVITLVFF 293 Query: 296 PTGILG 301 P G+ G Sbjct: 294 PQGLFG 299 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: 223 Number of extensions: 10 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: 308 Length of database: 305 Length adjustment: 27 Effective length of query: 281 Effective length of database: 278 Effective search space: 78118 Effective search space used: 78118 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