Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate 208249 DVU2743 high-affinity branched-chain amino acid ABC ransporter, permease protein
Query= ecocyc::LIVH-MONOMER (308 letters) >MicrobesOnline__882:208249 Length = 306 Score = 206 bits (523), Expect = 7e-58 Identities = 112/310 (36%), Positives = 186/310 (60%), Gaps = 16/310 (5%) Query: 8 FLQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMGID 67 F+Q +FN + GS YALIA+GYT+VYG++ +INFAHG+++M+G+Y+SF + A +++G Sbjct: 4 FIQNIFNALQWGSFYALIALGYTLVYGVLLLINFAHGDIFMVGAYISFFV--ASILLGQI 61 Query: 68 TGWLLVAAGFVGAI------VIASAYGWSIERVAYRPVRN--SKRLIALISAIGMSIFLQ 119 G+ ++ A+ V+ + G ++ERVAYRP+R + RL +I+A+ I L+ Sbjct: 62 GGFFELSGPMALALTVPLTMVLTAGVGVTLERVAYRPLRRKGAHRLYVVITALMCGIMLE 121 Query: 120 NYVSLTEGSRDVALPSLFNGQ-WVVGHSENFSASITTMQAVIWIVTFLAMLALTIFIRYS 178 N G+ ALP + + + +G + S+T ++ ++ + FL L + + Sbjct: 122 NGNLALLGASRKALPEMIDKVVYTIG-----TVSVTNLKLMVIVTAFLVFALLQFIVTRT 176 Query: 179 RMGRACRACAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMA 238 R+G A RA A D L+GI D +I TFV+G+ A +AG+L Y +++PY+G M Sbjct: 177 RIGMAMRAVAWDKFALPLMGIPLDSIIVFTFVLGSGFAGLAGLLFAMSYPILDPYMGAMV 236 Query: 239 GMKAFTAAVLGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVMPTG 298 G KAF AAV+GGIG I GA IGG +L E + +A + ++D+ +F++L+ ++ PTG Sbjct: 237 GWKAFIAAVVGGIGDIRGAFIGGFLLAFIEIMVAAVFPSTFRDLFAFSILLFIMWQRPTG 296 Query: 299 ILGRPEVEKV 308 + G + K+ Sbjct: 297 LFGVAKTTKI 306 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: 235 Number of extensions: 7 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: 306 Length adjustment: 27 Effective length of query: 281 Effective length of database: 279 Effective search space: 78399 Effective search space used: 78399 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