Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate GFF3786 Psest_3855 Branched-chain amino acid ABC-type transport system, permease components
Query= ecocyc::LIVH-MONOMER (308 letters) >FitnessBrowser__psRCH2:GFF3786 Length = 295 Score = 139 bits (351), Expect = 6e-38 Identities = 91/297 (30%), Positives = 160/297 (53%), Gaps = 17/297 (5%) Query: 8 FLQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMGID 67 FL Q+ G+ GS YA++++G +++G++ +INFAHG YMIG++ ++++A L GI Sbjct: 12 FLGQLLIGLINGSFYAMLSLGLAIIFGMLKIINFAHGAQYMIGAFAGYLLLATL---GIG 68 Query: 68 TGWLLVAAGFVGAIVIASAYGWSIERVAYRPVRNSKRLIALISAIGMSIFLQNYVSLTEG 127 L+ A + + A IER+A + N L +L+ G+++ L+ G Sbjct: 69 YWPALILAPIIVGLCSA-----VIERLALSRLYNLDHLYSLLFTFGLALALEGAFRYFYG 123 Query: 128 S--RDVALPSLFNGQWVVGHSENFSASITTMQAVIWIVTFLAMLALTIFIRYSRMGRACR 185 S + A+P G + +G + +A + + + + +A + I +++G R Sbjct: 124 SSGQPYAVPKELAGGYNLGF-----MFLPKYRAWVVLASLVICIASWLLIEKTKLGAYLR 178 Query: 186 ACAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAGMKAFTA 245 A E+ + GIN ++ T+ +GAA+A +AG+L Y V +P +G + F Sbjct: 179 AATENPTLVRTFGINVPLLLTFTYGMGAALAGLAGMLAAPIYQV-SPLMGSNLIIVVFAV 237 Query: 246 AVLGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVMPTGILGR 302 V+GG+GSI GA+I G +LGI E L+ + E ++V F ++ +VLLV P G++GR Sbjct: 238 VVVGGMGSILGAIITGYMLGILEGLTKVFY-PEASNIVIFVIMAIVLLVRPAGLMGR 293 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: 261 Number of extensions: 17 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: 295 Length adjustment: 27 Effective length of query: 281 Effective length of database: 268 Effective search space: 75308 Effective search space used: 75308 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