Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate GFF522 PS417_02660 branched-chain amino acid transporter permease subunit LivH
Query= ecocyc::LIVH-MONOMER (308 letters) >FitnessBrowser__WCS417:GFF522 Length = 304 Score = 336 bits (861), Expect = 5e-97 Identities = 168/301 (55%), Positives = 221/301 (73%), Gaps = 1/301 (0%) Query: 8 FLQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMGID 67 FLQQ+ NG+TLGS Y LIAIGYTMVYGIIGMINFAHGEVYMI +Y++ + +A L GI+ Sbjct: 5 FLQQLVNGLTLGSVYGLIAIGYTMVYGIIGMINFAHGEVYMISAYLAAISLALLAYFGIE 64 Query: 68 TGWLLVAAGFVGAIVIASAYGWSIERVAYRPVRNSKRLIALISAIGMSIFLQNYVSLTEG 127 + LL+ + +V+ YGW IERVAY+P+RNS RL LISAIG+S+ LQNY + +G Sbjct: 65 SFPLLILGTLIFTVVVTGVYGWVIERVAYKPLRNSTRLAPLISAIGISLILQNYAQIAQG 124 Query: 128 SRDVALPSLFNGQWVVGHSENFSASITTMQAVIWIVTFLAMLALTIFIRYSRMGRACRAC 187 ++ +P+L G W V F +T + I + F M LT I+Y+++GR CRA Sbjct: 125 AKQQGIPTLLAGAWRVDIGSGF-VQLTYTKVFILVAAFAGMALLTYVIKYTKLGRMCRAT 183 Query: 188 AEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAGMKAFTAAV 247 +D KMAS+LGINTDRVI+ FVIGAAMAA+AGVL+ YG + Y GF+ G+KAFTAAV Sbjct: 184 QQDRKMASILGINTDRVISYVFVIGAAMAALAGVLITLNYGTFDFYAGFIIGIKAFTAAV 243 Query: 248 LGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVMPTGILGRPEVEK 307 LGGIGS+PGAM+GG+ILGI+E+L S ++++YKDV SF+LL+++L+ P G+LGRP V K Sbjct: 244 LGGIGSLPGAMLGGIILGISESLFSGLINSDYKDVFSFSLLVVILIFRPQGLLGRPLVAK 303 Query: 308 V 308 V Sbjct: 304 V 304 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: 339 Number of extensions: 10 Number of successful extensions: 2 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: 304 Length adjustment: 27 Effective length of query: 281 Effective length of database: 277 Effective search space: 77837 Effective search space used: 77837 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