Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Ac3H11_4984 High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)
Query= uniprot:Q1MCU0 (300 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4984 Length = 296 Score = 137 bits (346), Expect = 2e-37 Identities = 95/303 (31%), Positives = 157/303 (51%), Gaps = 20/303 (6%) Query: 3 YFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSIFA 62 Y + L G+ G +Y L A+ + MVY ++N A G++ M+G + +F S+FA Sbjct: 9 YLFEISLTGIAGGGLYALAALAFVMVYKATRVVNIAIGELLMVGAY----LFFTFASMFA 64 Query: 63 GLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQVT 122 LP L + + A+L T L IER RPL G ++ + +G++ L +++ Sbjct: 65 -LP----LWLAIPAAVLGTGLLGALIERTMIRPLLGEPPISVFMVTVGLASVLVGLVEMI 119 Query: 123 QGPRNKPIPP-MVSSVYQFGNISVSLK----QIIIIVITAVLLTIFWYIVNRTALGRAQR 177 + +P M + G+ ++ K +I IV A +L +F + AL R Sbjct: 120 WTADQRRLPDFMPTQPIMVGDAFLAPKVFWGAVIAIVFIAAVLVVFRFWRGGVAL----R 175 Query: 178 ATEQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTA 237 AT D+ A +G+NV + S+ +V A LAA++G + G++S F G+ Sbjct: 176 ATASDQAAAYSVGINVPRVFSLAWVASAMLAAISGIIVGSIGGISSSMGVF--GLSVLVV 233 Query: 238 AVLGGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGRPEV 297 ++GG+ S+ GA+ GG+LIGLIE+L AY YK +ATF +L VL+ +P G+ G E+ Sbjct: 234 VIVGGLDSVLGALIGGILIGLIEALAGAYLGGEYKLLATFIVLVAVLLVRPYGLFGTHEI 293 Query: 298 EKV 300 E++ Sbjct: 294 ERL 296 Lambda K H 0.329 0.143 0.421 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: 315 Number of extensions: 27 Number of successful extensions: 7 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: 300 Length of database: 296 Length adjustment: 26 Effective length of query: 274 Effective length of database: 270 Effective search space: 73980 Effective search space used: 73980 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