Align Branched-chain amino acid ABC transporter permease LivH; SubName: Full=Branched-chain amino acid transporter permease subunit LivH; SubName: Full=L-leucine ABC transporter membrane protein /L-isoleucine ABC transporter membrane protein /L-valine ABC transporter membrane protein (characterized, see rationale)
to candidate WP_013258125.1 DEBA_RS06505 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A0D9B2B6 (307 letters) >NCBI__GCF_000143965.1:WP_013258125.1 Length = 302 Score = 207 bits (528), Expect = 2e-58 Identities = 118/308 (38%), Positives = 186/308 (60%), Gaps = 14/308 (4%) Query: 6 HFFQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVAFIAIAGLAMMGL 65 +FFQ ++N L GS YALIA+GYT+VYG++ +INFAHG+++M+G+YVA+ A A M L Sbjct: 3 YFFQNVLNALQWGSFYALIALGYTLVYGVLSLINFAHGDIFMVGAYVAYFA----ATMFL 58 Query: 66 DSVPLL--MTAAFIA--SIVVTSSYGYSIERIAYRPLR--GSNRLIPLISAIGMSIFLQN 119 V L +T A I +++ T+ G ++ERIAYRPLR G++RL +I+A+ + L+N Sbjct: 59 GEVGLGPGVTLALIVPLTMLATACVGVALERIAYRPLRRKGAHRLYVVITALMCGLILEN 118 Query: 120 TVLLSQDSKDKSIPNLIPGNFAIGPGGAHEVLISYMQIVVFVVTLVAMLGLTLFISRSRL 179 L + KS P L+P G + ++ +++ V + A L ++++++ Sbjct: 119 GNLALLGASRKSFPELVPTTVYAFAG----LSVTNLKLAVIATAVAAFAVLHFIVTKTKI 174 Query: 180 GRACRACAEDIKMANLLGINTNNIIALTFVIGAALAAIAAVLLSMQYGVINPNAGFLVGL 239 G A R A D L+G+ + II TF++G+ +A +A V+ +M Y V+ P G L+G Sbjct: 175 GLAMRGIAWDSFAIPLMGVPPDRIIVFTFILGSGMAGLAGVMFAMAYPVLEPYMGALIGW 234 Query: 240 KAFTAAVLGGIGSIPGAMLGGLVLGVAEAFGADIFGDQYKDVVAFGLLVLVLLFRPTGIL 299 KAF AAV+GGIG I GA LGG +L E A +F +D++AF +L++ + RPTG+ Sbjct: 235 KAFIAAVIGGIGDIRGAFLGGFLLAFLEIGVAAVFPSTMRDLIAFSVLLVFMWQRPTGVF 294 Query: 300 GRPEVEKV 307 G +K+ Sbjct: 295 GVARNQKI 302 Lambda K H 0.327 0.144 0.411 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: 292 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: 307 Length of database: 302 Length adjustment: 27 Effective length of query: 280 Effective length of database: 275 Effective search space: 77000 Effective search space used: 77000 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 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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