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_013258865.1 DEBA_RS10275 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A0D9B2B6 (307 letters) >NCBI__GCF_000143965.1:WP_013258865.1 Length = 288 Score = 155 bits (393), Expect = 8e-43 Identities = 95/297 (31%), Positives = 156/297 (52%), Gaps = 13/297 (4%) Query: 9 QQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVAFIAIAGLAMMGLDSV 68 Q L+NGL G YA A G ++++G++G++N AHGE+ M+G++V GL + L S+ Sbjct: 5 QALINGLLAGGVYAAFATGLSLIFGVMGVLNIAHGELVMLGAFVCAGLFHGLGLGPLWSL 64 Query: 69 PLLMTAAFIASIVVTSSYGYSIERIAYRPLRGSNRLIPLISAIGMSIFLQNTVLLSQDSK 128 PL F + GY ++R+ P+ G ++ I G+ + + N LL+ + Sbjct: 65 PLSFGLMF--------ALGYVMQRLFLAPIAGRPPVMSYILTFGLHLIIANLALLAWSAD 116 Query: 129 DKSIPNLIPGNFAIGPGGAHEVLISYMQIVVFVVTLVAMLGLTLFISRSRLGRACRACAE 188 +++ G + G L+ M V + L + GL LF+SR+ GRA RA A+ Sbjct: 117 PRAVTTPYSG-AGLRLWGLDLPLLKSM---VCLAALAMVGGLHLFLSRTAWGRAIRATAQ 172 Query: 189 DIKMANLLGINTNNIIALTFVIGAALAAIAAVLLSMQYGVINPNAGFLVGLKAFTAAVLG 248 D + A L+G++ + ALTF +GA L ++ L++M V + G + AF V+G Sbjct: 173 DRQAAELMGVDVGKVFALTFALGAGLTGLSGALVAMVRDV-DVAMGLPYTILAFCVVVVG 231 Query: 249 GIGSIPGAMLGGLVLGVAEAFGADIFGDQYKDVVAFGLLVLVLLFRPTGILGRPEVE 305 G+G +PGA++GG +LGV + + + F +L L LL RP G+ G+ VE Sbjct: 232 GMGYLPGALIGGALLGVVGELCTALISPGWSLAIMFTILYLTLLLRPAGLTGKGMVE 288 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: 251 Number of extensions: 19 Number of successful extensions: 3 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: 288 Length adjustment: 26 Effective length of query: 281 Effective length of database: 262 Effective search space: 73622 Effective search space used: 73622 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