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_068171602.1 HTA01S_RS12260 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A0D9B2B6 (307 letters) >NCBI__GCF_001592305.1:WP_068171602.1 Length = 306 Score = 137 bits (346), Expect = 2e-37 Identities = 88/267 (32%), Positives = 150/267 (56%), Gaps = 17/267 (6%) Query: 9 QQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVAFIAIAGLAMMGLDSV 68 + L+ GL +G YA++A G ++++G++ +IN AHG++ ++G AF IA GL Sbjct: 3 EALIQGLLLGGFYAILAAGLSLMFGVMRIINLAHGDLAIVG---AFGVIALTERFGLS-- 57 Query: 69 PLLMTAAFIASIVVTSSYGYSIERIAYRPLRGSNRLIPLISAIGMSIFLQNTVLLSQDSK 128 P L A + + V + G ++R + + L+PL+ G+ LQNT+ + S+ Sbjct: 58 PWL---ALLLVLPVMALIGIGLQRWLFARTLRAGILLPLLVTFGLGAVLQNTLYGAFGSE 114 Query: 129 DKSIPNLIPGNFAIG----PGGAHEVLISYMQIVVFVVTLVAMLGLTLFISRSRLGRACR 184 +S+ + + G+ A PGG +++ + ++ FV+ + + L L +S + LGRA R Sbjct: 115 ARSLGSAL-GDLAWASWELPGG---IVVGQLPVITFVIAVAVLGALQLLLSHTALGRAIR 170 Query: 185 ACAEDIKMANLLGINTNNIIALTFVIGAALAAIAAVLLSMQYGVINPNAGFLVGLKAFTA 244 A A D + A L G++ + I ALA +A LL+MQ + P G + ++AF A Sbjct: 171 AAASDPEAAALCGVDARRVHRAAAAIAVALAGLAGALLAMQ-ATVEPYGGPTLLIQAFEA 229 Query: 245 AVLGGIGSIPGAMLGGLVLGVAEAFGA 271 V+GGIGS+ G +LGG++LGVA++ GA Sbjct: 230 VVIGGIGSLWGTLLGGVLLGVAQSLGA 256 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: 246 Number of extensions: 12 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: 306 Length adjustment: 27 Effective length of query: 280 Effective length of database: 279 Effective search space: 78120 Effective search space used: 78120 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