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_011159344.1 TX73_RS19425 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A0D9B2B6 (307 letters) >NCBI__GCF_000195775.1:WP_011159344.1 Length = 305 Score = 318 bits (815), Expect = 1e-91 Identities = 158/303 (52%), Positives = 221/303 (72%), Gaps = 1/303 (0%) Query: 6 HFFQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVAFIAIAGLAMMGL 65 +F QQL+NGL +GS Y LIAIGYTMVYGI+GMINFAHG+++MIG ++A I+ L GL Sbjct: 3 YFAQQLINGLVLGSIYGLIAIGYTMVYGIVGMINFAHGDIFMIGGFIALISFLILVSFGL 62 Query: 66 DSVPLLMTAAFIASIVVTSSYGYSIERIAYRPLRGSNRLIPLISAIGMSIFLQNTVLLSQ 125 VPL++ + S+ +T+ YG+++ERIAYRPLR S RL P++SAIGMS L N +SQ Sbjct: 63 TFVPLILLVVLLVSMAITALYGWTVERIAYRPLRHSFRLAPMLSAIGMSFVLMNYAQVSQ 122 Query: 126 DSKDKSIPNLIPGNFAIGPGG-AHEVLISYMQIVVFVVTLVAMLGLTLFISRSRLGRACR 184 ++ K +P +I G + + V +S +QI+V V T+V + T ++++RLGR R Sbjct: 123 GARVKPVPPIITGGYTLHESADGFNVQLSNVQILVVVTTVVLLGIFTWLVAKTRLGRDMR 182 Query: 185 ACAEDIKMANLLGINTNNIIALTFVIGAALAAIAAVLLSMQYGVINPNAGFLVGLKAFTA 244 AC +D MA LLG++ + I++TFVIGAALA++A ++ + YG+I+ GF+ G+KAFTA Sbjct: 183 ACEQDQTMAALLGVDVDRTISMTFVIGAALASVAGMMYLLYYGLIDFFMGFIAGIKAFTA 242 Query: 245 AVLGGIGSIPGAMLGGLVLGVAEAFGADIFGDQYKDVVAFGLLVLVLLFRPTGILGRPEV 304 AVLGGIGS+PGAMLGGL++G+ E F + F +YKDV AF +L++VL+F PTG+LGRPEV Sbjct: 243 AVLGGIGSLPGAMLGGLLIGLIETFWSAYFSVEYKDVAAFSILIIVLIFMPTGLLGRPEV 302 Query: 305 EKV 307 EKV Sbjct: 303 EKV 305 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: 353 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: 307 Length of database: 305 Length adjustment: 27 Effective length of query: 280 Effective length of database: 278 Effective search space: 77840 Effective search space used: 77840 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