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_013075700.1 BTUS_RS08495 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A0D9B2B6 (307 letters) >NCBI__GCF_000092905.1:WP_013075700.1 Length = 292 Score = 258 bits (659), Expect = 1e-73 Identities = 142/301 (47%), Positives = 201/301 (66%), Gaps = 12/301 (3%) Query: 7 FFQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVAFIAIAGLAMMGLD 66 F QQLVNGL+VGS YALIA+GYTMVYGII +INFAHG+V+M+G++VA+ + + L Sbjct: 4 FIQQLVNGLSVGSIYALIALGYTMVYGIIKLINFAHGDVFMVGAFVAYFSYTVFHLGFLG 63 Query: 67 SVPLLMTAAFIASIVVTSSYGYSIERIAYRPLRGSNRLIPLISAIGMSIFLQNTVLLSQD 126 S+ + M A + +V IER AYRPLR S R+ LI+AIG+S+FL+N +++ Sbjct: 64 SLIVSMAACAVLGVV--------IERFAYRPLRKSTRIAALITAIGVSLFLENAGIIAVG 115 Query: 127 SKDKSIPNLIPGNFAIGPGGAHEVLISYMQIVVFVVTLVAMLGLTLFISRSRLGRACRAC 186 ++ + P+++P N +I GG V IS QI + V+++V M+ L + R+++G+A RA Sbjct: 116 AQARGYPSMLP-NSSINLGG---VTISVQQIGIIVLSVVLMVILQFIVHRTKMGKAMRAV 171 Query: 187 AEDIKMANLLGINTNNIIALTFVIGAALAAIAAVLLSMQYGVINPNAGFLVGLKAFTAAV 246 A D + A L+GI+ + I+ TF IG+ALAA A V+ Y I+P G + GLKAF AAV Sbjct: 172 AYDAEAAQLMGIDVDRTISFTFAIGSALAAAAGVIYGAYYSAIDPLMGIMPGLKAFIAAV 231 Query: 247 LGGIGSIPGAMLGGLVLGVAEAFGADIFGDQYKDVVAFGLLVLVLLFRPTGILGRPEVEK 306 LGGIG IPGAM+GGLVLG+ E + ++D VAF LL+L+LL +P G+ G+ EK Sbjct: 232 LGGIGVIPGAMVGGLVLGMIETLVQSLGFSLWRDAVAFALLILILLVKPEGLFGKHAREK 291 Query: 307 V 307 V Sbjct: 292 V 292 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: 314 Number of extensions: 13 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: 292 Length adjustment: 27 Effective length of query: 280 Effective length of database: 265 Effective search space: 74200 Effective search space used: 74200 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