Align ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale)
to candidate Ac3H11_1432 High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)
Query= uniprot:D8IUY4 (309 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1432 Length = 294 Score = 147 bits (371), Expect = 3e-40 Identities = 92/302 (30%), Positives = 167/302 (55%), Gaps = 24/302 (7%) Query: 5 IQQIINGLVLGSMYALIALGYTMVYGVLNLINFAHGDILMVGAMVGLSLLKVVQQVAPGL 64 + Q++ GLV GS YA+++LG +++G+LN+INFAHG + M GA++ + + G+ Sbjct: 12 LSQLLLGLVNGSFYAILSLGLAVIFGLLNVINFAHGALFMTGALITWMAMNYL-----GI 66 Query: 65 PGIVQLVIA--IVGAIPVCIVVSLLIERIAYRPLRNAPRLAPLITAIGVSILLQTLAMMI 122 + LV+A +VG + +LIER+ R + L L+ +G+++L++ + I Sbjct: 67 NYWLMLVLAPLVVG------LFGVLIERLLLRWIYKLDHLYGLLLTLGLTLLIEGVFRSI 120 Query: 123 WGRSPLPFPQVMPSDPVHIAGALISPT-QIMLLALAVLAMVGLVLIVEKTKMGRAMRATA 181 +G S L + + G +I P + ++ +++ V ++EKTK+G +RA Sbjct: 121 YGVSGLGYDTPELLEGATNLGFMIMPNYRAWVVVASIVVCVATWYVIEKTKLGAYLRAGT 180 Query: 182 ENPRIAGLMGVDANKVIVVTFAIGAGLAAIAGVMWAANYSTAQFAMGFVPGLKAFSAAVL 241 ENPR+ G++ ++ +T+A GA LAA AGV+ A Y MG + F+ V+ Sbjct: 181 ENPRLVEAFGINVPVMVTLTYAFGAALAAFAGVLAAPVYQVTPL-MGQNLIIVVFAVVVI 239 Query: 242 GGIGNIYGAMLGGILLGLIESLGAGYIGDLTGNFLGSNYQDIFAFIVLIIVLTLRPSGIM 301 GG+G+I G++L G+ LG+IE + + + + F++++IVL +RP+G+ Sbjct: 240 GGMGSIMGSILTGLGLGVIEGFTKVFYPEASSTVV---------FVIMVIVLLIRPAGLF 290 Query: 302 GE 303 G+ Sbjct: 291 GK 292 Lambda K H 0.328 0.144 0.416 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: 278 Number of extensions: 17 Number of successful extensions: 5 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: 309 Length of database: 294 Length adjustment: 27 Effective length of query: 282 Effective length of database: 267 Effective search space: 75294 Effective search space used: 75294 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 17 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