Align ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale)
to candidate GFF3786 Psest_3855 Branched-chain amino acid ABC-type transport system, permease components
Query= uniprot:D8IUY4 (309 letters) >FitnessBrowser__psRCH2:GFF3786 Length = 295 Score = 145 bits (365), Expect = 1e-39 Identities = 95/302 (31%), Positives = 162/302 (53%), Gaps = 24/302 (7%) Query: 4 FIQQIINGLVLGSMYALIALGYTMVYGVLNLINFAHGDILMVGAMVGLSLLKVVQQVAPG 63 F+ Q++ GL+ GS YA+++LG +++G+L +INFAHG M+GA G LL + G Sbjct: 12 FLGQLLIGLINGSFYAMLSLGLAIIFGMLKIINFAHGAQYMIGAFAGYLLLATL-----G 66 Query: 64 LPGIVQLVIA--IVGAIPVCIVVSLLIERIAYRPLRNAPRLAPLITAIGVSILLQTLAMM 121 + L++A IVG + S +IER+A L N L L+ G+++ L+ Sbjct: 67 IGYWPALILAPIIVG------LCSAVIERLALSRLYNLDHLYSLLFTFGLALALEGAFRY 120 Query: 122 IWGRSPLPFPQVMPSDPVHIAGALISPTQIMLLALAVLAM-VGLVLIVEKTKMGRAMRAT 180 +G S P+ + G + P + LA L + + L++EKTK+G +RA Sbjct: 121 FYGSSGQPYAVPKELAGGYNLGFMFLPKYRAWVVLASLVICIASWLLIEKTKLGAYLRAA 180 Query: 181 AENPRIAGLMGVDANKVIVVTFAIGAGLAAIAGVMWAANYSTAQFAMGFVPGLKAFSAAV 240 ENP + G++ ++ T+ +GA LA +AG++ A Y + MG + F+ V Sbjct: 181 TENPTLVRTFGINVPLLLTFTYGMGAALAGLAGMLAAPIYQVSPL-MGSNLIIVVFAVVV 239 Query: 241 LGGIGNIYGAMLGGILLGLIESLGAGYIGDLTGNFLGSNYQDIFAFIVLIIVLTLRPSGI 300 +GG+G+I GA++ G +LG++E L + + + +I F+++ IVL +RP+G+ Sbjct: 240 VGGMGSILGAIITGYMLGILEGLTKVFYPEAS---------NIVIFVIMAIVLLVRPAGL 290 Query: 301 MG 302 MG Sbjct: 291 MG 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: 274 Number of extensions: 18 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: 309 Length of database: 295 Length adjustment: 27 Effective length of query: 282 Effective length of database: 268 Effective search space: 75576 Effective search space used: 75576 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