Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate GFF2761 HP15_2705 inner-membrane translocator
Query= uniprot:Q1MCU1 (463 letters) >FitnessBrowser__Marino:GFF2761 Length = 335 Score = 148 bits (374), Expect = 2e-40 Identities = 102/350 (29%), Positives = 177/350 (50%), Gaps = 22/350 (6%) Query: 107 FLKIALIALLLYPMVVVAIKGPQGSLTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGY 166 F++ L L++ +++V + G+ + + Q+ I GLN++VG AG + LG+ Sbjct: 5 FMQSRLRGLVILALILVILPAFLGNPFHYE-LVTQMAIIAATVVGLNLLVGFAGQISLGH 63 Query: 167 VAFYAVGAYSYALLSSYFGLSFWVLLPLSGIFAALWGVILGFPVLRLRGDYLAIVTLAFG 226 F+ +GAY + + +G S L + I I+G P+LRL+G YL++ TLA G Sbjct: 64 AGFFGLGAYFTGIATGTYGWSSVPALVVGAIVVGAIAWIVGRPILRLKGHYLSMATLAVG 123 Query: 227 EIIRLVLINWTDVTKGTFGISSIPKATLFGIPFDATAGGFAKLFHLPISSAYYKIFLFYL 286 II ++L N +T G G+ +P +FG ++ +A G LF + I +Y+ Sbjct: 124 FIIAIILNNERALTGGPDGMP-VPAFEIFG--WELSAFGRYSLFGITIEGFQ----AWYI 176 Query: 287 ILALCMLTA-YVTIRLRRMPIGRAWEALREDEIACRSLGINTVTTKLTAFATGAMFAGFA 345 ++ +L A + + L PIGRA ++ E+A +G+NT K F A++A Sbjct: 177 FASVVLLVAVWFALNLIESPIGRALRSVHGSEVAASVVGVNTAKYKSLVFVISAIYASLM 236 Query: 346 GSFFAARQGFVSPESFVFLESAVILAIVVLGGMGSLTGIAIAAIVMVGGTELLREMSFLK 405 GS +A QGF++P F S + + +VVLGGMGS G+ + A+V+ ++L + L+ Sbjct: 237 GSLYAHFQGFITPAVASFEFSILFITMVVLGGMGSTFGVILGAVVLKLLPQVLADFQELE 296 Query: 406 LIFGPDFTPELYRMLIFGLAMVVVMLFKPRGFVGSREPTAFLRERKAISG 455 + +FGL +++ M+F P+G + + + RK G Sbjct: 297 HV-------------MFGLILMLTMIFMPKGLLPTLTAFVSKKMRKKAGG 333 Lambda K H 0.330 0.145 0.432 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: 473 Number of extensions: 29 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: 463 Length of database: 335 Length adjustment: 31 Effective length of query: 432 Effective length of database: 304 Effective search space: 131328 Effective search space used: 131328 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 (21.8 bits) S2: 50 (23.9 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