Align Inner-membrane translocator (characterized, see rationale)
to candidate 3606962 Dshi_0389 Monosaccharide-transporting ATPase (RefSeq)
Query= uniprot:A0KWY7 (320 letters) >FitnessBrowser__Dino:3606962 Length = 357 Score = 129 bits (325), Expect = 8e-35 Identities = 92/303 (30%), Positives = 149/303 (49%), Gaps = 23/303 (7%) Query: 11 ITASLLLTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGIDLSVGAVI 70 + A++ + L+G+ F FA +T +L+ + I A +LVI++ GIDLSVGA++ Sbjct: 52 LVAAIAVFGLLLGSKFFSPFA----LTLILQQVQIVGIVAAAQSLVILTAGIDLSVGAIM 107 Query: 71 ALSGVVTSLLITEYQWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFIVTL-------- 122 +S VV Y +A L GTL G + G ++ KL PFIVTL Sbjct: 108 VMSSVVMGQFTFRYGLPVEVAVACGLLCGTLLGFINGWLVAKVKLPPFIVTLGMWQIVLA 167 Query: 123 AGMFLARGLATTLSEESIAIDHP---FYDAVAEMSIALPGNGALDLSSLIFILFFVIIAV 179 A +R T+ + I P F+ E+ G L + +L +++A Sbjct: 168 ANFLYSRN--ETIRSQDIRDQAPLLQFFGTTLEI-----GGARLTYGVIFMVLLVIVLAY 220 Query: 180 VMHYTRFGTNVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYAL 239 + +T +G +VYA+G + +AEL G+ +++T IS+Y +S + AG S Sbjct: 221 ALRHTAWGRHVYAVGDDPEAAELSGVQVSRTLISVYMLSGLICAFAGWALIGRIGSVSPT 280 Query: 240 GAIGVELDAIAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVIG 299 +++I AVVIGG L GG G +LG G +++GV + G+ + WT ++IG Sbjct: 281 SGQLANIESITAVVIGGISLFGGRGSILGAFFGALIVGVFTLGLRLLGA-DAQWTFLLIG 339 Query: 300 LLL 302 LL+ Sbjct: 340 LLI 342 Lambda K H 0.330 0.145 0.424 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: 357 Number of extensions: 19 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: 320 Length of database: 357 Length adjustment: 28 Effective length of query: 292 Effective length of database: 329 Effective search space: 96068 Effective search space used: 96068 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: 49 (23.5 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