Align Inner-membrane translocator (characterized, see rationale)
to candidate GFF2762 PGA1_c28050 putative sugar transport system, permease protein
Query= uniprot:A0KWY7 (320 letters) >FitnessBrowser__Phaeo:GFF2762 Length = 353 Score = 137 bits (345), Expect = 4e-37 Identities = 96/296 (32%), Positives = 151/296 (51%), Gaps = 13/296 (4%) Query: 15 LLLTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGIDLSVGAVIALSG 74 L+L++ + G F S +T +L+ + I A +LVI++ GIDLSVGA++ LS Sbjct: 48 LVLSVIVFGLLLGSKFFSPFALTLILQQVGIVGIVACAQSLVILTAGIDLSVGAIMVLSS 107 Query: 75 VVTSLLITEYQWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFIVT-------LAGMFL 127 VV Y P +A L GT+ G + G ++ KL PFIVT LA FL Sbjct: 108 VVMGQFTFRYGLPPEVAVACGLICGTICGFINGWLVARMKLPPFIVTLGMWQIVLASNFL 167 Query: 128 ARGLATTLSEESIAIDHPFYDAVAEMSIALPGNGALDLSSLIF-ILFFVIIAVVMHYTRF 186 T+ ++IA + P E + GA+ +IF ++ V++A V+ +T + Sbjct: 168 -YSANETIRSQTIAAEAPLLQLFGE---KIKIGGAVFTYGVIFMVILVVLLAYVLRHTAW 223 Query: 187 GTNVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYALGAIGVEL 246 G +VYA+G + +AEL G+ + + IS+Y +S + AG S + Sbjct: 224 GRHVYAVGDDPEAAELSGVKVTRVLISVYMLSGLICAFAGWAMIGRIGSVSPTSGQLANI 283 Query: 247 DAIAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVIGLLL 302 ++I AVVIGG L GG G +LGT G +++GV + G+ + WT ++IGLL+ Sbjct: 284 ESITAVVIGGISLFGGRGSILGTFFGALIVGVFTLGLRLLGA-DAQWTYLLIGLLI 338 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: 342 Number of extensions: 24 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: 353 Length adjustment: 28 Effective length of query: 292 Effective length of database: 325 Effective search space: 94900 Effective search space used: 94900 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