Align Inner-membrane translocator (characterized, see rationale)
to candidate 3609043 Dshi_2432 Monosaccharide-transporting ATPase (RefSeq)
Query= uniprot:A0KWY7 (320 letters) >FitnessBrowser__Dino:3609043 Length = 327 Score = 139 bits (350), Expect = 9e-38 Identities = 95/310 (30%), Positives = 156/310 (50%), Gaps = 11/310 (3%) Query: 11 ITASLLLTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGIDLSVGAVI 70 + A++LL + L+ + +F F + + ++ D + L++ A+G +VI++ IDLSV A + Sbjct: 13 LIAAILLLLALIAS-RFPAFIAPSNLAHVFNDTSPLILLAIGQMIVILTRCIDLSVAANL 71 Query: 71 ALSGVVTSLLITEYQWHPLLAFVVI-LPLGTLFGALMGTIIHVYKLQPFIVTLAGMFLAR 129 AL+G+V S++ P++ + I + LGTL G G ++ ++ P +VTL M + R Sbjct: 72 ALTGMVVSMVNVAAPGLPIVVILAIAIGLGTLLGMFNGLLVWKLQIPPIVVTLGTMTIFR 131 Query: 130 GLATTLSEESIAIDH---PFYDAVAEMSIALPGNGALDLSSLIFILFFVIIAVVMHYTRF 186 G+ +S+ H P + A + L + S I IL ++ +VM T Sbjct: 132 GIIFLISDGKWVNSHEMSPAFKAFPRAELL-----GLPVLSWIAILAVILFTIVMTRTTL 186 Query: 187 GTNVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYALGAIGVEL 246 G YA GGN H+A GI + KT + IS LA L G ++ Y A G EL Sbjct: 187 GRAFYAAGGNPHAATYAGIDVGKTQFWAFTISGALAGLTGYLWVSRFAVSYVDIAGGFEL 246 Query: 247 DAIAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVIGLLLFFFI 306 D +AA VIGG + GG G V G +LG + +G+I+ + +S +W + G + + Sbjct: 247 DVVAACVIGGVSIMGGVGTVGGALLGALFLGIIKNALPV-VDISPFWQLAISGGAIIIAV 305 Query: 307 LLQKLLNGRK 316 L N +K Sbjct: 306 ALNAQANRKK 315 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: 340 Number of extensions: 21 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: 327 Length adjustment: 28 Effective length of query: 292 Effective length of database: 299 Effective search space: 87308 Effective search space used: 87308 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: 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