Align Inner-membrane translocator (characterized, see rationale)
to candidate WP_013402606.1 CALHY_RS03375 ABC transporter permease
Query= uniprot:A0KWY7 (320 letters) >NCBI__GCF_000166355.1:WP_013402606.1 Length = 332 Score = 151 bits (382), Expect = 2e-41 Identities = 90/289 (31%), Positives = 171/289 (59%), Gaps = 12/289 (4%) Query: 36 VTNLLRDNAFLLITALGMTLVIISGGIDLSVGAVIALSGVVTSLLITEYQ-WHPLLAFVV 94 +++LL + A L I +GM LVI++ GIDLSVG+V+AL+G++++L++++YQ P++A ++ Sbjct: 44 ISDLLTNTAILAILTVGMMLVIVTRGIDLSVGSVLALAGMISALIVSKYQNVSPIVAILI 103 Query: 95 ILPLGTLFGALMGTIIHVYKLQPFIVTLAGMFLARGLATTLSEES--IAIDHPF-YDAVA 151 + +G + G + G +I + P I TL M + RG+ +S+ A + P + +A Sbjct: 104 GIFVGAICGVINGFLISKTNILPIIATLGTMNIYRGITYMISKGQWVSADEMPLSFKRIA 163 Query: 152 EMSIALPGNGALDLSSLIFILFFVIIAVVMHYTRFGTNVYAIGGNQHSAELMGISIAKTT 211 SI L N + ++ + +I+F+ + +TR G +YAIG N +A + GI+++K Sbjct: 164 TGSI-LGINNLIVVAIITYIVFYYFV----QHTRTGRQIYAIGSNPEAARISGINVSKLI 218 Query: 212 ISIYAISSFLATLAGIVFTFYTFSGYALGAIGVELDAIAAVVIGGTLLTGGSGFVLGTVL 271 +++Y + L+ LAG+++ S + A G E++ IAA V+GG + GGSG + G +L Sbjct: 219 LTVYFLMGVLSGLAGVLWVSKFASAQSDTATGYEMNVIAAAVLGGVSIAGGSGRISGIIL 278 Query: 272 GVILMGVIQTYITFDGSLSSWWTKIVIGLLLFFFILLQKL--LNGRKTQ 318 G +L+G++ + ++S +W + + G ++ +++ L +N K Q Sbjct: 279 GTLLLGILNNALPL-VNVSPFWQQAIQGFIILIAVIVNVLVRMNMEKAQ 326 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: 349 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: 332 Length adjustment: 28 Effective length of query: 292 Effective length of database: 304 Effective search space: 88768 Effective search space used: 88768 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 24 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