Align Inner-membrane translocator (characterized, see rationale)
to candidate RR42_RS32895 RR42_RS32895 ABC transporter permease
Query= uniprot:A0KWY7 (320 letters) >FitnessBrowser__Cup4G11:RR42_RS32895 Length = 318 Score = 153 bits (387), Expect = 5e-42 Identities = 99/303 (32%), Positives = 167/303 (55%), Gaps = 14/303 (4%) Query: 9 LWITASLLLTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGIDLSVGA 68 +W+ L L + G GF S + N+ + LL+ AL MTL+I++ G+DLS+GA Sbjct: 22 VWVLLLLSLGFSVTGP----GFLSVENLLNIGAQSTILLLIALPMTLIIMTEGLDLSMGA 77 Query: 69 VIALSGVVTSLLITEYQWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFIVTLAGMFLA 128 V+ L GVV ++++ + PL +L G FG L G ++ ++ PF+ TL + +A Sbjct: 78 VLTLCGVVLAMVMVATESLPLALGAALLT-GLAFGLLNGALVSWLEIPPFVATLGTLGVA 136 Query: 129 RGLATTLSEESIAIDHPFYDAVAEMSIALPGNGALDLSSLIFI--LFFVIIAVVMHYTRF 186 +GLA +A D + E + L + I+I +F+ + ++++TRF Sbjct: 137 QGLAL------VATDGQSVTGIGEAIPLIYAGQLLGVPLPIWIAAVFYGLFHWLLYHTRF 190 Query: 187 GTNVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYALGAIGVEL 246 G V+A+GGN+ + + G+ I I++YA+ +A +A ++ T +G+ AIG+E Sbjct: 191 GAYVFALGGNREALKFSGVRINVYLIAVYALGGLMAGVAALLLTARMNAGHPTAAIGLEF 250 Query: 247 DAIAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVIGLLLFFFI 306 DAIAAV +GGT G+G++ GTVLGV+ +GV++ + G SS IGLL+ + Sbjct: 251 DAIAAVAVGGTTFDRGNGWLPGTVLGVLAVGVLRNGLNLVGVPSSVQV-AAIGLLVLVVL 309 Query: 307 LLQ 309 L++ Sbjct: 310 LIE 312 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: 339 Number of extensions: 28 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: 318 Length adjustment: 28 Effective length of query: 292 Effective length of database: 290 Effective search space: 84680 Effective search space used: 84680 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