Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate RR42_RS13775 RR42_RS13775 sugar ABC transporter permease
Query= uniprot:A8LLL4 (385 letters) >FitnessBrowser__Cup4G11:RR42_RS13775 Length = 277 Score = 111 bits (277), Expect = 3e-29 Identities = 70/232 (30%), Positives = 119/232 (51%), Gaps = 7/232 (3%) Query: 153 PPEFTFANYENMLLDPNNSEGMARAFFNTLTVTIPATIIPILVAAFAAYALAWMEFPGRA 212 P +FT +Y+ + DP+ G + N++ T+I I VA AAYA + F G Sbjct: 53 PNDFTLEHYKTIFTDPSWYSG----YINSMIYVAMNTVISITVALPAAYAFSRYRFIGDK 108 Query: 213 LLIALIVGLLVVPLQLALIPLLTLHNAIGIGKGYLGTWLAHTGFGMPLAIYLLRNYMVGL 272 + ++ + P + L+P L+ IG+ +LG LAH F +PLA+++L +M G+ Sbjct: 109 HVFFWLLTNRMTPPAVFLLPFFQLYTTIGLMDTHLGVALAHLVFNVPLAVWILEGFMSGV 168 Query: 273 PRDIIENAKVDGATDFQIFTKIVLPLSFPALASFAIFQFLWTWNDLLVAKVFLIDATGQT 332 PR+I E A VDG + + F I LPL + A F F+++W +LL+A+ L + Sbjct: 169 PREIDETAYVDGYSFGRFFITIFLPLIKAGVGVAAFFCFMFSWVELLLART-LTSVNAKP 227 Query: 333 TVMTNQIVELLGTRGGNWEILATAAFVSIAVPLLVFFSMQRFLVRGLLAGSV 384 V T + + G +W +LA A ++I +V + ++ ++ +G G V Sbjct: 228 IVAT--MTRTVSASGMDWGVLAAAGVLTIVPGGIVIWFVRHYIAKGFAMGRV 277 Score = 23.1 bits (48), Expect = 0.010 Identities = 16/57 (28%), Positives = 29/57 (50%), Gaps = 1/57 (1%) Query: 7 SKSSLTWAVQLSVVGLVVLWLLPTFGLFVSSFRTVEQI-SSSGWWKAMFPSEQNLTL 62 +K S T+ + +V +V +LP + + SF++ E+I S+ W F E T+ Sbjct: 8 AKQSATYWRAVFLVVYLVFAILPIYWMLNMSFKSNEEIVSTLSLWPNDFTLEHYKTI 64 Lambda K H 0.323 0.138 0.419 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: 283 Number of extensions: 20 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 385 Length of database: 277 Length adjustment: 28 Effective length of query: 357 Effective length of database: 249 Effective search space: 88893 Effective search space used: 88893 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 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