Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate RR42_RS18600 RR42_RS18600 ABC transporter permease
Query= uniprot:A3DE72 (327 letters) >FitnessBrowser__Cup4G11:RR42_RS18600 Length = 299 Score = 128 bits (322), Expect = 2e-34 Identities = 89/289 (30%), Positives = 149/289 (51%), Gaps = 21/289 (7%) Query: 35 LIPTFVCMMCIHFIPMLQGIYLSLLDLNQLTMTKFLNA-PFIGLKNYYEILFDEKSLIRR 93 ++PT + ++ P+ G++L T TK +IGL NY + D + + Sbjct: 17 MLPTALLLLVFLTYPLGLGVWLGF------TNTKIGGTGEWIGLSNYSYLAGDSLTQL-- 68 Query: 94 GFWFALRNTAIYTVVVTFATFALGIILAMLVNREFKGRGIVRTALLMPWVVPSYVVGMTW 153 AL NT YTVV + FALG+ LA+L+N+ + R +L+PW+VP+ + + + Sbjct: 69 ----ALFNTIFYTVVASVVKFALGLWLALLLNKNLPFKSFFRAIVLLPWIVPTALSALAF 124 Query: 154 GFLWRQDSGLINIILCDILHILPEKPYWLVGSNQI--WAIIIPTIWRGLPLSMILMLAGL 211 +++ +I+ L + I ++ +G + ++ I +WRG+P I +LAGL Sbjct: 125 WWIYDAQFSIISWTLVKLGLI--DRYIDFLGDPWLARFSTIAANVWRGIPFVAISLLAGL 182 Query: 212 QSISPDYYEAADIDGANGWQKFWHITLPLLKPILAINVMFSLISNIYSFNIVSMMFGNGA 271 Q+ISP YEAA IDG WQ+F ++TLPLL PI+A+ + FS++ F ++ ++ G Sbjct: 183 QTISPTLYEAASIDGVTPWQQFRYVTLPLLTPIIAVVMTFSVLFTFTDFQLIYVLTRGG- 241 Query: 272 GIPGEWGDLLMTYIQRNTFQMWRFGPGAA-ALMIVMFFVLGIVALWYTL 319 P L+ T + G GAA A M+V F + I+ ++ L Sbjct: 242 --PLNATHLMATLSFQRAIPGGSLGEGAAIATMMVPFLLAAILFSYFGL 288 Lambda K H 0.330 0.145 0.468 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: 343 Number of extensions: 22 Number of successful extensions: 2 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: 327 Length of database: 299 Length adjustment: 27 Effective length of query: 300 Effective length of database: 272 Effective search space: 81600 Effective search space used: 81600 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