Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate SM_b21459 SM_b21459 sugar uptake ABC transporter permease
Query= uniprot:A3DE72 (327 letters) >FitnessBrowser__Smeli:SM_b21459 Length = 297 Score = 149 bits (376), Expect = 8e-41 Identities = 91/295 (30%), Positives = 152/295 (51%), Gaps = 25/295 (8%) Query: 26 KQNLFAYAMLIPTFVCMMCIHFIPMLQGIYLSLLDLNQLTMTKFLNAP----FIGLKNYY 81 +Q A+ L+P + +M + P+ + I+ S D +L+AP F+G++N+ Sbjct: 10 QQRRTAWIFLLPLLLTLMAVAIWPLARSIFFSFTDA-------YLDAPSDYGFVGIENFV 62 Query: 82 EILFDEKSLIRRGFWFALRNTAIYTVVVTFATFALGIILAMLVNREFKGRGIVRTALLMP 141 E+ D FW A+RNT ++T+V LG+ +A+L++R F GRGIVR A+L+P Sbjct: 63 EVAEDPV------FWGAVRNTLVFTLVSVGLETLLGLAIALLLHRAFLGRGIVRAAILIP 116 Query: 142 WVVPSYVVGMTWGFLWRQDSGLINIILCDILHILPEKPYWLVGSNQI-WAIIIPTIWRGL 200 W +P V W ++ GLIN +L L ++ + W + I +I +W Sbjct: 117 WAMPMVVSARIWEWMLNDQFGLINKLLV-ALGLVEKGVAWTADPSLILGTVIFIDVWVTT 175 Query: 201 PLSMILMLAGLQSISPDYYEAADIDGANGWQKFWHITLPLLKPILAINVMFSLISNIYSF 260 P ++L+LAGLQ I + YEAAD+ G W++FW ITLPL P + + ++F + + F Sbjct: 176 PFMVLLILAGLQLIPEEIYEAADVSGVPQWKRFWSITLPLATPAIGVAILFRTLDALRMF 235 Query: 261 NIVSMMFGNGAGIPGEWGDLLMTYIQRNTFQMWRFGPGAAALMIVMFFVLGIVAL 315 ++ ++ N E + Y + G GAAA V F ++G++A+ Sbjct: 236 DLSYVLAAN-----NENTMTMSIYARDQLISFQDLGLGAAASTWV-FMIIGLIAI 284 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: 328 Number of extensions: 26 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: 297 Length adjustment: 27 Effective length of query: 300 Effective length of database: 270 Effective search space: 81000 Effective search space used: 81000 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