Align Solute-binding protein Bamb_6123 (characterized)
to candidate RR42_RS35000 RR42_RS35000 ABC transporter substrate-binding protein
Query= SwissProt::Q0B2F6 (328 letters) >FitnessBrowser__Cup4G11:RR42_RS35000 Length = 315 Score = 100 bits (250), Expect = 4e-26 Identities = 82/272 (30%), Positives = 130/272 (47%), Gaps = 16/272 (5%) Query: 11 ALAVALMAGFAMSAQARVFRSADVHGDSFPTNMAVKFMGDELSKLTGGKDSIKVFGNSAL 70 A VA +A AQ ++ + A V+ S P + + +E+ K + G+ I VF S L Sbjct: 2 ATCVASLACGGALAQTKL-KWAHVYETSEPFHKWSVWAAEEIRKRSNGRYQIDVFPASQL 60 Query: 71 GSEKDTVDQVRIGAIDMARVNGASFN-EIVPESLIPSFPFLFRDVDHFRKAMYGPAGQKI 129 G E D + +G++D+ ++G+SF + P + +P+ FRD +H +++ Sbjct: 61 GKENDINQGLAMGSVDII-ISGSSFAAKSFPRIGVTYYPYTFRDANHLLAYTKSDIYKEL 119 Query: 130 LDAFAAKG---MIALTFYESGARSIYAKRPVRTPADMKGLKVRVQPSDLMVDEIRAMGGT 186 + K ++A T+Y G R + +P A+MKGLK+RV + RA G Sbjct: 120 TRGYEEKSGNHIVATTYY--GTRQSTSNKPFSHCAEMKGLKMRVPDVPAYLAMPRACGVN 177 Query: 187 PTPMPFAEVYTGLKTGLVDAAENNLPSYEETKHFEVAPDYSETQHAMTPEVLVFSKKIWD 246 +P+ FAEVY L+ G V+A EN LP+ E K +EV T H + V S +W Sbjct: 178 TSPIAFAEVYLALQNGTVEAQENPLPTIEAKKFYEVQKYIVLTGHIVDHLNTVISGGLWK 237 Query: 247 TLSPQE--------QAAIRKAAADSVPYYQKL 270 LS + Q A +A AD V ++L Sbjct: 238 KLSEADRKMFSDVAQEAAMRATADVVAREKEL 269 Lambda K H 0.318 0.131 0.375 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: 240 Number of extensions: 8 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: 328 Length of database: 315 Length adjustment: 28 Effective length of query: 300 Effective length of database: 287 Effective search space: 86100 Effective search space used: 86100 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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