Align Solute-binding protein Bamb_6123 (characterized)
to candidate BWI76_RS24125 BWI76_RS24125 hypothetical protein
Query= SwissProt::Q0B2F6 (328 letters) >FitnessBrowser__Koxy:BWI76_RS24125 Length = 328 Score = 230 bits (586), Expect = 4e-65 Identities = 121/324 (37%), Positives = 197/324 (60%), Gaps = 6/324 (1%) Query: 5 FPRSRTALAV-ALMAGFAMSAQARVFRSADVHGDSFPTNMAVKFMGDELSKLTGGKDSIK 63 F RS +++ AL++ A +A+ + A S + A + M E+++L+ G I+ Sbjct: 6 FSRSLVCVSLLALLSSGASAAEKVTLKLAHNLERSHVVHQAFEEMSKEVNQLSNGSMKIR 65 Query: 64 VFGNSALGSEKDTVDQVRIGAIDMARVNGASFNEIVPESLIPSFPFLFRDVDHFRKAMYG 123 ++ +S +GS ++T++ ++ GA+DM + + + I + PFLF+D +HF K ++G Sbjct: 66 IYPSSQMGSARETLELLQNGALDMTKGSASDLESFDNVYAIYNLPFLFKDQNHFNKVVFG 125 Query: 124 PAGQKILDAFAAKGMIALTFYESGARSIYAKRPVRTPADMKGLKVRVQPSDLMVDEIRAM 183 G++I+++ KG AL+ Y +G RS YAK+P+ P D+KGLK+RVQ S + + M Sbjct: 126 EVGKEIMESTKDKGFFALSVYVAGTRSFYAKKPITKPEDLKGLKIRVQASPTTLKMVELM 185 Query: 184 GGTPTPMPFAEVYTGLKTGLVDAAENNLPSYEETKHFEVAPDYSETQHAMTPEVLVFSKK 243 GG+PTP+ F EVYT ++ G+VD AENN+PS+ +T+H E+A +SE +HA P+ LV S K Sbjct: 186 GGSPTPISFGEVYTAMQQGVVDGAENNVPSWVQTRHIEIAKVFSEDEHASIPDFLVISSK 245 Query: 244 IWDTLSPQEQAAIRKAAADSVPYYQKLWTAREASAQ-QAVTKGGANILPAAQVDRAAFVK 302 WD L+P +Q + KAA S Y QKLW +A + QA GG + +VD+A F Sbjct: 246 TWDKLTPDQQQILIKAAKASEVYQQKLWDKIDADTRAQAKAMGGEIV----KVDKAPFRA 301 Query: 303 AMQPLWTKYEKTPQMKQIVDEIEA 326 A+QPL+ ++K P+ ++ + EA Sbjct: 302 AVQPLFDDFKKDPKQAALLAKFEA 325 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: 286 Number of extensions: 20 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: 328 Length adjustment: 28 Effective length of query: 300 Effective length of database: 300 Effective search space: 90000 Effective search space used: 90000 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: 49 (23.5 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