Align Solute-binding protein Bamb_6123 (characterized)
to candidate AZOBR_RS15915 AZOBR_RS15915 ABC transporter substrate-binding protein
Query= SwissProt::Q0B2F6 (328 letters) >FitnessBrowser__azobra:AZOBR_RS15915 Length = 337 Score = 143 bits (361), Expect = 5e-39 Identities = 89/274 (32%), Positives = 151/274 (55%), Gaps = 6/274 (2%) Query: 10 TALAVALMAGFAMSAQ---ARVFRSADVHGDSFPTNMAVKFMGDELSKLTGGKDSIKVFG 66 T LA A++A A SAQ R+ R +S AVKF ++++K +GGK +K F Sbjct: 11 TGLAAAILAPVAASAQDIKPRLIRFGYGLSESSNQGRAVKFFVEDMAKRSGGKLKVKGFA 70 Query: 67 NSALGSEKDTVDQVRIGAIDMARVNGASFNEIVPESLIPSFPFLFRDVDHFRKAMYGPAG 126 +++LGS+ + + GA +M + A+ IV + + PFLF + GP G Sbjct: 71 DASLGSDIQMQNALIGGAQEMMVGSTATLVGIVKDFAVFDLPFLFNNEQEADAVFDGPFG 130 Query: 127 QKILDAFAAKGMIALTFYESGARSIY-AKRPVRTPADMKGLKVRVQPSDLMVDEIRAMGG 185 QK+ KG++ L ++E+G R++ +KRPV D+KG+K+RV + + +D G Sbjct: 131 QKLAAKLNDKGLVGLVYWENGFRNLTNSKRPVEKVEDLKGIKLRVMQNPVYIDMFNGFGA 190 Query: 186 TPTPMPFAEVYTGLKTGLVDAAENNLPSYEETKHFEVAPDYSETQHAMTPEVLVFSKKIW 245 P+ F+E++T ++TG VD EN + + + +K +EV + ++H +P +++ SK+ + Sbjct: 191 NAVPLSFSELFTAMETGTVDGQENPVTTIQSSKFYEVQKYLTISKHVYSPWIVLASKRWY 250 Query: 246 DTLSPQEQAAIRKAAADSVPYYQKLWTAREASAQ 279 D LS E+ I +AA S + +K +REAS Q Sbjct: 251 DGLSADERKIINEAAVASRDFERK--DSREASKQ 282 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: 209 Number of extensions: 6 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: 337 Length adjustment: 28 Effective length of query: 300 Effective length of database: 309 Effective search space: 92700 Effective search space used: 92700 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