Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate AZOBR_RS15915 AZOBR_RS15915 ABC transporter substrate-binding protein
Query= SwissProt::P37735 (333 letters) >FitnessBrowser__azobra:AZOBR_RS15915 Length = 337 Score = 175 bits (443), Expect = 2e-48 Identities = 102/326 (31%), Positives = 184/326 (56%), Gaps = 8/326 (2%) Query: 5 RILGALVGATALSLALSVPALA-----EPIVIKFSHVVAPDTPKGKGAAKFEELAEKYTN 59 ++L +++ AT L+ A+ P A +P +I+F + ++ + +G+ F E K + Sbjct: 2 KLLRSVLLATGLAAAILAPVAASAQDIKPRLIRFGYGLSESSNQGRAVKFFVEDMAKRSG 61 Query: 60 GAVDVEVYPNSQLYKDKEELEALQLGAVQMLAPSLAKFGPLGVQDFEVFDLPYIFKDYEA 119 G + V+ + ++ L D + AL GA +M+ S A + V+DF VFDLP++F + + Sbjct: 62 GKLKVKGFADASLGSDIQMQNALIGGAQEMMVGSTATLVGI-VKDFAVFDLPFLFNNEQE 120 Query: 120 LHKVTQGEAGKMLLSKLEAKGITGLAFWDNGFK-IMSANTPLTMPDDFLGLKMRIQSSKV 178 V G G+ L +KL KG+ GL +W+NGF+ + ++ P+ +D G+K+R+ + V Sbjct: 121 ADAVFDGPFGQKLAAKLNDKGLVGLVYWENGFRNLTNSKRPVEKVEDLKGIKLRVMQNPV 180 Query: 179 LEAEMNALGAVPQVMAFSEVYQALQTGVVDGTENPPSNMFTQKMNEVQKHATVSNHGYLG 238 N GA ++FSE++ A++TG VDG ENP + + + K EVQK+ T+S H Y Sbjct: 181 YIDMFNGFGANAVPLSFSELFTAMETGTVDGQENPVTTIQSSKFYEVQKYLTISKHVYSP 240 Query: 239 YAVIVNKQFWDGLPADVRTGLEKAMAESTDYANGIAKEENEKALQAMKDAGTTEFHELTA 298 + V+ +K+++DGL AD R + +A S D+ ++E +++++ +KD G + +EL+ Sbjct: 241 WIVLASKRWYDGLSADERKIINEAAVASRDFERKDSREASKQSIAYLKDKG-MQINELSD 299 Query: 299 EERAAWEEVLTPVHDEMAERIGAETI 324 E E++ P D+ A GA+ + Sbjct: 300 AELGRMREMVKPAMDKFAADGGADLL 325 Lambda K H 0.314 0.130 0.364 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: 239 Number of extensions: 7 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: 333 Length of database: 337 Length adjustment: 28 Effective length of query: 305 Effective length of database: 309 Effective search space: 94245 Effective search space used: 94245 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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