Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate SM_b20036 SM_b20036 ABC transporter substrate-binding protein
Query= SwissProt::P37735 (333 letters) >FitnessBrowser__Smeli:SM_b20036 Length = 338 Score = 192 bits (489), Expect = 8e-54 Identities = 114/329 (34%), Positives = 186/329 (56%), Gaps = 8/329 (2%) Query: 2 LTRRILGALVGATALSLALSVPALAE--PIVIKFSHVVAPDTPKGKGAAKFEELAEKYTN 59 LT+ LG A L+L + PALAE +KF+ P+ G KF EL ++ + Sbjct: 5 LTKLTLGL---AVPLALMTAGPALAEIRDQTVKFASANNKGHPQVTGMEKFAELVKEKSG 61 Query: 60 GAVDVEVYPNSQLYKDKEELEALQLGAVQMLAPSLAKFGPLGVQDFEVFDLPYIFKDYEA 119 G ++V+++P L D + + ALQ G ++M + V++F DLP++F E Sbjct: 62 GKIEVKLFPGGTLGGDVQTVSALQGGVIEMTVLNAGILAS-NVKEFGAVDLPFLFDSGEE 120 Query: 120 LHKVTQGEAGKMLLSKLEAKGITGLAFWDNGFKIMSANT-PLTMPDDFLGLKMRIQSSKV 178 KV G G L+ +L A G+ G+A+W+ GF+ ++ N P+T +D GLK+R S + Sbjct: 121 ADKVMDGPFGTSLMERLPATGLVGVAYWELGFRNLTNNRHPVTKLEDIKGLKIRTIQSPI 180 Query: 179 LEAEMNALGAVPQVMAFSEVYQALQTGVVDGTENPPSNMFTQKMNEVQKHATVSNHGYLG 238 NALGA + ++E+Y AL+TG VDG ENP +N+ K EVQK+ T++ H Y Sbjct: 181 PVELFNALGANAVPLPYTELYTALETGTVDGQENPSANIINAKFYEVQKYMTLTRHQYNP 240 Query: 239 YAVIVNKQFWDGLPADVRTGLEKAMAESTDYANGIAKEENEKALQAMKDAGTTEFHELTA 298 V+V+K+FWDGL + +T L++A E+ D+ +++E++ AL+ ++ G E EL+A Sbjct: 241 QIVLVSKKFWDGLNDEEKTVLQQAAVEARDFQRKVSREQDAAALEEIRKTG-MEVSELSA 299 Query: 299 EERAAWEEVLTPVHDEMAERIGAETIAAV 327 EE + + P+ ++ + IG ET+ A+ Sbjct: 300 EETQKLRDAVKPMIEKFSADIGQETVEAL 328 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: 234 Number of extensions: 13 Number of successful extensions: 3 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: 338 Length adjustment: 28 Effective length of query: 305 Effective length of database: 310 Effective search space: 94550 Effective search space used: 94550 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