Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate HSERO_RS02540 HSERO_RS02540 ABC transporter substrate-binding protein
Query= SwissProt::P37735 (333 letters) >FitnessBrowser__HerbieS:HSERO_RS02540 Length = 345 Score = 132 bits (331), Expect = 2e-35 Identities = 99/310 (31%), Positives = 165/310 (53%), Gaps = 15/310 (4%) Query: 2 LTRRIL---GALVGATALSLALSVPALAEPIVIKFSHVVAPDTPKGKGAAKFEELAEKYT 58 +TRR + GA+ A L LS PA A KF+ P P K A + + T Sbjct: 10 VTRRNMLKAGAVGAALPLFSILSRPASAAEFSYKFATGQDPSHPVNKRAQEAIDRIRNAT 69 Query: 59 NGAVDVEVYPNSQLYKDKEELEALQLGAVQMLAPSLAKFGPLGVQDFEVFDLPYIFKDYE 118 NG ++++++P +QL D + + ++ G V+ + L V + + + F DY Sbjct: 70 NGRLEIKLFPANQLGSDTDLMSQVRNGGVEFFNQANTVLSTL-VPAAGIVNTGFAFHDYG 128 Query: 119 ALHKVTQGEAGKMLLSKLEAKGITGLAF-WDNGFKIMSANT-PLTMPDDFLGLKMRIQSS 176 A+ K G G + +++E G+ ++ WDNGF+ ++ +T P+ D GLK+R+ ++ Sbjct: 129 AVWKAMDGPLGAHVRAQIEKVGLLTMSKPWDNGFRQITTSTKPVRNAGDVKGLKLRVPAA 188 Query: 177 KVLEAEMNALGAVPQVMAFSEVYQALQTGVVDGTENPPSNMFTQKMNEVQKHATVSNHGY 236 +L + +ALGA P + F+EVY +LQT +V+G ENP + + T ++ EVQK T+SNH + Sbjct: 189 PMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEVQKFCTISNHVW 248 Query: 237 LGYAVIVNKQFWDGLPAD----VRTGLEKAMA-ESTDYA--NGIAKEE-NEKALQAMKDA 288 Y ++ N++ ++ LP D VR L+KA + E D A +G A+ + K LQ + +A Sbjct: 249 DAYWILGNRRAFEKLPKDIQEIVRRELDKAASDERADIAAFSGFARNDLASKGLQIV-EA 307 Query: 289 GTTEFHELTA 298 F E A Sbjct: 308 DKDSFKEALA 317 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: 264 Number of extensions: 12 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: 345 Length adjustment: 28 Effective length of query: 305 Effective length of database: 317 Effective search space: 96685 Effective search space used: 96685 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