Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate HSERO_RS05560 HSERO_RS05560 ABC transporter substrate-binding protein
Query= SwissProt::P37735 (333 letters) >FitnessBrowser__HerbieS:HSERO_RS05560 Length = 348 Score = 129 bits (323), Expect = 1e-34 Identities = 90/300 (30%), Positives = 157/300 (52%), Gaps = 10/300 (3%) Query: 8 GALVGATALSLALSVPALAEPIVIKFSHVVAPDTPKGKGAAKFEELAEKYTNGAVDVEVY 67 GA+ A L +S PA A KF+ P P K A + + + T G +D++++ Sbjct: 22 GAVGAALPLFSIMSRPANAAEFNYKFATGQDPSHPVNKRAQQAIDRIREATGGRLDIKLF 81 Query: 68 PNSQLYKDKEELEALQLGAVQMLAPSLAKFGPLGVQDFEVFDLPYIFKDYEALHKVTQGE 127 P +QL D + + ++ G V+ + L V + + + F DY+ + + G Sbjct: 82 PANQLGSDTDLMSQIRNGGVEFFNQASVVLSTL-VPAAGIVNTGFAFHDYKEVWQAMDGP 140 Query: 128 AGKMLLSKLEAKGITGLAF-WDNGFKIMSANT-PLTMPDDFLGLKMRIQSSKVLEAEMNA 185 G + +++E G+ ++ WDNGF+ ++ +T P+ D GLK+R+ ++ +L + +A Sbjct: 141 LGAYVRAQIEKVGLLTMSKPWDNGFRQITTSTKPIKTAADLKGLKLRVPAAPMLTSLFSA 200 Query: 186 LGAVPQVMAFSEVYQALQTGVVDGTENPPSNMFTQKMNEVQKHATVSNHGYLGYAVIVNK 245 LGA P + F+EVY +LQT +V+G ENP + + T ++ EVQK T+SNH + Y ++ N+ Sbjct: 201 LGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEVQKFCTISNHVWDAYWILGNR 260 Query: 246 QFWDGLPAD----VRTGLEKAMA-ESTDYA--NGIAKEENEKALQAMKDAGTTEFHELTA 298 + ++ LP D VR L+KA E D A +G A+ + + + +A F E A Sbjct: 261 RAFEKLPKDIQEIVRRELDKAATDERADIASLSGFARNDLQGKGVQIIEADKNSFKEALA 320 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: 245 Number of extensions: 14 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: 348 Length adjustment: 28 Effective length of query: 305 Effective length of database: 320 Effective search space: 97600 Effective search space used: 97600 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