Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate AZOBR_RS26640 AZOBR_RS26640 ABC transporter substrate-binding protein
Query= SwissProt::P37735 (333 letters) >FitnessBrowser__azobra:AZOBR_RS26640 Length = 339 Score = 176 bits (446), Expect = 7e-49 Identities = 101/320 (31%), Positives = 174/320 (54%), Gaps = 3/320 (0%) Query: 11 VGATALSLALSVPALAEPIVIKFSHVVAPDTPKGKGAAKFEELAEKYTNGAVDVEVYPNS 70 V AL A A ++ S VA D P G + A + + G + ++ + N+ Sbjct: 12 VAVAALFAAAPAKAQTAERTMRLSAAVAQDHPFAAGVSALTACAAEKSGGKMKIQSFWNA 71 Query: 71 QLYKDKEELEALQLGAVQMLAPSLAKFGPLGVQDFEVFDLPYIFKDYEALHKVTQGEAGK 130 L D + ++ ++ G++ M+ S + L V VFDLP++F++ ++ G G+ Sbjct: 72 ALGSDMQAVQLVRGGSLDMVVASTSPLASL-VPAMGVFDLPFLFENETEADRILDGAVGQ 130 Query: 131 MLLSKLEAKGITGLAFWDNGFK-IMSANTPLTMPDDFLGLKMRIQSSKVLEAEMNALGAV 189 L KL+ G+ LA+W+NGF+ + ++ P+ +D G K+R+ + V + LGA Sbjct: 131 QLSEKLQGVGLVNLAYWENGFRNLTNSRRPIQKWEDLGGTKIRVMQNPVFMDTFSTLGAN 190 Query: 190 PQVMAFSEVYQALQTGVVDGTENPPSNMFTQKMNEVQKHATVSNHGYLGYAVIVNKQFWD 249 MAFSE++ AL+T VDG ENP +N+ T K E QK+ +V+NH Y ++ +K+ WD Sbjct: 191 AVPMAFSELFTALETRAVDGQENPYANIETGKFYEAQKYLSVTNHAYTPAVILYSKKIWD 250 Query: 250 GLPADVRTGLEKAMAESTDYANGIAKEENEKALQAMKDAGTTEFHELTAEERAAWEEVLT 309 GL + R L+ A + + +E++EK+L +KD G + +EL+AEER + + Sbjct: 251 GLSSAERDVLQSCAAVARTEERRVNREQSEKSLARLKDLG-MQVNELSAEERKRMLQKVA 309 Query: 310 PVHDEMAERIGAETIAAVKA 329 PV+++ A IGAET+ +++ Sbjct: 310 PVYEKHAATIGAETMTLLQS 329 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: 228 Number of extensions: 10 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: 339 Length adjustment: 28 Effective length of query: 305 Effective length of database: 311 Effective search space: 94855 Effective search space used: 94855 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