Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate 8501198 DvMF_1932 TRAP dicarboxylate transporter, DctP subunit (RefSeq)
Query= SwissProt::P37735 (333 letters) >FitnessBrowser__Miya:8501198 Length = 335 Score = 132 bits (333), Expect = 9e-36 Identities = 99/321 (30%), Positives = 144/321 (44%), Gaps = 24/321 (7%) Query: 10 LVGATALSLALSVPALAEPIVIKFSHVVAPDTPKGKGAA----KFEELAEKYTNGAVDVE 65 LV A +++AL+ P A K +A TP G KF +L + + G + V+ Sbjct: 7 LVAALLMTVALAAPVQAAYDGPKIKFRLAHTTPPGNHITLAYQKFADLVAEKSGGKITVQ 66 Query: 66 VYPNSQLYKDKEELEALQLGAVQM---LAPSLAKFGPLGVQDFEVFDLPYIFKDYEALHK 122 V+PN+ L D+ +E Q G +++ P+LA F L + VFDLPYI + Sbjct: 67 VFPNAILGSDRVLVEGAQKGTLEIGVSSTPNLANFSKL----YSVFDLPYITSPKFQKNL 122 Query: 123 VTQGEAGKML----LSKLEAKGITGLAFWDNGFK-IMSANTPLTMPDDFLGLKMRIQSSK 177 + + G L L G+ + + + G++ +S PL D GLKMR S Sbjct: 123 YSAIDPGGTLYDYFLKVANDVGLQPIMYAEYGYRHFVSVKRPLGKASDLAGLKMRTTDSP 182 Query: 178 VLEAEMNALGAVPQVMAFSEVYQALQTGVVDGTENPPSNMFTQKMNEVQKHATVSNHGYL 237 V AL P +A+ EVY ALQ G +D N ++F K +EV K+A S H Y Sbjct: 183 VEVGVAKALNTNPSPIAWGEVYTALQQGTIDAEGNTFPHLFGAKHHEVLKYAITSAHNYC 242 Query: 238 GYAVIVNKQFWDGLPADVRTGLEKAMAESTDYANGIAKEENEKALQ--------AMKDAG 289 + NK +WDGLP + + A E+T Y + ENEKA + + DA Sbjct: 243 MQVAMANKAWWDGLPDAAKQVINAAAREATQYQRDVLYPENEKAAREGFIKAGITIHDAT 302 Query: 290 TTEFHELTAEERAAWEEVLTP 310 E E R W+ V P Sbjct: 303 DAEIDEFRKLTRPVWDTVTLP 323 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: 236 Number of extensions: 13 Number of successful extensions: 1 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: 335 Length adjustment: 28 Effective length of query: 305 Effective length of database: 307 Effective search space: 93635 Effective search space used: 93635 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