Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate GFF2914 PS417_14910 C4-dicarboxylate ABC transporter
Query= SwissProt::Q9HU18 (331 letters) >FitnessBrowser__WCS417:GFF2914 Length = 327 Score = 517 bits (1332), Expect = e-151 Identities = 257/329 (78%), Positives = 295/329 (89%), Gaps = 2/329 (0%) Query: 1 MLKHTAKALVCALSLTVAGIVQAADPIVIKFSHVVAEHTPKGQGALLFKKLVEERLPGKV 60 MLK ++AL+CA +L AG+ QAADPIVIKF+HVVAE+TPKGQGALLFKKL +ERLPG+V Sbjct: 1 MLK-LSRALLCAATLFAAGLAQAADPIVIKFAHVVAENTPKGQGALLFKKLAQERLPGRV 59 Query: 61 KVEVYPNSSLFGDGKEMEALLLGDVQIIAPSLAKFEQYTKKLQIFDLPFLFDNIQAVDRF 120 KVEVYPNSSLFGDGKEMEALLLGDVQ++APSLAKFEQYT+++QI+DLPFLF+++ AVDRF Sbjct: 60 KVEVYPNSSLFGDGKEMEALLLGDVQMLAPSLAKFEQYTQQVQIYDLPFLFNDLAAVDRF 119 Query: 121 QQSPQGKELLTSMQDKGITGLGYWHNGMKQLSANKPLREPKDARGLKFRVQASKVLEEQF 180 Q + QGK LLT+MQDK I GL YWHNG+KQLS+NK L EPKDARGLKFRVQAS VLEEQF Sbjct: 120 QAA-QGKALLTAMQDKNILGLAYWHNGLKQLSSNKALHEPKDARGLKFRVQASSVLEEQF 178 Query: 181 KAVRANPRKMSFAEVYQGLQTGVVNGTENPWSNIYSQKMHEVQKYITESDHGVLDYMVIT 240 KA+RANPRKMSFAEVYQGLQTG VNGTEN WSN SQK++EVQKY TES+HG++DYMVIT Sbjct: 179 KAIRANPRKMSFAEVYQGLQTGTVNGTENTWSNYESQKVNEVQKYFTESNHGLIDYMVIT 238 Query: 241 NTKFWNGLPEDVRGVLAKTMDEVTVEVNKQAEALNQGDKQRIVEAKTSEIIELTPEQRAE 300 N FWNGLP D+R L + M EVTVEVNKQAEALNQ KQ+I++AKTSEIIELTPEQR Sbjct: 239 NATFWNGLPPDIRSTLEQIMVEVTVEVNKQAEALNQSAKQKIIDAKTSEIIELTPEQRQL 298 Query: 301 WRKAMQPVWKKFEGEIGADLIKAAEAANQ 329 WR+AM+PVW+KFEGEIGADLIKAA+A+NQ Sbjct: 299 WREAMRPVWQKFEGEIGADLIKAADASNQ 327 Lambda K H 0.316 0.132 0.376 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: 402 Number of extensions: 9 Number of successful extensions: 2 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: 331 Length of database: 327 Length adjustment: 28 Effective length of query: 303 Effective length of database: 299 Effective search space: 90597 Effective search space used: 90597 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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