Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate GFF2613 Psest_2664 tripartite ATP-independent periplasmic transporter solute receptor, DctP family
Query= SwissProt::Q9HU18 (331 letters) >FitnessBrowser__psRCH2:GFF2613 Length = 329 Score = 516 bits (1330), Expect = e-151 Identities = 253/330 (76%), Positives = 289/330 (87%), Gaps = 1/330 (0%) Query: 1 MLKHTAKALVCALSLTVAGIVQAADPIVIKFSHVVAEHTPKGQGALLFKKLVEERLPGKV 60 ML + KAL CALS ++AG+V A DP+ IKF+HVVA++TPKGQGALLFKKL EERLPGKV Sbjct: 1 MLSNKLKALACALSFSIAGLVHA-DPVTIKFAHVVADNTPKGQGALLFKKLAEERLPGKV 59 Query: 61 KVEVYPNSSLFGDGKEMEALLLGDVQIIAPSLAKFEQYTKKLQIFDLPFLFDNIQAVDRF 120 KVEVYPNSSLFGDGKEMEALLLGDV ++APSLAKFE Y K +QI+DLPFLFD++ A DRF Sbjct: 60 KVEVYPNSSLFGDGKEMEALLLGDVHMLAPSLAKFEHYAKAIQIYDLPFLFDDLAAADRF 119 Query: 121 QQSPQGKELLTSMQDKGITGLGYWHNGMKQLSANKPLREPKDARGLKFRVQASKVLEEQF 180 Q PQGK LL +M+DK ITGL YWHNGMKQLSANKPLREPKDARGLKFRVQAS VL+EQF Sbjct: 120 QSGPQGKALLRAMEDKNITGLAYWHNGMKQLSANKPLREPKDARGLKFRVQASAVLDEQF 179 Query: 181 KAVRANPRKMSFAEVYQGLQTGVVNGTENPWSNIYSQKMHEVQKYITESDHGVLDYMVIT 240 KAVRANPRKMSFAEVYQGLQTGVVNGTEN WSN SQK+HEVQ Y+T SDHG++DYMVIT Sbjct: 180 KAVRANPRKMSFAEVYQGLQTGVVNGTENTWSNYESQKVHEVQPYMTASDHGLIDYMVIT 239 Query: 241 NTKFWNGLPEDVRGVLAKTMDEVTVEVNKQAEALNQGDKQRIVEAKTSEIIELTPEQRAE 300 NTKFWNGLPED+RG L M+EVT EVN+QA+ LNQ +Q I + +EIIELTPEQRA+ Sbjct: 240 NTKFWNGLPEDLRGELETIMEEVTAEVNRQADDLNQQARQAIAASGKTEIIELTPEQRAQ 299 Query: 301 WRKAMQPVWKKFEGEIGADLIKAAEAANQA 330 WR+AM+PVWKKFE EIGA+LI+AA+AAN++ Sbjct: 300 WREAMKPVWKKFENEIGAELIEAAQAANRS 329 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: 411 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: 329 Length adjustment: 28 Effective length of query: 303 Effective length of database: 301 Effective search space: 91203 Effective search space used: 91203 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 Apr 09 2024. 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