Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate WP_090447096.1 BLS63_RS17680 C4-dicarboxylate ABC transporter
Query= SwissProt::Q9HU18 (331 letters) >NCBI__GCF_900100495.1:WP_090447096.1 Length = 335 Score = 521 bits (1342), Expect = e-153 Identities = 261/334 (78%), Positives = 293/334 (87%), Gaps = 5/334 (1%) Query: 1 MLKHTAKALVCALSLTVAGIVQAAD-----PIVIKFSHVVAEHTPKGQGALLFKKLVEER 55 MLK TAKALVCALSL++ +VQAA PIVIKF+HVVA++TPKGQGALLFK+L EER Sbjct: 1 MLKLTAKALVCALSLSLGSLVQAAGSSQTAPIVIKFAHVVADNTPKGQGALLFKQLAEER 60 Query: 56 LPGKVKVEVYPNSSLFGDGKEMEALLLGDVQIIAPSLAKFEQYTKKLQIFDLPFLFDNIQ 115 LPG+V+VEVYPNSSLFGDGKEMEALLLGDVQ++APSLAKFEQY K +QIFDLPFLFD++ Sbjct: 61 LPGRVRVEVYPNSSLFGDGKEMEALLLGDVQLLAPSLAKFEQYAKPIQIFDLPFLFDDLA 120 Query: 116 AVDRFQQSPQGKELLTSMQDKGITGLGYWHNGMKQLSANKPLREPKDARGLKFRVQASKV 175 A +RFQ SPQGK LLTSM+DK ITGL YWHNG KQ+SANKPLREPKDARGLKFRVQAS V Sbjct: 121 AAERFQSSPQGKALLTSMEDKNITGLAYWHNGTKQMSANKPLREPKDARGLKFRVQASAV 180 Query: 176 LEEQFKAVRANPRKMSFAEVYQGLQTGVVNGTENPWSNIYSQKMHEVQKYITESDHGVLD 235 LEEQFKAVRANPRKMSFAEVYQGLQTGVVNGTEN WSN SQK+HEVQKY+TES+HG++D Sbjct: 181 LEEQFKAVRANPRKMSFAEVYQGLQTGVVNGTENTWSNYQSQKVHEVQKYMTESNHGLID 240 Query: 236 YMVITNTKFWNGLPEDVRGVLAKTMDEVTVEVNKQAEALNQGDKQRIVEAKTSEIIELTP 295 YM+ITNT FW GLP DVR L M EVTVEVNKQA+ LNQ KQ I A T+EIIELT Sbjct: 241 YMLITNTTFWKGLPADVRSELQAIMAEVTVEVNKQADELNQSAKQAIAAAGTTEIIELTA 300 Query: 296 EQRAEWRKAMQPVWKKFEGEIGADLIKAAEAANQ 329 EQRA+WR+AM+PVW+KFE EIGA+LI+AA+AANQ Sbjct: 301 EQRAQWREAMKPVWQKFEAEIGAELIEAAQAANQ 334 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: 410 Number of extensions: 11 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: 335 Length adjustment: 28 Effective length of query: 303 Effective length of database: 307 Effective search space: 93021 Effective search space used: 93021 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 24 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