Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate Ac3H11_1949 TRAP-type transport system, periplasmic component, predicted N-acetylneuraminate-binding protein
Query= SwissProt::Q9HU18 (331 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1949 Length = 345 Score = 160 bits (406), Expect = 3e-44 Identities = 108/335 (32%), Positives = 172/335 (51%), Gaps = 8/335 (2%) Query: 5 TAKALVCALSLTV-AGIVQAADPIVIKFSHVVAEHTPKGQGALLFKKLVEERLPGKVKVE 63 +A A AL+ T A I Q + S V+ P G+G L+ V ER G++ ++ Sbjct: 9 SAVAAAAALAFTAPAAIAQTTYKSEYRMSLVLGTAFPWGKGGELWANKVRERTQGRINIK 68 Query: 64 VYPNSSLF-GDG-KEMEALLLGDVQIIAPSLAKFEQYTKKLQIFDLPFLFDNIQAVDRFQ 121 +YP SL GD +E AL G + + S + K+L +F LPFLF + AVD Sbjct: 69 LYPGVSLIQGDQTREFSALRQGVIDMAVGSTINWSPQVKQLNLFSLPFLFPDYAAVDAVT 128 Query: 122 QSPQGKELLTSMQDKGITGLGYWHNGMKQLS-ANKPLREPKDARGLKFRVQASKVLEEQF 180 Q GK + ++ G+ L + NG +++S + K ++ P+D +GLK RV S + + F Sbjct: 129 QGDVGKSIFATLDKAGVVPLAWGENGYREISNSKKAIKTPEDLKGLKIRVVGSPLFLDTF 188 Query: 181 KAVRANPRKMSFAEVYQGLQTGVVNGTENPWSNIYSQKMHEV-QKYITESDHGVLDYMVI 239 A+ ANP +MS+A+ +G V+G ENP S + K+H V QK IT + + + Sbjct: 189 TALGANPTQMSWADAQPAFASGAVDGQENPLSIFTAAKLHSVAQKNITLWGYVNDPLIFV 248 Query: 240 TNTKFWNG-LPEDVRGVLAKTMDEVTVEVNKQAEALNQGDKQRI--VEAKTSEIIELTPE 296 N + WN P D V +D E+ + + + DK + + A + +L+P Sbjct: 249 VNKEIWNSWTPADREIVKQAAIDAGKEEIAIARKGVVEADKPLLKDISALGVTVTQLSPA 308 Query: 297 QRAEWRKAMQPVWKKFEGEIGADLIKAAEAANQAQ 331 +RA + K +PV+ K++G+IGADL+ AE A A+ Sbjct: 309 ERAAFVKVTRPVYDKWKGQIGADLVNMAEKAIAAR 343 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: 227 Number of extensions: 13 Number of successful extensions: 4 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: 345 Length adjustment: 28 Effective length of query: 303 Effective length of database: 317 Effective search space: 96051 Effective search space used: 96051 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