Align TRAP dicarboxylate transporter DctP subunit; Flags: Precursor (characterized, see rationale)
to candidate AZOBR_RS02715 AZOBR_RS02715 C4-dicarboxylate ABC transporter
Query= uniprot:Q2IUT5 (332 letters) >FitnessBrowser__azobra:AZOBR_RS02715 Length = 342 Score = 157 bits (396), Expect = 5e-43 Identities = 109/337 (32%), Positives = 175/337 (51%), Gaps = 14/337 (4%) Query: 3 KSIFVVASIAALALVG-----PAAAQQPIVVKFSHVVADNTPKGQAAIKFKELAEKYTNG 57 K++F ++AA+ L G AAA K S V+ P G ++ EL ++ TNG Sbjct: 2 KALFAGLALAAMVLPGVVANGAAAADYKAEYKLSTVLGKPFPWGIGGDRWAELVKEKTNG 61 Query: 58 KVKVEVYPNSQLF-GD-AKEMEAVALGDVQFIAPSLSKFDKFTKQIQVFDLPFLFNDIAA 115 ++ V++YP S L GD KE A+ G + S + K++ +F LPFL D A Sbjct: 62 RINVKMYPGSALVNGDQTKEFTALRQGVIDMAVGSTINWSPQVKELNLFSLPFLMPDHKA 121 Query: 116 VDRFQAGKQGQALLRSMESKNFLGLAYWHNGMKQISANRPLL-KPEDAKGLKFRIQASDI 174 +D G G+ L + +K+ + LA+ NG +++S ++ + KPED KGLK R+ S + Sbjct: 122 MDALTQGPVGKQLFDLLATKDVVPLAWGENGFREVSNSKHAISKPEDLKGLKIRVVGSPL 181 Query: 175 LAAQFQGLNATPQKLAFSEVYQALQVGTVDGQENTWSNIFSQKFYEV-QKDITESDHGVI 233 F L A P ++++++ AL G VDGQEN + + K + QK +T + Sbjct: 182 YLDTFTALGANPTQMSWADAQPALSTGAVDGQENPVAVFTAAKLPTLGQKHLTLWGYVAD 241 Query: 234 DYMVVVNAKWWNGLSKDLQDAMKKAMDEATKVNNDVAGK----LNDEAKQKIASSGASKI 289 + VVN + WN SK+ Q+A++ A +A +A K +D +++A G + + Sbjct: 242 PLIFVVNKEVWNSWSKEDQEAVRAAAVQAAAEEVAIARKGITAQDDSLLKELAGQGVAVV 301 Query: 290 HQLTPEQRKQWVEAMKPVWAKFESAIGKDLIDAAVAS 326 QLTPEQ+K + A + V+ K+ IG DL+ AA S Sbjct: 302 -QLTPEQQKAFQAATRAVYDKWAKTIGPDLVKAAETS 337 Lambda K H 0.316 0.129 0.367 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: 267 Number of extensions: 12 Number of successful extensions: 5 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: 332 Length of database: 342 Length adjustment: 28 Effective length of query: 304 Effective length of database: 314 Effective search space: 95456 Effective search space used: 95456 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