Align C4-dicarboxylate-binding periplasmic protein DctP (characterized, see rationale)
to candidate WP_044620695.1 H744_RS01505 TRAP transporter substrate-binding protein
Query= uniprot:I7END8 (333 letters) >NCBI__GCF_000940995.1:WP_044620695.1 Length = 351 Score = 147 bits (370), Expect = 5e-40 Identities = 98/326 (30%), Positives = 167/326 (51%), Gaps = 11/326 (3%) Query: 4 VTAAATAVALTMSAGTAMAACDDGEIVVKFSHVTNTDKHPKGIAASLLEKRINEEMNGTM 63 + AA + T AC+ ++FS +NT +HP AS ++ + E + Sbjct: 18 IIGAAIVTNGNNTTNTTNLACESQIKTLRFSMSSNT-QHPIYDGASKFKELV--EKTTDL 74 Query: 64 CLEVYPNSTLYNDNKVLEAMLQGDVQLAAPSLSKFEKFTKQFRLFDLPFMFKNIDAVDAF 123 +++YP++ L +D +E + G + ++ PS + F ++ +FDLPFM N D Sbjct: 75 TVDIYPSAQLGDDRAAIEMLQLGTLDVSIPSTAPLANFYPEYNVFDLPFMIPNEAVADKV 134 Query: 124 QGSENGQAMLDSMQRRGLQGLSYWHNGMKQMS-ANKPLINPSDANGLKFRVQSSDVLVAQ 182 S+ ML+ +Q R L GL +W NG + ++ + + + + D GLK R S + + Sbjct: 135 LRSDFAGDMLEMLQSRRLIGLDFWENGFRHLTNSRRTVTSVDDVKGLKVRTMESPLHLDA 194 Query: 183 MEAIGGSPQKMAFSEVYGALQQGVVDGQENTWSNIYGKKFFEVQDGVTETNHGALD-YLV 241 +A+G +P MAF+E++ ALQQG VDGQEN + NI +EVQ +T+T H L+ Sbjct: 195 WKALGATPTPMAFNELFTALQQGTVDGQENPYPNIALNNLYEVQKQMTDTGHVYTPLVLI 254 Query: 242 VTSVDW--LDSLDPAVREQFLTILGEVTATRNSESTKVNAEARQSIIDAGGVVRELTPEQ 299 + W L + D A Q G+ + + +VN ++ + I A V ELTPE Sbjct: 255 FSEASWNKLSAHDQAAVRQAAIEAGDY---QREVNRRVNNDS-LATIKANMQVTELTPEA 310 Query: 300 RAAWVEAMKPVWEQFAGDVGQDMIDA 325 R+ + +A + V +++ +G D+ID+ Sbjct: 311 RSEFRKATESVVDKYRDVIGGDIIDS 336 Lambda K H 0.316 0.130 0.371 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: 278 Number of extensions: 19 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: 333 Length of database: 351 Length adjustment: 29 Effective length of query: 304 Effective length of database: 322 Effective search space: 97888 Effective search space used: 97888 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