Align TRAP dicarboxylate transport system, periplasmic component (DctP-like) (characterized, see rationale)
to candidate 202248 SO3134 C4-dicarboxylate-binding periplasmic protein (NCBI ptt file)
Query= uniprot:G8AR24 (337 letters) >FitnessBrowser__MR1:202248 Length = 339 Score = 153 bits (387), Expect = 5e-42 Identities = 106/315 (33%), Positives = 166/315 (52%), Gaps = 12/315 (3%) Query: 18 LAPVAASAQDI--KPRLIRFGYGLSESSNQGRAVKFFVEDMAKRSGGKLKVKGFADASLG 75 LA V A++ ++ P I+F + ++E++ +G+ F E + +R G+ V F ++ L Sbjct: 22 LASVFATSFNVFAAPVEIKFSHVVAENTPKGQMALKFKELVEQRLPGEYTVSVFPNSQLF 81 Query: 76 SDIQMQNALIGGAQEMMVGSTATLVGIVKDFAVFDLPFLFNNEQEADAVFDGPFGQKLAA 135 D AL+ + + S + K VFDLPFLFN+ + G GQ L Sbjct: 82 GDNNELAALLLNDVQFVAPSLSKFERYTKRLQVFDLPFLFNDMDAVNRFQQGEAGQALLN 141 Query: 136 KLNDKGLVGLVYWENGFRNLTNSKRPVEKVEDLKGIKLRVMQNPVYIDMFNGFGANAVPL 195 ++ KG+VGL Y NG + T + P+++ D KG+K RVM + V F+ GA V Sbjct: 142 SMSRKGIVGLGYLHNGMKQFT-ANTPLKQPSDAKGLKFRVMASDVLAAQFDAVGAIPVKK 200 Query: 196 SFSELFTAMETGTVDGQENPVTTIQSSKFYEVQKYLTISKHVYSPWIVLASKRWYDGLSA 255 FSE+FT ++T +DGQEN + S KFYEVQ ++T S H ++V+ S ++ L A Sbjct: 201 PFSEVFTLLQTRAIDGQENTWSNTYSQKFYEVQSHITESNHGVLDYMVVTSDAFWKSLPA 260 Query: 256 DERKIINEA-----AVASRDFERKDSREASKQSIAYLKDKGMQINELSDAELGRMREMVK 310 D+RK+I EA A+ ++ KD+ + KQ I L K Q+ LS AE + +++K Sbjct: 261 DKRKVIKEALDESIALGNKIAAEKDNED--KQLI--LDSKLSQLVTLSPAERQQWVDVMK 316 Query: 311 PAMDKFAADGGADLL 325 P KF G D++ Sbjct: 317 PVWSKFEDQVGKDVI 331 Lambda K H 0.317 0.134 0.372 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: 231 Number of extensions: 11 Number of successful extensions: 3 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: 337 Length of database: 339 Length adjustment: 28 Effective length of query: 309 Effective length of database: 311 Effective search space: 96099 Effective search space used: 96099 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 (21.7 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