Align TRAP dicarboxylate transporter DctP subunit; Flags: Precursor (characterized, see rationale)
to candidate AZOBR_RS15915 AZOBR_RS15915 ABC transporter substrate-binding protein
Query= uniprot:Q2IUT5 (332 letters) >FitnessBrowser__azobra:AZOBR_RS15915 Length = 337 Score = 176 bits (445), Expect = 1e-48 Identities = 109/326 (33%), Positives = 177/326 (54%), Gaps = 11/326 (3%) Query: 3 KSIFVVASIAALALVGPAAAQQ---PIVVKFSHVVADNTPKGQAAIKFKELAEKYTNGKV 59 +S+ + +AA L AA+ Q P +++F + +++++ +G+A F E K + GK+ Sbjct: 5 RSVLLATGLAAAILAPVAASAQDIKPRLIRFGYGLSESSNQGRAVKFFVEDMAKRSGGKL 64 Query: 60 KVEVYPNSQLFGDAKEMEAVALGDVQFIAPSLSKFDKFTKQIQVFDLPFLFNDIAAVDRF 119 KV+ + ++ L D + A+ G + + S + K VFDLPFLFN+ D Sbjct: 65 KVKGFADASLGSDIQMQNALIGGAQEMMVGSTATLVGIVKDFAVFDLPFLFNNEQEADAV 124 Query: 120 QAGKQGQALLRSMESKNFLGLAYWHNGMKQIS-ANRPLLKPEDAKGLKFRIQASDILAAQ 178 G GQ L + K +GL YW NG + ++ + RP+ K ED KG+K R+ + + Sbjct: 125 FDGPFGQKLAAKLNDKGLVGLVYWENGFRNLTNSKRPVEKVEDLKGIKLRVMQNPVYIDM 184 Query: 179 FQGLNATPQKLAFSEVYQALQVGTVDGQENTWSNIFSQKFYEVQKDITESDHGVIDYMVV 238 F G A L+FSE++ A++ GTVDGQEN + I S KFYEVQK +T S H ++V+ Sbjct: 185 FNGFGANAVPLSFSELFTAMETGTVDGQENPVTTIQSSKFYEVQKYLTISKHVYSPWIVL 244 Query: 239 VNAKWWNGLSKDLQDAMKKAMDEATKVNNDVAGKLNDEA-KQKIA--SSGASKIHQLTPE 295 + +W++GLS D +K ++EA + D K + EA KQ IA +I++L+ Sbjct: 245 ASKRWYDGLSAD----ERKIINEAAVASRDFERKDSREASKQSIAYLKDKGMQINELSDA 300 Query: 296 QRKQWVEAMKPVWAKFESAIGKDLID 321 + + E +KP KF + G DL++ Sbjct: 301 ELGRMREMVKPAMDKFAADGGADLLN 326 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: 263 Number of extensions: 10 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: 332 Length of database: 337 Length adjustment: 28 Effective length of query: 304 Effective length of database: 309 Effective search space: 93936 Effective search space used: 93936 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