Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate GFF2099 Psest_2142 tripartite ATP-independent periplasmic transporter solute receptor, DctP family
Query= SwissProt::Q9HU18 (331 letters) >FitnessBrowser__psRCH2:GFF2099 Length = 330 Score = 417 bits (1072), Expect = e-121 Identities = 201/324 (62%), Positives = 259/324 (79%), Gaps = 7/324 (2%) Query: 15 LTVAGIVQA-------ADPIVIKFSHVVAEHTPKGQGALLFKKLVEERLPGKVKVEVYPN 67 +T+AG++ A A+PIVIKFSHVVA+ TPKG+GAL+FK+L EERL G+V+VEVYPN Sbjct: 5 ITLAGVLLALASACAQAEPIVIKFSHVVADDTPKGKGALMFKRLAEERLAGQVRVEVYPN 64 Query: 68 SSLFGDGKEMEALLLGDVQIIAPSLAKFEQYTKKLQIFDLPFLFDNIQAVDRFQQSPQGK 127 S+LFGD E+EAL +VQ++APSLAKFEQYTK+LQ+FDLPFLFD+I+AV+RFQ+ +GK Sbjct: 65 STLFGDATELEALRNDEVQLLAPSLAKFEQYTKQLQVFDLPFLFDDIEAVNRFQKRAKGK 124 Query: 128 ELLTSMQDKGITGLGYWHNGMKQLSANKPLREPKDARGLKFRVQASKVLEEQFKAVRANP 187 +LL SM+DK ITGL YWHNGMKQLSA + LR+P DA GL FR+Q S VLE QF V A+ Sbjct: 125 QLLRSMEDKNITGLAYWHNGMKQLSATRMLRQPSDASGLSFRIQPSAVLEAQFGTVGAST 184 Query: 188 RKMSFAEVYQGLQTGVVNGTENPWSNIYSQKMHEVQKYITESDHGVLDYMVITNTKFWNG 247 +K+ FA+VY L+ G V G ENPWSNIYS+KMH VQ YI E+DHGVLDYMV++NT+FW G Sbjct: 185 QKIPFADVYDALRAGTVQGAENPWSNIYSKKMHTVQPYIIETDHGVLDYMVVSNTRFWMG 244 Query: 248 LPEDVRGVLAKTMDEVTVEVNKQAEALNQGDKQRIVEAKTSEIIELTPEQRAEWRKAMQP 307 +P +R L +DEV+ VN++A+ LN+ D++RI +A TSEI+ L+PE+R WR+AM+P Sbjct: 245 MPHKIRFELEAILDEVSFMVNREADELNRADRERIRQAGTSEIVALSPEERERWREAMRP 304 Query: 308 VWKKFEGEIGADLIKAAEAANQAQ 331 VW++FE IGAD+IKAAE N+ Q Sbjct: 305 VWQQFEPVIGADIIKAAETVNRKQ 328 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: 343 Number of extensions: 7 Number of successful extensions: 1 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: 330 Length adjustment: 28 Effective length of query: 303 Effective length of database: 302 Effective search space: 91506 Effective search space used: 91506 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 Apr 09 2024. 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