Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate AZOBR_RS27150 AZOBR_RS27150 membrane protein
Query= uniprot:Q88NP0 (426 letters) >FitnessBrowser__azobra:AZOBR_RS27150 Length = 433 Score = 344 bits (883), Expect = 3e-99 Identities = 172/425 (40%), Positives = 283/425 (66%), Gaps = 5/425 (1%) Query: 3 AFILLGSFIVLILIGMPVAYALGLSALIGAWWIDIPLQAMMI---QVASGVNKFSLLAIP 59 A +L +F+ L+ G+P++YA GL+++ I PL A+ + ++A+G++ F+LLAIP Sbjct: 6 ALVLSAAFVALLAFGVPISYATGLASITALLTIMPPLPAISVTAQRIATGLDSFALLAIP 65 Query: 60 FFVLAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGS 119 FF +AG+IM GG++RRL+ A V VG++ G L+ + I+A+ FG +SGS+VA +++G Sbjct: 66 FFFMAGSIMNRGGIARRLIDCAKVFVGWMPGPLAQITILANMMFGCVSGSAVAAASAIGG 125 Query: 120 VLIPEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPG 179 + P M++ GY R ++ AV +S + LL PPS ++YSL +GGT SIA+LF+AG +PG Sbjct: 126 TMQPSMDKAGYDRSYTAAVNISSCITGLLIPPSGAFIVYSLVSGGT-SIAALFVAGYLPG 184 Query: 180 LLLSAVMMGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTAT 239 +LL +M + AKKR Y + L ++ + AL L +V+++GGI+ GVFTAT Sbjct: 185 ILLGLAVMIPAWMMAKKRGYARLPSPTLSQSSRALLSALPSLGLIVVVIGGIVGGVFTAT 244 Query: 240 ESAAVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQIP 299 E +A+AVV++ + + YR+ D+ +++ T+ ++V +++G + + YVM+L +IP Sbjct: 245 EGSAIAVVYALALAL-AYRELSLDDIGQILVDTIVATAVVALMVGTSMAMAYVMSLAEIP 303 Query: 300 SKITTAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHFG 359 I ++S N + L+ +N +L+L+GT +D+ P ILI TPI LPV+ +GVDPVHFG Sbjct: 304 QIIGDWVQSVSGNWIIALLLVNIVLLLMGTFLDITPGILIFTPIFLPVLVELGVDPVHFG 363 Query: 360 MIMLVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAISL 419 +I++ NL +G+++PP G+ LF+G A+ +VSIE ++ L+P + L+ VTY+P +SL Sbjct: 364 VILVFNLSLGIVSPPTGSALFIGCAVARVSIEQVIRPLIPLFAWSTAALLVVTYVPGLSL 423 Query: 420 WLPSV 424 WLPS+ Sbjct: 424 WLPSL 428 Lambda K H 0.329 0.142 0.418 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: 558 Number of extensions: 29 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: 426 Length of database: 433 Length adjustment: 32 Effective length of query: 394 Effective length of database: 401 Effective search space: 157994 Effective search space used: 157994 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 51 (24.3 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