Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate AZOBR_RS27150 AZOBR_RS27150 membrane protein
Query= SwissProt::O07838 (440 letters) >FitnessBrowser__azobra:AZOBR_RS27150 Length = 433 Score = 293 bits (749), Expect = 9e-84 Identities = 157/440 (35%), Positives = 261/440 (59%), Gaps = 16/440 (3%) Query: 3 ALIIFGLLIALMLTGMPISISLGLTVLTFLFT-MTQVP-IDTVALKLFTGIEKFEIMAIP 60 AL++ +AL+ G+PIS + GL +T L T M +P I A ++ TG++ F ++AIP Sbjct: 6 ALVLSAAFVALLAFGVPISYATGLASITALLTIMPPLPAISVTAQRIATGLDSFALLAIP 65 Query: 61 FFILAGNFLTHGGVAKRMINFATAMVGHWHGGLGLAGVIACALFAAVSGSSPATVVAIGS 120 FF +AG+ + GG+A+R+I+ A VG G L ++A +F VSGS+ A AIG Sbjct: 66 FFFMAGSIMNRGGIARRLIDCAKVFVGWMPGPLAQITILANMMFGCVSGSAVAAASAIGG 125 Query: 121 VILPAMVNQGFPKQFGAGVITTSGALGILIPPSIVMVMYAVATSGMVVTGPDGQPVSSAS 180 + P+M G+ + + A V +S G+LIPPS ++Y++ + G S Sbjct: 126 TMQPSMDKAGYDRSYTAAVNISSCITGLLIPPSGAFIVYSLVSGG-------------TS 172 Query: 181 VGELFMAGVVPGLMLAGFLAFTTWNRARKFGYPRLEKASLRQRWTAFREAAWGLMLIVVV 240 + LF+AG +PG++L + W A+K GY RL +L Q A A L LIVVV Sbjct: 173 IAALFVAGYLPGILLGLAVMIPAWMMAKKRGYARLPSPTLSQSSRALLSALPSLGLIVVV 232 Query: 241 IGGIYAGIFTPTEAAAMSAVYAFFISVFVYKDLTLRDVPRVLLSSANMSAMLLYIITNAV 300 IGGI G+FT TE +A++ VYA +++ Y++L+L D+ ++L+ + +A++ ++ ++ Sbjct: 233 IGGIVGGVFTATEGSAIAVVYALALAL-AYRELSLDDIGQILVDTIVATAVVALMVGTSM 291 Query: 301 LFSFLMAHEGIPQALGEWMVNAGLSWWMFLIIVNILLLAAGNFMEPSSIVLIMAPILFPV 360 +++M+ IPQ +G+W+ + +W + L++VNI+LL G F++ + +LI PI PV Sbjct: 292 AMAYVMSLAEIPQIIGDWVQSVSGNWIIALLLVNIVLLLMGTFLDITPGILIFTPIFLPV 351 Query: 361 AVRLGIDPVHFGIMIVVNMEVGMCHPPVGLNLYVASGITKMGITELTVAVWPWLLTMLAF 420 V LG+DPVHFG+++V N+ +G+ PP G L++ + ++ I ++ + P A Sbjct: 352 LVELGVDPVHFGVILVFNLSLGIVSPPTGSALFIGCAVARVSIEQVIRPLIPLFAWSTAA 411 Query: 421 LVLVTYVPAISLALPNLLGM 440 L++VTYVP +SL LP+L G+ Sbjct: 412 LLVVTYVPGLSLWLPSLFGL 431 Lambda K H 0.329 0.142 0.431 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: 577 Number of extensions: 36 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: 440 Length of database: 433 Length adjustment: 32 Effective length of query: 408 Effective length of database: 401 Effective search space: 163608 Effective search space used: 163608 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