Align C4-dicarboxylate transport protein 2 (characterized)
to candidate Dsui_3158 Dsui_3158 Na+/H+ dicarboxylate symporter
Query= SwissProt::Q9I4F5 (436 letters) >FitnessBrowser__PS:Dsui_3158 Length = 448 Score = 555 bits (1430), Expect = e-162 Identities = 286/419 (68%), Positives = 337/419 (80%), Gaps = 1/419 (0%) Query: 1 MTKQPFYKSLYVQVLVAIAIGIALGHWYPETAVAMKPFGDGFVKLIKMAIAPIIFCTVVT 60 M+ +PFYK LYVQVL AIA+G+ALG ++PET MKP GD F+KLIKM IAPIIF TVV Sbjct: 1 MSHKPFYKRLYVQVLFAIALGVALGAFFPETGATMKPLGDAFIKLIKMMIAPIIFATVVV 60 Query: 61 GIAGMQSMKSVGKTGGMALLYFEVVSTVALIIGLVVVNVVQPGAGMHVDPNTLDTSKIAA 120 GIA M MK VG+ G AL+YFEVVSTVAL IGL+VVN++QPGAGM+VDP+TLDT IA Sbjct: 61 GIAKMGDMKEVGRVGLKALIYFEVVSTVALAIGLIVVNILQPGAGMNVDPSTLDTKAIAN 120 Query: 121 YAAAGEKQSTVDFLMNVIPGTVVGAFANGDILQVLFFSVLFGYALHRLGSYGKPVFEFIE 180 YAAA QST DFLMN+IP +VV AFA G+ILQVL FSVLFG AL RLG KP+ + ++ Sbjct: 121 YAAAAHNQSTTDFLMNIIPNSVVDAFAKGEILQVLLFSVLFGLALSRLGDKAKPLVKILD 180 Query: 181 RVSHVMFNIINVIMKVAPIGAFGAMAFTIGAYGVGSLVQLGQLMLCFYITCILFVLIVLG 240 SH +F +I +IM APIGAFGAMAFTIG YG+GSL QLG LM YITC LFV +VLG Sbjct: 181 EFSHGLFGVIGMIMHFAPIGAFGAMAFTIGKYGIGSLKQLGFLMANVYITCALFVFVVLG 240 Query: 241 GIARAHGFSILRFIRYIREELLIVLGTSSSESALPRMIDKMEKLGCNKSVVGLVIPTGYS 300 IA+ GFS+L+F+ YI+EELLIVLGTSSSESALPRM+ K+E LGC+K VVG+VIPTGYS Sbjct: 241 LIAKFTGFSLLKFLAYIKEELLIVLGTSSSESALPRMMTKLENLGCHKPVVGMVIPTGYS 300 Query: 301 FNLDGTSIYLTMAAVFIAQATDTPMDITHQITLLLVLLIASKGAAGVTGSGFIVLAATLS 360 FNLDGTSIYLTMAA+FIAQA + P+ +T Q+T+L VLL+ SKGAA VTG GFI LAATL+ Sbjct: 301 FNLDGTSIYLTMAAIFIAQALNVPLTLTEQLTILGVLLLTSKGAAAVTGGGFITLAATLA 360 Query: 361 AV-GHLPVAGLALILGIDRFMSEARALTNLVGNGVATVVVSKWCKQLDEGTLQRELAGE 418 + G LPV GLAL+LG+DRFMSEARA+TNL+GNGVAT+VVSKW L+ + R L GE Sbjct: 361 TLGGKLPVEGLALLLGVDRFMSEARAITNLIGNGVATIVVSKWENALNTDRMTRVLNGE 419 Lambda K H 0.325 0.140 0.406 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: 642 Number of extensions: 27 Number of successful extensions: 2 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: 436 Length of database: 448 Length adjustment: 32 Effective length of query: 404 Effective length of database: 416 Effective search space: 168064 Effective search space used: 168064 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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