GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctA in Dechlorosoma suillum PS

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.

Links

Downloads

Related tools

About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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