GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dctA in Pseudomonas fluorescens GW456-L13

Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate PfGW456L13_1449 probable dicarboxylate transporter

Query= CharProtDB::CH_014038
         (428 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1449 probable
           dicarboxylate transporter
          Length = 420

 Score =  399 bits (1024), Expect = e-115
 Identities = 201/400 (50%), Positives = 283/400 (70%), Gaps = 1/400 (0%)

Query: 19  IGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIAGMESMKAVGRTGAVAL 78
           +GI+ G   PE   Q+KPLGDGF+KLIKM+I  ++FC VV+GI+G   +K VGR G  ++
Sbjct: 2   LGIVCGLTLPEYSAQLKPLGDGFIKLIKMLIGLIVFCVVVSGISGAGDLKKVGRIGLKSV 61

Query: 79  LYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYADQAKDQGIVA-FIMDVI 137
           +YFE+++TIAL+IGL+       G+G N+    L A  +   A + +       F+MD+I
Sbjct: 62  IYFEVLTTIALVIGLVFAFSTGIGSGANIHLEQLSAADMGDIAQRGQHMHTTTQFLMDLI 121

Query: 138 PASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESFSQVIFGIINMIMRLAP 197
           P SVIGAFA  NILQVLLF+VLFG AL+ +G     I  +I   S VIF I+ MI+RLAP
Sbjct: 122 PTSVIGAFADNNILQVLLFSVLFGSALNLVGEAASGISRLINELSHVIFRIMGMIVRLAP 181

Query: 198 IGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSIAKATGFSIFKFIRYIR 257
           IG FGA+AFT  KYG+ +L  LG L+  FY+TC+ FV L+LG + + +G  ++  ++Y+R
Sbjct: 182 IGVFGAIAFTTSKYGLDSLQHLGSLVGLFYLTCVAFVALILGLVMRLSGLKMWPLLKYLR 241

Query: 258 EELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNLDGTSIYLTMAAVFIA 317
           EELLIV+GT+SS++ LP+++ K+E LG   S VGLVIPTGYSFNLDG SIYLT+A VFIA
Sbjct: 242 EELLIVMGTASSDAVLPQIMRKLEHLGIGSSTVGLVIPTGYSFNLDGFSIYLTLAIVFIA 301

Query: 318 QATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAVGHLPVAGLALILGIDR 377
            AT + + +   +T+L+V L++SKGA G+ GS  ++LAATL+A+  +PV GL L+L +D 
Sbjct: 302 NATGTPLAMTDLLTILLVSLITSKGAHGIPGSALVILAATLTAIPAIPVVGLVLVLAVDW 361

Query: 378 FMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVLNNR 417
           FM   RALTNL+GN VAT+ +A+W K++D ++ + VL+ +
Sbjct: 362 FMGIGRALTNLIGNCVATVAIARWEKDIDIQRANKVLSGQ 401


Lambda     K      H
   0.327    0.142    0.401 

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: 546
Number of extensions: 37
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 428
Length of database: 420
Length adjustment: 32
Effective length of query: 396
Effective length of database: 388
Effective search space:   153648
Effective search space used:   153648
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 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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