GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpC in Pseudomonas simiae WCS417

Align 2-methylcitrate synthase; 2-MCS; MCS; Citrate synthase; EC 2.3.3.5; EC 2.3.3.16 (characterized)
to candidate GFF1744 PS417_08870 type II citrate synthase

Query= SwissProt::O34002
         (379 letters)



>FitnessBrowser__WCS417:GFF1744
          Length = 429

 Score =  191 bits (486), Expect = 3e-53
 Identities = 131/394 (33%), Positives = 197/394 (50%), Gaps = 33/394 (8%)

Query: 5   TIHKGLAGVTADVTAISKVNSDTNSLLYRGYPVQELAAKCSFEQVAYLLWNSELPNDSEL 64
           T   G     +  + I+ ++ D   LL+RGYP+++LA K  + +  YLL N ELP   + 
Sbjct: 42  TFDPGFMSTASCESKITYIDGDNGILLHRGYPIEQLAEKSDYLETCYLLLNGELPTAEQK 101

Query: 65  KAFVNFERSHRKLDENVKGAIDLLSTACHPMDVARTAVSVLGANHARAQD-SSPEANLEK 123
             FV+  ++H  + E +K   +      HPM V    V  L A +  + D ++P+     
Sbjct: 102 AQFVSTVKNHTMVHEQLKTFFNGFRRDAHPMAVMCGVVGALSAFYHDSLDINNPQHREIS 161

Query: 124 AMSLLATFPSVVAYDQRRRRGEELIEPREDLDYSANFLWMTFG-----EEAAPEVVEAFN 178
           A+ L+A  P++ A   +   G+ ++ PR DL Y+ NFL M F      +  +P + +A +
Sbjct: 162 AIRLVAKMPTLAAMVYKYSMGQPMMYPRNDLTYAENFLHMMFNTPCEIKPISPVLAKAMD 221

Query: 179 VSMILYAEHSFNASTFTARVITSTLADLHSAVTGAIGALKGPLHGGANEAVMHTFEEIGI 238
              IL+A+H  NAST T R+  S+ A+  + +   I AL GP HGGANEAV+   +EIG 
Sbjct: 222 RIFILHADHEQNASTSTVRLAGSSGANPFACIAAGIAALWGPAHGGANEAVLTMLDEIG- 280

Query: 239 RKDESLDEAATRSKAWMVDALAQKKKVMGFGHRVYKNGDSRVPTMKSALDAMIKHYDRPE 298
               ++D+   ++K           K+MGFGHRVYKN D R   MK   D ++K      
Sbjct: 281 -DVSNIDKFIAKAK-----DKNDPFKLMGFGHRVYKNRDPRATVMKQTCDEVLKE----- 329

Query: 299 MLGLYNG--LEAAM--EE---------AKQIKPNLDYPAGPTYNLMGFDTEMFTPLFIAA 345
            LG+ N   LE AM  EE          + + PN+D+ +G     +G  T MFT +F  A
Sbjct: 330 -LGIKNDPQLELAMRLEEIALTDPYFIERSLYPNVDFYSGIILKAIGIPTSMFTVIFALA 388

Query: 346 RITGWTAHIMEQVADNALI-RPLSEYNGPEQRQV 378
           R  GW +H  E ++    I RP   Y G E R +
Sbjct: 389 RTVGWISHWKEMLSSPYKIGRPRQLYTGYESRDI 422


Lambda     K      H
   0.316    0.130    0.376 

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: 351
Number of extensions: 17
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: 379
Length of database: 429
Length adjustment: 31
Effective length of query: 348
Effective length of database: 398
Effective search space:   138504
Effective search space used:   138504
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 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:

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