GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpC in Dechlorosoma suillum PS

Align 2-methylcitrate synthase; 2-MCS; MCS; Citrate synthase; EC 2.3.3.5; EC 2.3.3.16 (characterized)
to candidate Dsui_2216 Dsui_2216 citrate synthase I, hexameric type

Query= SwissProt::O34002
         (379 letters)



>FitnessBrowser__PS:Dsui_2216
          Length = 431

 Score =  200 bits (509), Expect = 5e-56
 Identities = 132/391 (33%), Positives = 198/391 (50%), Gaps = 26/391 (6%)

Query: 5   TIHKGLAGVTADVTAISKVNSDTNSLLYRGYPVQELAAKCSFEQVAYLLWNSELPNDSEL 64
           T   G     +  + I+ ++ D   LLYRGYP+++LA  C+F +VAYLL N ELPN S+ 
Sbjct: 43  TYDSGFLSTASCKSKITFIDGDKGELLYRGYPIEQLAENCNFLEVAYLLKNGELPNASQK 102

Query: 65  KAFVNFERSHRKLDENVKGAIDLLSTACHPMDVARTAVSVLGANHARAQDSSPEANLEKA 124
            AF +  ++H  + E +           HPM V    V  L A +  A D S   +   +
Sbjct: 103 TAFEDTIKNHTMVHEQLAKFFSGFRRDAHPMAVMVGVVGALSAFYHEAMDFSDAEHRSIS 162

Query: 125 MS-LLATFPSVVAYDQRRRRGEELIEPREDLDYSANFLWMTFGE-----EAAPEVVEAFN 178
            + ++A  P++VA   +   G+  + PR DLDY+ANF+ M FG      +  P +V A +
Sbjct: 163 FNRIIAKMPTIVAMAYKYTTGQPFMYPRNDLDYTANFMHMMFGTPCETYKPNPVLVRALD 222

Query: 179 VSMILYAEHSFNASTFTARVITSTLADLHSAVTGAIGALKGPLHGGANEAVMHTFEEIG- 237
           +   L+A+H  NAST T R+  S+ A+  + ++  I  L GP HGGANEA +   EEIG 
Sbjct: 223 IIFTLHADHEQNASTSTVRLAGSSGANPFACISAGIACLWGPAHGGANEACLQMLEEIGD 282

Query: 238 -IRKDESLDEAATRSKAWMVDALAQKKKVMGFGHRVYKNGDSRVPTMKSALDAMIKH--Y 294
             R  E +  A  ++ ++         K+MGFGHRVYKN D R   M+   + ++K    
Sbjct: 283 VSRVGEYIARAKDKNDSF---------KLMGFGHRVYKNFDPRAKLMRQVCNDVLKELGL 333

Query: 295 DRPEMLGLYNGLE-AAMEE----AKQIKPNLDYPAGPTYNLMGFDTEMFTPLFIAARITG 349
           +   +  L   LE  A+E+     K++ PN+D+ +G     +G  T MFT +F  AR  G
Sbjct: 334 ENDRLFKLAMELEKIALEDPYFVEKKLYPNVDFYSGIVQKALGIPTSMFTCIFALARTVG 393

Query: 350 WTAHIMEQVAD--NALIRPLSEYNGPEQRQV 378
           W     E + D    + RP   Y G  +R V
Sbjct: 394 WMTQWEEMITDPEYKIGRPRQLYIGAAKRDV 424


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: 381
Number of extensions: 14
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: 431
Length adjustment: 31
Effective length of query: 348
Effective length of database: 400
Effective search space:   139200
Effective search space used:   139200
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