GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpC in Rhodobacter ovatus JA234

Align 2-methylcitrate synthase; 2-MCS; MCS; Citrate synthase; EC 2.3.3.5; EC 2.3.3.16 (characterized)
to candidate WP_097029597.1 CRO07_RS05055 citrate (Si)-synthase

Query= SwissProt::O34002
         (379 letters)



>NCBI__GCF_900207575.1:WP_097029597.1
          Length = 428

 Score =  184 bits (466), Expect = 5e-51
 Identities = 130/398 (32%), Positives = 189/398 (47%), Gaps = 44/398 (11%)

Query: 5   TIHKGLAGVTADVTAISKVNSDTNSLLYRGYPVQELAAKCSFEQVAYLLWNSELPNDSEL 64
           T   G     A  + I+ ++ D   LLYRGYP+++LA +  + +V YLL   ELPN ++ 
Sbjct: 41  TYDPGFTSTAACESTITYIDGDKGELLYRGYPIEQLAERSHYLEVCYLLLYGELPNAAQA 100

Query: 65  KAFVNFERSHRKLDENVKGAIDLLSTACHPMDVARTAVSVLGANHARAQDS----SPEAN 120
             F      H  L E +           HPM    T V V+GA  A   DS     P   
Sbjct: 101 ADFEYRITRHTMLHEQIHYFFRGFRRDSHPM---ATMVGVVGAMSAFYHDSLDINDPWQR 157

Query: 121 LEKAMSLLATFPSVVAYDQRRRRGEELIEPREDLDYSANFLWMTFGEEAAPEVV-----E 175
              A+ ++A  P++ A   +   G+    P+  LDY+ NFL M F   A P  V     +
Sbjct: 158 EVAAVRMIAKLPTIAAMAYKYSLGQPFNYPQNHLDYAGNFLHMCFAVPAEPYTVNPILSK 217

Query: 176 AFNVSMILYAEHSFNASTFTARVITSTLADLHSAVTGAIGALKGPLHGGANEAVMHTFEE 235
           A +  M+L+A+H  NAST T R+  S+ A+  + +   I  L GP HGGAN+A +    E
Sbjct: 218 AMDRIMMLHADHEQNASTSTVRLAGSSGANPFACIAAGIACLWGPAHGGANQACLEMLRE 277

Query: 236 IGI--RKDESLDEAATRSKAWMVDALAQKKKVMGFGHRVYKNGDSRVPTMKSALDAMIKH 293
           IG   R  E +  A  +   +         ++MGFGHRVYKN D R   MK + D ++  
Sbjct: 278 IGTVDRIPEYIKRAKDKDDPF---------RLMGFGHRVYKNFDPRAKVMKESADEVL-- 326

Query: 294 YDRPEMLGLYNG--LEAAME-----------EAKQIKPNLDYPAGPTYNLMGFDTEMFTP 340
                +LG+ N   L+ A E            +K++ PN+D+ +G   + MGF T MFTP
Sbjct: 327 ----GLLGIENNPTLQVAKELERIALEDDYFVSKKLYPNVDFYSGIILDAMGFPTSMFTP 382

Query: 341 LFIAARITGWTAHIMEQVAD--NALIRPLSEYNGPEQR 376
           +F  +R  GW +   E + D    + RP   Y G +QR
Sbjct: 383 IFAISRTVGWISQWKEMIGDPTQRIGRPRQLYKGEKQR 420


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: 391
Number of extensions: 18
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: 428
Length adjustment: 31
Effective length of query: 348
Effective length of database: 397
Effective search space:   138156
Effective search space used:   138156
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 24 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