GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpC in Sedimenticola selenatireducens DSM 17993

Align 2-methylcitrate synthase; 2-MCS; MCS; Citrate synthase; EC 2.3.3.5; EC 2.3.3.16 (characterized)
to candidate WP_029132263.1 A3GO_RS0103745 citrate synthase

Query= SwissProt::O34002
         (379 letters)



>NCBI__GCF_000428045.1:WP_029132263.1
          Length = 431

 Score =  202 bits (514), Expect = 1e-56
 Identities = 136/393 (34%), Positives = 199/393 (50%), Gaps = 27/393 (6%)

Query: 5   TIHKGLAGVTADVTAISKVNSDTNSLLYRGYPVQELAAKCSFEQVAYLLWNSELPNDSEL 64
           T   G     +  +AI+ ++ D   L YRGYP+++LA + SF +VAYLL   +LP+  E+
Sbjct: 44  TYDPGFVATASCRSAITYIDGDKGILRYRGYPIEQLAKEASFLEVAYLLMYGDLPSAEEM 103

Query: 65  KAFVNFERSHRKLDENVKGAIDLLSTACHPMDVARTAVSVLGANHARAQD-SSPEANLEK 123
             F N  R H  + E +K   D      HPM +    V  L A +  + D ++P      
Sbjct: 104 AKFDNTIRHHTMIKETLKNFFDGFQYDAHPMGIMVGVVGSLSAFYHDSLDINNPRHREIS 163

Query: 124 AMSLLATFPSVVAYDQRRRRGEELIEPREDLDYSANFLWMTFG---EEAAPE--VVEAFN 178
           A  L+A  P++ A   +   GE  I PR DLDY  NFL M F    EE +P+   V+A N
Sbjct: 164 AHRLIAKMPTIAAASYKHNVGEPFIYPRNDLDYCENFLRMMFSNPCEEYSPDPVAVKAIN 223

Query: 179 VSMILYAEHSFNASTFTARVITSTLADLHSAVTGAIGALKGPLHGGANEAVMHTFEEIG- 237
              IL+A+H  NAST T R+  S+ A+  + +   I +L GP HGGANEAV+    EIG 
Sbjct: 224 TLFILHADHEQNASTSTVRLSGSSQANPFACIAAGIASLWGPSHGGANEAVLDMLNEIGD 283

Query: 238 -IRKDESLDEAATRSKAWMVDALAQKKKVMGFGHRVYKNGDSRVPTMKSALDAMI---KH 293
             + D+ + +A  +   +         ++MGFGHRVYKN D R   ++     ++   K 
Sbjct: 284 VSQIDKYIAKAKDKDDPF---------RLMGFGHRVYKNFDPRATLIREVCHEVLENMKD 334

Query: 294 YDRPEMLGLYNGLEAAMEE----AKQIKPNLDYPAGPTYNLMGFDTEMFTPLFIAARITG 349
            D P         + A+E+     +++ PN+D+ +G  Y  +G  T MFT +F  AR  G
Sbjct: 335 NDNPLFELALRLEQVALEDEYFVERKLYPNVDFYSGIIYQALGIPTSMFTVMFAVARTVG 394

Query: 350 WTAHIMEQVADN--ALIRPLSEYNG-PEQRQVP 379
           W AH ME + D    + RP   Y G P++  VP
Sbjct: 395 WVAHWMEMMDDPEFRIGRPRQLYTGAPKRDYVP 427


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: 355
Number of extensions: 15
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 Apr 09 2024. 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