GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpC in Sedimenticola selenatireducens DSM 17993

Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate WP_029131970.1 A3GO_RS0101980 citrate synthase

Query= reanno::pseudo6_N2E2:Pf6N2E2_6062
         (375 letters)



>NCBI__GCF_000428045.1:WP_029131970.1
          Length = 430

 Score =  184 bits (466), Expect = 5e-51
 Identities = 120/364 (32%), Positives = 188/364 (51%), Gaps = 22/364 (6%)

Query: 26  GQSGAGLTYRGYDVRDLAADAQFEEVAYLLLYGELPTQAQLDAYTGKLRQLRDLPQALKE 85
           G+ G  L YRG  +  L     F EVA +L++GELP +AQ + ++  L    +L + +K 
Sbjct: 61  GEKGI-LRYRGISLDALEHHPNFVEVALMLIFGELPNKAQYERFSTSLTNNANLDEDMKH 119

Query: 86  VLERIPADAHPMDVMRTGCSFLGNLEPE----QDFSQQHDKTDRLLAAFPAIMCYWYRFS 141
                P  A PM V+    S L    PE    +D +Q      RL++    +  Y YR S
Sbjct: 120 HFAGFPRSAPPMAVLSAMISTLSCFHPEFLELEDATQVERAAARLISKVRTLAAYAYRRS 179

Query: 142 HQGQRIECVTDEVSIGGHFLHLLHGKKPSELHV-----KVMNVSLILYAEHEFNASTFTA 196
            +G         +    +FLH++  +   +  +       +N+ LIL+A+HE N ST T 
Sbjct: 180 -RGLPYNYPDPSLPYVSNFLHMMFSEPYRQYTIDDDVLSALNMVLILHADHEQNCSTSTV 238

Query: 197 RVCASTLSDLFSCITAAIGSLRGPLHGGANEAAMEMIERFSSPQEAIEGTLGMLARKD-- 254
           R+  S+ ++LF+   A + +L GPLHGGAN A +EM+E   +     E  + +   KD  
Sbjct: 239 RMVGSSGANLFASCAAGVSALWGPLHGGANMAVIEMLEAIHNGNMTAEEYVALAKDKDSP 298

Query: 255 -KIMGFGHAIYKDNDPRNEVIKGWSKKLADEVG--DTVLFPVSE----AIDKTMWEQKKL 307
            ++MGFGH +Y++ DPR  +++  S+KL + +G  D +L    +    A+  + +  +KL
Sbjct: 299 VRLMGFGHRVYRNFDPRATILREVSEKLLERMGKKDPLLSIARKLEEIALKDSYFIDRKL 358

Query: 308 FPNADFYHASAYHFMGIPTKLFTPIFVCSRLTGWAAHVFEQR--ANNRIIRPSAEYTGVE 365
           +PN DFY       +GIPT +FT IF   RL GW AH +EQ+  A+ +I RP   Y G +
Sbjct: 359 YPNVDFYSGIILRAIGIPTNMFTVIFAIGRLPGWIAHWYEQKRQADGKIWRPRQVYIGNK 418

Query: 366 QRKF 369
           Q  +
Sbjct: 419 QSAY 422


Lambda     K      H
   0.321    0.135    0.406 

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: 363
Number of extensions: 18
Number of successful extensions: 4
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: 375
Length of database: 430
Length adjustment: 31
Effective length of query: 344
Effective length of database: 399
Effective search space:   137256
Effective search space used:   137256
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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