GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpC in Rhodococcus qingshengii djl-6-2

Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate WP_003940025.1 C1M55_RS23230 citrate synthase 2

Query= BRENDA::Q9I5E3
         (375 letters)



>NCBI__GCF_002893965.1:WP_003940025.1
          Length = 375

 Score =  160 bits (404), Expect = 7e-44
 Identities = 117/375 (31%), Positives = 186/375 (49%), Gaps = 43/375 (11%)

Query: 10  AGLRGQVAGQTALSTVGQEGAGLTYRGYDVRDLAAAAI-FEEVAYLLLYGELPNKQQLDA 68
           +GL G VA  + ++   ++G  L YRG D+ DL    + F  V  LL+ G          
Sbjct: 13  SGLEGVVAFTSDIAEPDKDGGALRYRGVDIEDLVGQRVTFGNVWALLVDGRFGP------ 66

Query: 69  YLKKLQGQRDLPQALKEVLERIPKDAHPMDV---MRTGASVLGTL---EPELSFDQQRDV 122
                     LP A     E  P   H  DV   ++ G ++L  +   +P L  D +   
Sbjct: 67  ---------GLPPA-----EPFPLPIHTGDVRVDVQAGLAMLAPIWGYQPLLDIDDET-A 111

Query: 123 ADRLLAAFPAIMTYW-------YRFTHEGQRIDCNSDEPTIGGHFLALLHGKKPSELHVK 175
            D+L  A    ++Y        Y+      RID   +  T+   F+    G+ P   HV+
Sbjct: 112 RDQLARASVMALSYVAQSARGIYQPAVPQSRID---EAKTVTERFMVRWKGE-PDPAHVE 167

Query: 176 VMNVSLILYAEHEFNASTFTARVCASTLSDLYSCVTGAIGSLRGPLHGGANEAAMELIER 235
            ++   +  AEH  NASTFTARV AST +D+ + ++GAIG++ GPLHGGA    + +IE 
Sbjct: 168 AIDAYWVSAAEHGMNASTFTARVIASTGADVAASLSGAIGAMSGPLHGGAPARVLPMIEE 227

Query: 236 FSSPQEATAELLKMLERKDKIMGFGHAIYKDSDPRNEVIKGWSKQLADEVGDKVLFAVSE 295
                +A A +  +L+RK+K+MGFGH +Y+  DPR  V++  +K+L +    +   A+ +
Sbjct: 228 TEKTGDARALVKGILDRKEKLMGFGHRVYRAEDPRARVLRATAKRL-NAPRYEAAAALEQ 286

Query: 296 AIDKTMWEQ---KKLFPNADFYHASAYHFMGIPTKLFTPIFVCSRTSGWTAHVFEQRANN 352
           A    + E+   + +  N +F+ A    F  +P  +   +F C RT+GW AH+ EQ+   
Sbjct: 287 AALAELRERRPDRAIETNVEFWAAVILDFAEVPAHMMPAMFTCGRTAGWCAHILEQKRLG 346

Query: 353 RIIRPSAEYTGVEQR 367
           +++RP+A YTG   R
Sbjct: 347 KLVRPAAIYTGPAPR 361


Lambda     K      H
   0.319    0.134    0.396 

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: 316
Number of extensions: 13
Number of successful extensions: 3
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: 375
Length adjustment: 30
Effective length of query: 345
Effective length of database: 345
Effective search space:   119025
Effective search space used:   119025
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 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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