GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpB in Caulobacter crescentus NA1000

Align 2-methylisocitrate lyase; 2-MIC; MICL; (2R,3S)-2-methylisocitrate lyase; EC 4.1.3.30 (characterized)
to candidate CCNA_01980 CCNA_01980 PEP phosphonomutase related enzyme

Query= SwissProt::P77541
         (296 letters)



>FitnessBrowser__Caulo:CCNA_01980
          Length = 255

 Score = 83.2 bits (204), Expect = 6e-21
 Identities = 72/222 (32%), Positives = 111/222 (50%), Gaps = 21/222 (9%)

Query: 9   AFRAALTKENPLQIVGTINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVL 68
           AFRA L  E    +    +A  A   +R G++A+  +  G+A  ++G  D G  T D+V+
Sbjct: 11  AFRA-LHAEGCFVLPNPWDAGGARRLERRGFKALASTSAGMA-WAMGRDD-GQVTRDEVI 67

Query: 69  TDIRRITDVCSLPLLVDADIGFGSSAFNVARTVKSMIKAGAAGLHIEDQVGAKRCGHRPN 128
             +R +     LP+  D + GFG +   VA +V   I+AG AGL IED  G++       
Sbjct: 68  AHLRTLCSATELPVNADFENGFGETPAEVAESVTLAIQAGVAGLSIEDWSGSE------- 120

Query: 129 KAIVSKEEMVDRI---RAAVDAKTDPDFVIMARTDAL--AVEGLDAAIERAQAYVEAGAE 183
             +   E  VDR+   RAA+DA +  D +++ART+        L   +ER  AY  AGA+
Sbjct: 121 --LYPLEVAVDRLKAARAAIDA-SGQDVILVARTEGYLRGCRDLQPTLERLGAYAAAGAD 177

Query: 184 MLFPEAITELAMYRQFADAVQVPILANITEFGATPLFTTDEL 225
            L+  A+++ A  +   DAV  P   N+  +G  P  T + L
Sbjct: 178 CLYAPAVSDPAEIKAIVDAV-APKPVNVLLWG--PEMTVESL 216


Lambda     K      H
   0.319    0.133    0.369 

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: 144
Number of extensions: 8
Number of successful extensions: 2
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: 296
Length of database: 255
Length adjustment: 25
Effective length of query: 271
Effective length of database: 230
Effective search space:    62330
Effective search space used:    62330
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: 47 (22.7 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