Alignments for a candidate for mcmA in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcmA in Caulobacter crescentus NA1000

Align Methylmalonyl-CoA mutase; MCM; EC 5.4.99.2 (characterized)
to candidate CCNA_03177 CCNA_03177 methylmalonyl-CoA mutase MeaA-like protein

Query= SwissProt::P27253
         (714 letters)



>FitnessBrowser__Caulo:CCNA_03177
          Length = 662

 Score =  410 bits (1055), Expect = e-119
 Identities = 260/656 (39%), Positives = 364/656 (55%), Gaps = 32/656 (4%)

Query: 72  PWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLATHRGYDSDNPRVAGDVGKAGVA 131
           PW  R YAG STA++SNA YR NLA GQ GLSVAFDL T  GYD D+    G+VGK GV 
Sbjct: 13  PWIFRTYAGHSTAEKSNALYRANLAKGQTGLSVAFDLPTQTGYDPDHILARGEVGKVGVP 72

Query: 132 IDTVEDMKVLFDQIPLDKMSVSMTMNGAVLPVLAFYIVAAEEQGVTPDKLTGTIQNDILK 191
           I  + DM+ LF +IPL+KM+ SMT+N     +LA Y+  A+EQG     L GT QND++K
Sbjct: 73  ISHLGDMRQLFSEIPLEKMNTSMTINAPAAWLLAMYVALADEQGADRKLLQGTTQNDLIK 132

Query: 192 EYLCRNTYIYPPKPSMRIIADIIAWCSGNMPRFNTISISGYHMGEAGANCVQQVAFTLAD 251
           EYL R TYI+PP PS+R+I D+IAWC   +P++N +++  YH+ EAGA   Q++AF LA 
Sbjct: 133 EYLSRGTYIFPPGPSLRLIGDMIAWCYREVPKWNPMNVCSYHLQEAGATPEQELAFALAT 192

Query: 252 GIEYIKAAISAGLKIDD-----FAPRLSFFFGIGMDLFMNVAMLRAARYLWSE-AVSGFG 305
            I  +   + AG ++ D      A R+SFF   G+     +  +R+   LW +  +  +G
Sbjct: 193 AISVLD-TVKAGGQVPDEDFEIVASRISFFVNAGVRFVTELCKMRSFTKLWDQILLERYG 251

Query: 306 AQDPKSLALRTHCQTSGWSLTEQDPYNNVIRTTIEALAATL---GGTQSLHTNAFDEALG 362
            QDPK+   R   Q +   LTEQ P NNV R  IEALA TL      ++L   A++EALG
Sbjct: 252 VQDPKARRFRYGVQVNSLGLTEQQPENNVYRILIEALAVTLSKDARCRALQLPAWNEALG 311

Query: 363 LPTDFSARIARNTQIIIQEESELCRTVDPLAGSYYIESLTDQIVKQARAIIQQIDEAGGM 422
           LP  F  + +   Q ++  E++L    D   GS+ +E+   ++ K A A +  IDE GG 
Sbjct: 312 LPRPFDQQWSLRLQQVLAYETDLLEYEDLFDGSHVVEAKVAELSKGALAQLTLIDEMGGA 371

Query: 423 AKAIEAGLPKRMIEEASAREQSLIDQGKRVIVGVNKYKLDHEDETDVLE-----IDNVMV 477
             AI+    K  +  ++A+    ++ G+  +VGVN++    E E   L      I+ V  
Sbjct: 372 QNAID--YMKSELVASNAKRVRAVETGEMTVVGVNRWT---ETEASPLSAGESAIETVDP 426

Query: 478 RNEQIASLERIRA---TRDDAAVTAALNALTHAAQHNENLLAAAVNAARVRATLGEISDA 534
           R E    +ERI+A    RD  AV AAL AL  AA+   N++  ++ AA+   T GE S A
Sbjct: 427 RLE-AGVVERIKAWREARDAVAVEAALAALKAAAREGRNVMEPSIAAAKAGVTTGEWSGA 485

Query: 535 LEVAFDRYLVPSQCVTGVIAQSYHQSEKSASEFDAIVAQTEQFLADNGRRPRILIAKMGQ 594
           L   F  Y  P    TGV   +   S   A + +A+  + E+     GR    L+ K G 
Sbjct: 486 LREVFGEYRGP----TGV---AVVVSTGEAEDVEAVKREVERVSELLGRTLTYLVGKPGL 538

Query: 595 DGHDRGAKVIASAYSDLGFDVDLSPMFSTPEEIARLAVENDVHVVGASSLAAGHKTLIPE 654
           DGH  GA+ IA+     G +V    + STPEEI R A E+  HVVG S L+  H  L+ E
Sbjct: 539 DGHSNGAEQIATRARACGMEVVYDGIRSTPEEIVRRAKESRAHVVGLSILSGSHLDLVQE 598

Query: 655 LVEALKKWGREDICVVAGGVIPPQDYAFLQERGVAAIYGPGTPMLDSVR-DVLNLI 709
           ++  ++  G   I VVAGG+IPP+D   L++ GVA IY P    +  +  DV+ L+
Sbjct: 599 VIRVMRAEGLGHIPVVAGGIIPPEDALILKQMGVARIYTPKDFKITQIMGDVVKLV 654


Lambda     K      H
   0.318    0.133    0.381 

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: 992
Number of extensions: 54
Number of successful extensions: 6
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: 714
Length of database: 662
Length adjustment: 39
Effective length of query: 675
Effective length of database: 623
Effective search space:   420525
Effective search space used:   420525
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 (21.7 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources