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 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