Alignments for a candidate for mcm-large in Ruegeria conchae TW15

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcm-large in Ruegeria conchae TW15

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_010441942.1 G7G_RS0113370 methylmalonyl-CoA mutase

Query= BRENDA::P11653
         (728 letters)



>NCBI__GCF_000192475.1:WP_010441942.1
          Length = 708

 Score =  815 bits (2105), Expect = 0.0
 Identities = 416/682 (60%), Positives = 514/682 (75%), Gaps = 6/682 (0%)

Query: 39  ETAEQIPVGTLFNEDVYKDMDWLDTYAGIPPFVHGPYATMYAFRPWTIRQYAGFSTAKES 98
           ET E I V  L+ +D   D+  + +  G  PF  G  ATMYA RPWTIRQYAGFSTA+ES
Sbjct: 26  ETLEGIDVKPLYTQDDTADLPHMGSLPGFGPFTRGVKATMYAGRPWTIRQYAGFSTAEES 85

Query: 99  NAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPRVAGDVGMAGVAIDSIYDMRELFAGIPL 158
           NAFYRRNLAAGQ+G+SVAFDL THRGYDSD+PRV GDVG AGVAIDS+ DM+ LF GIPL
Sbjct: 86  NAFYRRNLAAGQQGVSVAFDLATHRGYDSDHPRVVGDVGKAGVAIDSVEDMKILFDGIPL 145

Query: 159 DQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQNDILKEFMVRNTYIYPPQPSM 218
           D++SVSMTMNGAV+P+LA ++V  EEQG     L+GTIQNDILKEFMVRNTYIYPP+PSM
Sbjct: 146 DKVSVSMTMNGAVIPVLASFIVAGEEQGHDKAVLSGTIQNDILKEFMVRNTYIYPPEPSM 205

Query: 219 RIISEIFAYTSANMPKWNSISISGYHMQEAGATADIEMAYTLADGVDYIRAGESVGLNVD 278
           +IIS+I  +TS  MPK+NSISISGYHMQEAGA    E+AYTLADG +Y+RA    G++VD
Sbjct: 206 KIISDIIEFTSNEMPKFNSISISGYHMQEAGANLVQELAYTLADGREYVRAATQSGMDVD 265

Query: 279 QFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKLVHQFGPKNPKSMSLRTHSQTSGWSLTA 338
           +FA RLSFF+ IGMNFFME+AKLRAAR LW +++ +FG K+ +S  LRTH QTSG SL  
Sbjct: 266 KFAGRLSFFFAIGMNFFMEIAKLRAARTLWHRVMTEFGAKSERSKMLRTHCQTSGVSLQE 325

Query: 339 QDVYNNVVRTCIEAMAATQGHTQSLHTNSLDEAIALPTDFSARIARNTQLFLQQESGTTR 398
           QD YNNVVRT  EAM+A  G TQSLHTN+LDEAIALPTDFSARIARNTQL LQ+E+G T 
Sbjct: 326 QDPYNNVVRTAYEAMSAVLGGTQSLHTNALDEAIALPTDFSARIARNTQLVLQEETGVTD 385

Query: 399 VIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAIEKGIPKMRIEEAAARTQARID 458
           V+DP +GS YVE LT +L  KAW  ++EVE++GGM KA+  G+PK+RIEE+AAR QA ID
Sbjct: 386 VVDPLAGSYYVESLTNELVEKAWALMEEVEEMGGMTKAVASGMPKLRIEESAARRQAMID 445

Query: 459 SGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKLVKLRAERDPEKVKAALDKITWA 518
            G + ++GVNKYR E E P+D+L VDN  V   Q A+L ++RA RD    + ALD +T  
Sbjct: 446 RGEEVIVGVNKYRKEQEDPIDILDVDNVAVREAQVARLERIRATRDEAACQQALDALTTT 505

Query: 519 AGNPDDKDPDRNLLKLCIDAGRAMATVGEMSDALEKVFGRYTAQIRTISGVYSKEVKNTP 578
           A          NLL   ++A RA A+VGE+S A+EK FGR+ A+++T++GVY    +   
Sbjct: 506 ARE------GGNLLAAAVEAARARASVGEISMAMEKEFGRHRAEVKTLAGVYGAAYEGDE 559

Query: 579 EVEEARELVEEFEQAEGRRPRILLAKMGQDGHDRGQKVIATAYADLGFDVDVGPLFQTPE 638
                ++ +E+F +AEGRRPR+L+ KMGQDGHDRG KVIATA+AD+GFDVDVGPLFQTP 
Sbjct: 560 GFAAIQKSIEKFAEAEGRRPRLLVVKMGQDGHDRGAKVIATAFADIGFDVDVGPLFQTPA 619

Query: 639 ETARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKLGRPDILITVGGVIPEQDFDELRK 698
           E A+ AV+ DVHV+G+SS A GH TL P L +EL K G  DI++  GGVIP+QD+  L  
Sbjct: 620 EAAQDAVDNDVHVIGISSQAAGHKTLAPQLVEELKKAGAEDIIVICGGVIPQQDYQFLYD 679

Query: 699 DGAVEIYTPGTVIPESAISLVK 720
            G   I+ PGT IP++A  +++
Sbjct: 680 HGVKAIFGPGTNIPDAAQDILR 701


Lambda     K      H
   0.317    0.133    0.389 

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: 1275
Number of extensions: 35
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: 728
Length of database: 708
Length adjustment: 40
Effective length of query: 688
Effective length of database: 668
Effective search space:   459584
Effective search space used:   459584
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: 55 (25.8 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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

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 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