Aligments for a candidate for mcm-large in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Aligments for a candidate for mcm-large in Dechlorosoma suillum PS

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate Dsui_0519 Dsui_0519 methylmalonyl-CoA mutase

Query= BRENDA::P11653
         (728 letters)



>FitnessBrowser__PS:Dsui_0519
          Length = 721

 Score =  861 bits (2225), Expect = 0.0
 Identities = 442/723 (61%), Positives = 546/723 (75%), Gaps = 11/723 (1%)

Query: 9   SVDLGNAPVP-ADAARRFEELAAKAGTGEA-----WETAEQIPVGTLFNEDVYKDMDWLD 62
           S D     +P +D    + + AAK+  G       W T E + V  L+ +   +D+ + D
Sbjct: 2   SADASKPQLPNSDNLDAWAKAAAKSAPGGDVNALNWITPEGLTVKPLYTKKDVEDLPYAD 61

Query: 63  TYAGIPPFVHGPYATMYAFRPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLPTH 122
           T  G  P++ GP ATMYA RPWTIRQYAGFSTA+ESNAFYR+ LAAG +G+SVAFDL TH
Sbjct: 62  TLPGFAPYLRGPQATMYAVRPWTIRQYAGFSTAEESNAFYRKALAAGGQGVSVAFDLATH 121

Query: 123 RGYDSDNPRVAGDVGMAGVAIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVTA 182
           RGYDSDNPRV GDVG AGVAIDS+ DM+ LF GIPLD++SVSMTMNGAVLPILA Y+V A
Sbjct: 122 RGYDSDNPRVLGDVGKAGVAIDSVEDMKILFDGIPLDKISVSMTMNGAVLPILAGYIVAA 181

Query: 183 EEQGVKPEQLAGTIQNDILKEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISG 242
           EEQGV  EQL+GTIQNDILKEFMVRNTYIYPP+PSM+IIS+IF YT+ +MPK+NSISISG
Sbjct: 182 EEQGVSQEQLSGTIQNDILKEFMVRNTYIYPPKPSMKIISDIFGYTAQHMPKFNSISISG 241

Query: 243 YHMQEAGATADIEMAYTLADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLR 302
           YH+QEAGA   IE+A+TLADG++Y+R G + GL+VD FA RLSFFW +GMNF++E+AK+R
Sbjct: 242 YHIQEAGANQAIELAFTLADGMEYVRTGIASGLDVDAFAGRLSFFWAVGMNFYLEIAKMR 301

Query: 303 AARMLWAKLVHQFGPKNPKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHTQS 362
           A RMLW +++ QF PK+ KS+ LRTHSQTSGWSLT QD YNNVVRT IEAMAA  G TQS
Sbjct: 302 AGRMLWHRIMSQFNPKSAKSLMLRTHSQTSGWSLTEQDPYNNVVRTTIEAMAAVFGGTQS 361

Query: 363 LHTNSLDEAIALPTDFSARIARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKAWG 422
           LHTN+LDEAIALPT+FSARIARNTQL +Q+E+    V+DPW+GS  +E+LT D+A KAW 
Sbjct: 362 LHTNALDEAIALPTEFSARIARNTQLIIQEETHICNVVDPWAGSYMMEKLTQDMADKAWS 421

Query: 423 HIQEVEKVGGMAKAIEKGIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLK 482
            IQE+E +GGM KA+E G  KM++E  AA  QARIDSG+  ++GVNKY+L  E  +D+L 
Sbjct: 422 IIQEIEAMGGMTKAVESGWAKMQVETCAADKQARIDSGKDVIVGVNKYKLAKEDQIDILD 481

Query: 483 VDNSTVLAEQKAKLVKLRAERDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGRAM 542
           +DN  V   Q A+L K+RA RD   V+AALD +T  A     +  + NLL L + A R  
Sbjct: 482 IDNHAVREAQIARLKKIRASRDSAAVQAALDALTQCA-----ESGEGNLLDLSVKAIRLR 536

Query: 543 ATVGEMSDALEKVFGRYTAQIRTISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPRILL 602
           ATVGE+SDALEKVFGR+ A  +TISGVY   V+     E  +  + +F + EGRRPRI++
Sbjct: 537 ATVGEVSDALEKVFGRFRANNQTISGVYGGVVEGQESWESIKADIAKFAEEEGRRPRIMI 596

Query: 603 AKMGQDGHDRGQKVIATAYADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGGHL 662
           AK+GQDGHDRG KV+ATA+ADLGFD+D+GPLFQTPEE ARQAVE DVH +GVSSLA GH 
Sbjct: 597 AKLGQDGHDRGAKVVATAFADLGFDIDMGPLFQTPEEAARQAVENDVHAIGVSSLAAGHK 656

Query: 663 TLVPALRKELDKLGRPDILITVGGVIPEQDFDELRKDGAVEIYTPGTVIPESAISLVKKL 722
           TL+PAL   L + G  DI++  GGVIP QD+D L   GA  I+ PGT I +SA  +++++
Sbjct: 657 TLLPALVNSLKEQGADDIIVFAGGVIPAQDYDTLYAAGAKAIFGPGTRIEDSAKRVLEEI 716

Query: 723 RAS 725
           R S
Sbjct: 717 RKS 719


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: 1361
Number of extensions: 47
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: 721
Length adjustment: 40
Effective length of query: 688
Effective length of database: 681
Effective search space:   468528
Effective search space used:   468528
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 17 2021. The underlying query database was built on Sep 17 2021.

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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, or view the source code.

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