GapMind for catabolism of small carbon sources

 

Alignments 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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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