GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mcmA in Paraburkholderia bryophila 376MFSha3.1

Align Methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate H281DRAFT_01038 H281DRAFT_01038 methylmalonyl-CoA mutase

Query= reanno::PS:Dsui_0519
         (721 letters)



>FitnessBrowser__Burk376:H281DRAFT_01038
          Length = 703

 Score =  651 bits (1680), Expect = 0.0
 Identities = 334/663 (50%), Positives = 448/663 (67%), Gaps = 2/663 (0%)

Query: 45  VKPLYTKKDVEDLPYADTLPGFAPYLRGPQATMYAVRPWTIRQYAGFSTAEESNAFYRKA 104
           +K +YT+ D+E + + D++PG AP++RGP A+MY  +PWTIRQYAG++ A ++N  +R A
Sbjct: 14  LKRVYTRADIEGIAHIDSMPGEAPFVRGPFASMYTQKPWTIRQYAGYAQASDTNLAFRTA 73

Query: 105 LAAGGQGVSVAFDLATHRGYDSDNPRVLGDVGKAGVAIDSVEDMKILFDGIPLDKISVSM 164
           LA G QG+SVAFDL T RGYDSD+P V  DVG  GVAID+VEDM  LF+ I LD++SVSM
Sbjct: 74  LAEGAQGLSVAFDLPTQRGYDSDDPAVSADVGMTGVAIDTVEDMTRLFEDIALDRVSVSM 133

Query: 165 TMNGAVLPILAGYIVAAEEQGVSQEQLSGTIQNDILKEFMVRNTYIYPPKPSMKIISDIF 224
           TMNGAVLP+LA +IVAAEE GV   QL GTIQNDILKEFMVRNT I+ P+PS++I +D+ 
Sbjct: 134 TMNGAVLPVLAAFIVAAEESGVGASQLRGTIQNDILKEFMVRNTSIFAPEPSLRIAADVV 193

Query: 225 GYTAQHMPKFNSISISGYHIQEAGANQAIELAFTLADGMEYVRTGIASGLDVDAFAGRLS 284
            Y  +++P+FN++S+SGYH QEAGA+  +ELA T+A+  +Y+      G+  D    R+S
Sbjct: 194 EYLGKNVPRFNALSVSGYHFQEAGADPVLELALTMANARKYITALAGRGMQADDVCQRMS 253

Query: 285 FFWAVGMNFYLEIAKMRAGRMLWHRIMSQFNPKSAKSLMLRTHSQTSGWSLTEQDPYNNV 344
           FF+ VGM+FY+EIAK+RA R+LW  I S     S ++  LR H QTSGWSLT Q P NNV
Sbjct: 254 FFFGVGMDFYVEIAKLRAARILWADIASASGATSDRARALRMHCQTSGWSLTAQKPMNNV 313

Query: 345 VRTTIEAMAAVFGGTQSLHTNALDEAIALPTEFSARIARNTQLIIQEETHICNVVDPWAG 404
           VRTT+EA+AAVFGGTQSLHTN  DEA++LP   ++R+AR+TQL++Q ET +C+VVDPWAG
Sbjct: 314 VRTTVEALAAVFGGTQSLHTNGYDEALSLPCADASRLARDTQLVLQHETGVCDVVDPWAG 373

Query: 405 SYMMEKLTQDMADKAWSIIQEIEAMGGMTKAVESGWAKMQVETCAADKQARIDSGKDVIV 464
           SYMMEK T ++  KA +++ EIE  GG+   VESGW + Q+   A + QA I+S K  +V
Sbjct: 374 SYMMEKFTAEICQKALTVMAEIERRGGVVDVVESGWVRDQIHRSALNIQAEIESRKRTVV 433

Query: 465 GVNKYKL-AKEDQIDILDIDNHAVREAQIARLKKIRASRDSAAVQAALDALTQCAESGEG 523
           GVN +     ED  +   +D   VR  Q  RL  I+A RD   V+  LDALT+ A   +G
Sbjct: 434 GVNDFMTGCDEDLGEPQTVDGRRVRVLQTQRLAHIKARRDPTRVRNTLDALTRAARGRDG 493

Query: 524 NLLDLSVKAIRLRATVGEVSDALEKVFGRFRANNQTISGVYGGVVEGQESWESIKADIAK 583
           NLL+L+V  +R RATVGE + ALE V+ R++     +   YG  +E  + W+     +A 
Sbjct: 494 NLLELTVACMRARATVGECTQALEAVWPRYQIGLPLLRDHYGANLESDKDWQDTCRAVAD 553

Query: 584 FAEEEGRRPRIMIAKLGQDGHDRGAKVVATAFADLGFDIDMGPLFQTPEEAARQAVENDV 643
             +  GR PR++IAKLGQDGHDRGA+++A A +D GF +  G +F +P +  + A    V
Sbjct: 554 ATKRLGRAPRVLIAKLGQDGHDRGARIIAAALSDAGFAVFTGSMFASPSDTVQLAEGERV 613

Query: 644 HAIGVSSLAAGHKTLLPALVNSLKEQGADDIIVFAGGVIPAQDYDTLYAAGAKAIFGPGT 703
             IGVSSLA     L+ AL + L  +G   I +  GG+I       L  +G  A F  GT
Sbjct: 614 DVIGVSSLAGAQNDLITALHDQLTVRGL-RIPIVVGGIIDQASQLVLRRSGVAACFPAGT 672

Query: 704 RIE 706
            I+
Sbjct: 673 PIK 675


Lambda     K      H
   0.317    0.132    0.380 

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: 1122
Number of extensions: 39
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: 721
Length of database: 703
Length adjustment: 39
Effective length of query: 682
Effective length of database: 664
Effective search space:   452848
Effective search space used:   452848
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 (21.6 bits)
S2: 55 (25.8 bits)

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

Links

Downloads

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:

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