GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuB in Sinorhizobium meliloti 1021

Align Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial; MCCase subunit alpha; 3-methylcrotonyl-CoA carboxylase 1; 3-methylcrotonyl-CoA carboxylase biotin-containing subunit; 3-methylcrotonyl-CoA:carbon dioxide ligase subunit alpha; EC 6.4.1.4 (characterized)
to candidate SM_b20756 SM_b20756 propionyl-CoA carboxylase subunit alpha

Query= SwissProt::Q99MR8
         (717 letters)



>FitnessBrowser__Smeli:SM_b20756
          Length = 670

 Score =  504 bits (1298), Expect = e-147
 Identities = 288/684 (42%), Positives = 402/684 (58%), Gaps = 29/684 (4%)

Query: 42  GGSITKVLIANRGEIACRVIRTAKKMGVQSVAVYSEADRNSMHVDMADEAYSIGPAPSQQ 101
           G    K+LIANRGEIACRVIRT K +G+ +VAVYS+ADR++MHV MADEA  IGP+PS Q
Sbjct: 2   GHMFKKILIANRGEIACRVIRTTKALGIPTVAVYSDADRDAMHVRMADEAVHIGPSPSSQ 61

Query: 102 SYLAMEKIIQVAKSSAAQAIHPGYGFLSENMEFAELCKQEGIIFIGPPSSAIRDMGIKST 161
           SY+ +E I+   + + A A+HPGYGFLSEN  FAE  +++G+ FIGPP  AI  MG K T
Sbjct: 62  SYIVIENILAAIRRTGADAVHPGYGFLSENAAFAEALEKDGVTFIGPPVRAIEAMGDKIT 121

Query: 162 SKSIMAAAGVPVVEGYHGKDQSDQCLREHAGKIGYPVMIKAVRGGGGKGMRIVRSEREFQ 221
           SK + A AGV  V G+ G  +        A +IG+PVMIKA  GGGGKGMRI  +ERE +
Sbjct: 122 SKKLAAEAGVFTVPGHMGLIEDADEAARIAAEIGFPVMIKASAGGGGKGMRIAWNEREAR 181

Query: 222 EQLESARREAKKSFNDDAMLIEKFVDTPRHVEVQVFGDHHGNAVYLFERDCSVQRRHQKI 281
           E  +S+R EAK SF DD + IEKFV  PRH+E+QV GD HGN +YL ER+CS+QRR+QK+
Sbjct: 182 EGFQSSRNEAKSSFGDDRIFIEKFVTEPRHIEIQVLGDKHGNILYLGERECSIQRRNQKV 241

Query: 282 IEEAPAPGINPEVRRKLGEAAVRAAKAVKYVGAGTVEFIMDSRHNFYFMEMNTRLQVEHP 341
           IEEAP+P ++ + RR +GE AV  AKAV Y  AGTVEFI+D+  NFYF+EMNTRLQVEHP
Sbjct: 242 IEEAPSPFLDEKTRRAMGEQAVALAKAVGYHSAGTVEFIVDAGRNFYFLEMNTRLQVEHP 301

Query: 342 VTEMITGTDLVEWQLRIAAGEKIPLSQEEIPLQGHAFEARIYAEDPDNNFMPGAGPLVHL 401
           VTE++TG DLVE  +R+AAG K+  +Q+++ L G A E+R+YAEDP   F+P  G L   
Sbjct: 302 VTELVTGLDLVEQMIRVAAGAKLAFAQKDVKLDGWAIESRLYAEDPYRTFLPSIGRLTRY 361

Query: 402 STPSADMST-----RIETGVRQGDEVSVHYDPMIAKLVVWASDRQSALSKLRYCLHQYNI 456
             P           R +TGV +G E+S++YDPMIAKL  W  DR +A+  +   L  + +
Sbjct: 362 RPPEEGTQADGTVIRNDTGVFEGGEISMYYDPMIAKLCTWGPDRLTAVRAMADALDAFEV 421

Query: 457 VGLRSNVDFLLRLSGHPEFEAGNVHTDFIPQHHKDLLPSHSTIAKESVCQAALGLILKEK 516
            G+  N+ FL  +     F  G + T +I +   +       +A +      L  +    
Sbjct: 422 EGIGHNLPFLAAVMQQERFHEGRLTTAYIAE---EFAGGFHGVALDDASARKLAAVAATV 478

Query: 517 EMTSAFKLHTQDQFSPFSFSSGRRLNISYTRNMTLRSGKSDIVIAVTYNRDGSYDMQIDN 576
             T       Q++ S  S + G    +     +T   G  +I +    + DG+Y    D 
Sbjct: 479 NQT------LQERASRISGTIGNHRRVVGHEWVTSLDG-HEIQVTCEVSADGTYVRFADG 531

Query: 577 KSFRVLGD---------LSSEDGCTYLKSSINGVARKSKFILLDNTVHLFSMEGSIEVGI 627
            S  V  D          + ++    +K  + G   + ++  +D    + S     E+  
Sbjct: 532 TSVSVATDWAPGRTRAAFNIDNQPMSVKVELAGPGIRLRWRGIDVVARVRSPR-IAELAR 590

Query: 628 PVPKYLSPVSAEGAQGGTIAPMTGTIEKVFVKAGDRVKAGDSLMVMIAMKMEHTIKAPKD 687
            +PK L P +++      + PM G +  + VKAG+ V+AG ++ V+ AMKME+ ++A K 
Sbjct: 591 LMPKKLPPDTSK----MLLCPMPGVVTSITVKAGETVEAGQAIAVVEAMKMENILRAEKR 646

Query: 688 GRIKKVFFSEGAQANRHAPLVEFE 711
             +K+V    GA       ++EFE
Sbjct: 647 AIVKRVAIEAGASLAVDELIMEFE 670


Lambda     K      H
   0.318    0.133    0.382 

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: 1024
Number of extensions: 34
Number of successful extensions: 3
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: 717
Length of database: 670
Length adjustment: 39
Effective length of query: 678
Effective length of database: 631
Effective search space:   427818
Effective search space used:   427818
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