Alignments for a candidate for liuB in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuB in Phaeobacter inhibens BS107

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 GFF2122 PGA1_c21540 propionyl-CoA carboxylase alpha chain

Query= SwissProt::Q99MR8
         (717 letters)



>FitnessBrowser__Phaeo:GFF2122
          Length = 681

 Score =  501 bits (1290), Expect = e-146
 Identities = 283/693 (40%), Positives = 404/693 (58%), Gaps = 43/693 (6%)

Query: 47  KVLIANRGEIACRVIRTAKKMGVQSVAVYSEADRNSMHVDMADEAYSIGPAPSQQSYLAM 106
           K+LIANRGEIACRVI+TA+KMG+++VA+YS+AD+ S+HV MADEA  IGP P+ QSY+ +
Sbjct: 4   KILIANRGEIACRVIKTARKMGIKTVAIYSDADKQSLHVKMADEAVHIGPPPANQSYIVI 63

Query: 107 EKIIQVAKSSAAQAIHPGYGFLSENMEFAELCKQEGIIFIGPPSSAIRDMGIKSTSKSIM 166
           +K+++  +++ AQA+HPGYGFLSEN +FAE    EG+ F+GPP  AI  MG K TSK I 
Sbjct: 64  DKVMEAIRATGAQAVHPGYGFLSENAKFAEALAAEGVAFVGPPVGAIESMGDKITSKKIA 123

Query: 167 AAAGVPVVEGYHGKDQSDQCLREHAGKIGYPVMIKAVRGGGGKGMRIVRSEREFQEQLES 226
             AGV  V GY G         + + +IGYPVMIKA  GGGGKGMRI  S+ E +E  +S
Sbjct: 124 QEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSDAEAREGFQS 183

Query: 227 ARREAKKSFNDDAMLIEKFVDTPRHVEVQVFGDHHGNAVYLFERDCSVQRRHQKIIEEAP 286
           ++ EA  SF DD + IEKFV  PRH+E+QV  D HGN +YL ER+CS+QRR+QK++EEAP
Sbjct: 184 SKNEAANSFGDDRIFIEKFVTQPRHIEIQVLCDAHGNGIYLGERECSIQRRNQKVVEEAP 243

Query: 287 APGINPEVRRKLGEAAVRAAKAVKYVGAGTVEFIMDSRHNFYFMEMNTRLQVEHPVTEMI 346
           +P ++ + RR +GE AV  AKAV Y  AGTVEFI+D   NFYF+EMNTRLQVEHPVTE+I
Sbjct: 244 SPFLDEDTRRAMGEQAVALAKAVGYASAGTVEFIVDGDKNFYFLEMNTRLQVEHPVTELI 303

Query: 347 TGTDLVEWQLRIAAGEKIPLSQEEIPLQGHAFEARIYAEDPDNNFMPGAGPLVHL----- 401
           TG DLVE  +RIA GE + ++Q ++ L G A E R+YAEDP   F+P  G L        
Sbjct: 304 TGVDLVEQMIRIAGGEPLSITQNDVKLNGWAIENRLYAEDPYRGFLPSIGRLTRYRPPAE 363

Query: 402 --------------STPSADMSTRIETGVRQGDEVSVHYDPMIAKLVVWASDRQSALSKL 447
                           P+ +++ R +TGV +G E+S++YDPMIAKL  W   R +A++ +
Sbjct: 364 VAAGPLHDSGKWQGDAPAGELAVRNDTGVFEGGEISMYYDPMIAKLCTWGPTRDAAIAAM 423

Query: 448 RYCLHQYNIVGLRSNVDFLLRLSGHPEFEAGNVHTDFIPQHHKD-----LLPSHSTIAKE 502
           R  L  + + G+  N+ FL  +  HP F AG + T FI + + +      LP    + K 
Sbjct: 424 RDALDGFEVEGIGHNLPFLSAVMDHPIFIAGTMTTAFIEEQYPEGFNGVELPEQD-LRKI 482

Query: 503 SVCQAALGLILKEKEMTSAFKLHTQDQFSPFSFSSGRRLNISYTRNMTLRSGKSDIVIAV 562
           +   AA+  + + +    + ++   +          R++   +   +TL+    +  + V
Sbjct: 483 AAASAAMHRVAEIRRTRVSGRMDNHE----------RKVGSDWV--VTLQDVSFN--VTV 528

Query: 563 TYNRDGSYDMQIDNKSFRVLGDLSSEDGCTYLKSSINGVARKSKFILLDNTVHLFSMEGS 622
             +RDGS     D  + RV  D +  D    L    + +  K   I     +     +  
Sbjct: 529 DADRDGSTVRFDDGSALRVASDWTPGDQLARLTVGDDSLVVKVGKISGGFRIRSRGADLK 588

Query: 623 IEVGIPVPKYLSPVSAEGAQGGT----IAPMTGTIEKVFVKAGDRVKAGDSLMVMIAMKM 678
           + V  P    L+ +  E     T    + PM G + K+ V+ GD V+ G +L  + AMKM
Sbjct: 589 VHVRTPRQAELAKLMPEKIAPDTSKLLLCPMPGLVVKLEVEVGDEVQEGQALCTIEAMKM 648

Query: 679 EHTIKAPKDGRIKKVFFSEGAQANRHAPLVEFE 711
           E+ ++A K G +  +  + G        ++EFE
Sbjct: 649 ENILRAEKKGVVSAINAAAGDSLAVDEVIMEFE 681


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: 1104
Number of extensions: 41
Number of successful extensions: 4
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: 681
Length adjustment: 39
Effective length of query: 678
Effective length of database: 642
Effective search space:   435276
Effective search space used:   435276
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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