Alignments for a candidate for liuB in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuB in Dinoroseobacter shibae DFL-12

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 3607308 Dshi_0723 Carbamoyl-phosphate synthase L chain ATP-binding (RefSeq)

Query= SwissProt::Q99MR8
         (717 letters)



>FitnessBrowser__Dino:3607308
          Length = 681

 Score =  506 bits (1303), Expect = e-147
 Identities = 291/699 (41%), Positives = 408/699 (58%), Gaps = 55/699 (7%)

Query: 47  KVLIANRGEIACRVIRTAKKMGVQSVAVYSEADRNSMHVDMADEAYSIGPAPSQQSYLAM 106
           K+LIANRGEIACRVI+TA+KMG+Q+VA+YS+ADRN++HV MADEA  IGP+P+ QSY+ +
Sbjct: 4   KILIANRGEIACRVIKTARKMGIQTVAIYSDADRNALHVRMADEAVHIGPSPANQSYIVI 63

Query: 107 EKIIQVAKSSAAQAIHPGYGFLSENMEFAELCKQEGIIFIGPPSSAIRDMGIKSTSKSIM 166
           +K++   + + A+A+HPGYGFLSEN  FAE  ++EG+ FIGPP++AI  MG K TSK I 
Sbjct: 64  DKVMDAIRQTGAEAVHPGYGFLSENKLFAEALEKEGVAFIGPPANAIEAMGDKITSKKIA 123

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

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

Query: 287 APGINPEVRRKLGEAAVRAAKAVKYVGAGTVEFIMDSRHNFYFMEMNTRLQVEHPVTEMI 346
           +P ++   R+ +GE +   A+AV Y  AGTVEFI+D   NFYF+EMNTRLQVEHPVTE+I
Sbjct: 244 SPFLDEATRKAMGEQSCALAQAVGYASAGTVEFIVDGDRNFYFLEMNTRLQVEHPVTELI 303

Query: 347 TGTDLVEWQLRIAAGEKIPLSQEEIPLQGHAFEARIYAEDPDNNFMP------------- 393
           TG DLVE  +R+AAGEK+P++Q+++ L G A E R+YAEDP  NF+P             
Sbjct: 304 TGVDLVEQMIRVAAGEKLPMTQDDVTLTGWAIENRLYAEDPYRNFLPSIGRLTRYRPPVE 363

Query: 394 -GAGPLV-----HLSTPSADMSTRIETGVRQGDEVSVHYDPMIAKLVVWASDRQSALSKL 447
             AGPL      H   PS   + R +TGV +G E+S++YDPMIAKL  W  DR +A+  +
Sbjct: 364 VAAGPLEANGKWHGDAPSGPTAVRNDTGVYEGGEISMYYDPMIAKLCTWGPDRPAAIEAM 423

Query: 448 RYCLHQYNIVGLRSNVDFLLRLSGHPEFEAGNVHTDFIPQHHKDLLPSHSTIAKESVCQA 507
           R  L  + + G+  N+ F+  +  HP F  G + T FI + + D          E V   
Sbjct: 424 RNALDGFEVEGIGHNLPFVAAVMDHPVFIKGEMTTAFIKEQYPD--------GFEGVTLG 475

Query: 508 ALGLILKEKEMTSAFKLHTQDQFSPFSFSSGRRLNISYTRNMTLRSGKSDIVIA------ 561
           A  L        + F++           +  RR  IS T +   R   +D V+       
Sbjct: 476 AADLTRLAAAAAAMFRV-----------AEIRRTRISGTLDNHERMVGTDWVVTAQDARF 524

Query: 562 -VTYNRD--GSYDMQIDNKSFRVLGDLSSEDGCTYLKSSINGVARKSKFILLDNTVHLFS 618
            VT + D  GS     D  + RV    +  D    ++  I+G     K   + +   +  
Sbjct: 525 DVTIDADPGGSTVRFADGTAHRVTSRWTPGDSLATVE--IDGAPMVLKVDKITSGFRMRF 582

Query: 619 MEGSIEVGIPVPKY--LSPVSAEGAQGGT----IAPMTGTIEKVFVKAGDRVKAGDSLMV 672
               ++V +  P+   L+ +  E     T    + PM G + K+ V+ GD V+ G +L  
Sbjct: 583 RGADVKVHVRTPRQAELNDLMPEKLPPDTSKMLLCPMPGLVVKIDVEVGDEVQEGQALCT 642

Query: 673 MIAMKMEHTIKAPKDGRIKKVFFSEGAQANRHAPLVEFE 711
           + AMKME+ ++A K   + K+    G        ++EFE
Sbjct: 643 VEAMKMENILRAEKTATVTKINAGAGDSLAVDDVIMEFE 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: 1096
Number of extensions: 44
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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