Alignments for a candidate for liuB in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuB in Dechlorosoma suillum PS

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate Dsui_0982 Dsui_0982 acetyl/propionyl-CoA carboxylase, alpha subunit

Query= reanno::SB2B:6937189
         (673 letters)



>FitnessBrowser__PS:Dsui_0982
          Length = 667

 Score =  652 bits (1682), Expect = 0.0
 Identities = 357/662 (53%), Positives = 453/662 (68%), Gaps = 8/662 (1%)

Query: 1   MFNKLLIANRGEIACRVIRTARDMGIKTVAVYSDADRDARHVALADESFYLGESAPASSY 60
           MF+K+LIANRGEIACRVI+TAR +GI+TVAVYS+AD +ARHV LADE+  LG +A   SY
Sbjct: 1   MFSKILIANRGEIACRVIKTARRLGIRTVAVYSEADANARHVRLADEAVLLGPAAARESY 60

Query: 61  LRGELIIDIAKKCGAEAIHPGYGFLSENAAFARACEASGIAFVGPGSDAIDAMGSKSAAK 120
           L  E I+D A++ GA+AIHPGYGFLSENA FA AC A+G+ F+GP + AI AMGSKSAAK
Sbjct: 61  LVAEKILDAARRTGAQAIHPGYGFLSENADFAEACAAAGVVFIGPPASAIRAMGSKSAAK 120

Query: 121 LIMEKAGVPLVPGYHGDDQSDATLLAEAKKIGYPLLIKAAYGGGGKGMRIVESESELKAA 180
            +MEKA VPL PGYHGD+Q    L  +A  IGYP+LIKAA GGGGKGMR+V+   +  AA
Sbjct: 121 ALMEKAAVPLTPGYHGDNQEPEFLKQQADAIGYPVLIKAAAGGGGKGMRLVDKGEDFIAA 180

Query: 181 IDSARREAASSFGNDKLLMERYLRQPRHVEVQVFADSQGNCVYLSDRDCSIQRRHQKVVE 240
           + S +REA SSFGND++L+E+Y+ +PRH+E+QVF DSQGNCVYL +RDCS+QRRHQKV+E
Sbjct: 181 LASCQREARSSFGNDQVLVEKYITRPRHIEIQVFGDSQGNCVYLFERDCSVQRRHQKVLE 240

Query: 241 EAPAPGLPDSLRKQMGEAAVAAAKAIDYRGAGTVEFLLDVDMSFFFMEMNTRLQVEHPVT 300
           EAPAPG+    R+QMGEAAVAAAKA+ Y GAGTVEF+ + D SF+FMEMNTRLQVEHPVT
Sbjct: 241 EAPAPGMTPERRRQMGEAAVAAAKAVGYVGAGTVEFIANQDGSFYFMEMNTRLQVEHPVT 300

Query: 301 EMVTGQDLVKWQLLVAAGAQLPLEQHEIQIHGHAFEVRIYAEDPNNEFLPASGKLTFLRE 360
           EM+TGQDLV+WQL VAAG  LPL Q ++QI GHA E RIYAED    FLP++G+L  L  
Sbjct: 301 EMITGQDLVEWQLRVAAGEALPLRQEQLQIRGHALEARIYAEDAGKGFLPSTGRLLHLVP 360

Query: 361 PEPSRHVRIDSGVRENDVISNYYDPMIAKLIVWDESRPRALARLTRALGDYRVGGLKHNI 420
           P    +VR+D+GV E D I+ +YDPMIAKLIVWDE R  ALAR+ +AL DYRV G+  NI
Sbjct: 361 PAEGLNVRVDTGVEEGDEITPHYDPMIAKLIVWDEDREAALARMRQALADYRVVGVTTNI 420

Query: 421 EFLSNIAEHPAFAQANFSTDFIGRYGDALIGDSRDEADTAFVLAVLTQLRLRE---AVSQ 477
           +FLS +   PAFA A+  T  I R  D L  +S +      + A + +L LRE   A  Q
Sbjct: 421 DFLSRLVSCPAFAGADLDTGLIERQQDFLFPESPEVPRDVILTATVAEL-LRERDLAAQQ 479

Query: 478 DVAGHDPFSPWSSLKGFRLSSPRRHSVTLLDDAHQSRSAELTESNGRYQLCL-NDKLIEL 536
                DP+SPW+   G+R++   R +V+      Q     +  +   +QL L ND L+  
Sbjct: 480 GRRSGDPWSPWNRRDGWRMNIAARRTVSFRVGETQV-DVGVAYAGEDWQLTLRNDTLLVR 538

Query: 537 SGSIEDSELKCEINGHKMKVTVSLEDGGLTVFLSSGSYHF-REVLGQVLEETASSEDKLK 595
              +    L  E+   ++  +V        VFL+SG+Y   R     ++E   +    L 
Sbjct: 539 GRLLAHDRLAVELEDRRLMASVVAVAEKRHVFLNSGTYVIERHDPLHLVEAGGAQGGGLT 598

Query: 596 APMNGTVVTHLVAAGDKVSAGQGLLVMEAMKMEYTIEAPFDGVVSEFFFAPGELVSDGTL 655
           APM G VV  L+A    V+ G  LL++EAMKME+TI AP  G +  F +A GE V+DG  
Sbjct: 599 APMPGKVVA-LLAQPGPVAKGTPLLILEAMKMEHTITAPKQGNLKGFRYAVGEQVADGAE 657

Query: 656 LL 657
           L+
Sbjct: 658 LV 659


Lambda     K      H
   0.317    0.134    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: 1160
Number of extensions: 59
Number of successful extensions: 5
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: 673
Length of database: 667
Length adjustment: 39
Effective length of query: 634
Effective length of database: 628
Effective search space:   398152
Effective search space used:   398152
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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Protein sequences (fasta format)
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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