Alignments for a candidate for liuB in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuB in Dyella japonica UNC79MFTsu3.2

Align methylcrotonoyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.4) (characterized)
to candidate N515DRAFT_0927 N515DRAFT_0927 3-methylcrotonyl-CoA carboxylase alpha subunit

Query= BRENDA::Q9I299
         (655 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0927
          Length = 665

 Score =  614 bits (1584), Expect = e-180
 Identities = 341/664 (51%), Positives = 430/664 (64%), Gaps = 29/664 (4%)

Query: 9   QRLLVANRGEIACRVMRSARALGIGSVAVHSDIDRHARHVAEADIAVDLGGAKPADSYLR 68
           +R+L+ANRGEIACRV+R+ R LGI ++AV+S+ D  A+HV  AD A  +GG +PADSYLR
Sbjct: 3   ERVLIANRGEIACRVIRTCRRLGIRTIAVYSEADADAQHVRLADEAWPIGGPRPADSYLR 62

Query: 69  GDRIIAAALASGAQAIHPGYGFLSENADFARACEEAGLLFLGPPAAAIDAMGSKSAAKAL 128
           G+ I+  A  SGAQAIHPGYGFLSEN  FARAC EAG+ F+GP  A+IDAMGSK+AAKAL
Sbjct: 63  GETILEVARRSGAQAIHPGYGFLSENTAFARACTEAGIAFIGPRPASIDAMGSKAAAKAL 122

Query: 129 MEEAGVPLVPGYHGEAQDLETFRREAGRIGYPVLLKAAAGGGGKGMKVVEREAELAEALS 188
           ME+  VPLVPGYHG+ QD +    +A   G+P+++KAAAGGGGKGM++V  E E A+AL+
Sbjct: 123 MEKHAVPLVPGYHGDNQDADFLAGQARSTGFPLMIKAAAGGGGKGMRIVRAEREFADALA 182

Query: 189 SAQREAKAAFGDARMLVEKYLLKPRHVEIQVFADRHGHCLYLNERDCSIQRRHQKVVEEA 248
           SAQREA  AFGD R+++E+Y+  PRH+E QVF D HG+ ++LNER+CS QRR+QKV+EE 
Sbjct: 183 SAQREAANAFGDTRVILERYVEHPRHIEFQVFGDTHGNVIHLNERECSAQRRYQKVLEET 242

Query: 249 PAPGLGAELRRAMGEAAVRAAQAIGYVGAGTVEFLLDERGQFFFMEMNTRLQVEHPVTEA 308
           P+P L    R AMG AAV AA+A+ YVGAGTVEF++ + G+FFFMEMNTRLQVEHPVTE 
Sbjct: 243 PSPFLTPARRAAMGAAAVAAARAVDYVGAGTVEFIVGQDGEFFFMEMNTRLQVEHPVTEE 302

Query: 309 ITGLDLVAWQIRVARGEALPLTQEQVPLNGHAIEVRLYAEDPEGDFLPASGRLMLYREAA 368
             GLDLV WQ+RVA GEALPL QE V   GHAIEVRLYAEDPE +FLP SG+L+  R   
Sbjct: 303 TLGLDLVEWQLRVAAGEALPLRQEDVHAQGHAIEVRLYAEDPEQNFLPGSGKLLRLRLPE 362

Query: 369 AGPGRRVDSGVREGDEVSPFYDPMLAKLIAWGETREEARQRLLAMLAETSVGGLRTNLAF 428
                R+D GV EGD V+ FYDPM+AKLI     R +A QRL   L    + G ++N+AF
Sbjct: 363 TSRHVRLDGGVIEGDTVTIFYDPMIAKLIVHDRDRAQALQRLREALMACEIAGPKSNIAF 422

Query: 429 LRRILGHPAFAAAELDTGFIARHQDDLL-----PAPQALPEHFWQAAAEAWLQSE----P 479
           L R++ HP      +DTG++ RH D+ L     PAPQ L    + AA  A L  E     
Sbjct: 423 LERLVRHPVVVEGRIDTGYLDRHLDEFLAGDAAPAPQLL----FAAAVAALLHDERTVVA 478

Query: 480 GHRRDDDPHSPWSRNDGWRSALARESDLMLRCRDERRCVRLRHASPSQYRLDGDDLVSRV 539
                 DPHSPW+R D WR   A +  + L  R++R  V   H     Y+L   D    V
Sbjct: 479 QAAHGVDPHSPWARADAWRIGHAGKRIVALSLREQRYEVE-AHGHDGDYQLCHGDASCHV 537

Query: 540 DGVTRRSAALRR---GRQLFLEWEGELLAIEAVD--------PIAEAEAAHAHQGG---- 584
            G     AAL     G+ L L    +   +   D          A A A  A QG     
Sbjct: 538 QGARHDGAALSARFDGQSLRLPLHADAQRVLLHDSDGRRHSFARAAAFAWEARQGAGGNQ 597

Query: 585 LSAPMNGSIVRVLVEPGQTVEAGATLVVLEAMKMEHSIRAPHAGVVKALYCSEGELVEEG 644
           + APM G IV V   PG  VE G  L+V+EAMKME +++AP AG + ++  ++G+ VE  
Sbjct: 598 VLAPMPGRIVLVKARPGDQVEEGQELLVMEAMKMELALKAPRAGTIDSIGATQGDFVEAD 657

Query: 645 TPLV 648
             LV
Sbjct: 658 AVLV 661


Lambda     K      H
   0.319    0.135    0.397 

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: 1180
Number of extensions: 57
Number of successful extensions: 6
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: 655
Length of database: 665
Length adjustment: 38
Effective length of query: 617
Effective length of database: 627
Effective search space:   386859
Effective search space used:   386859
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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