Alignments for a candidate for liuB in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuB in Cupriavidus basilensis 4G11

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate RR42_RS32735 RR42_RS32735 3-methylcrotonyl-CoA carboxylase

Query= reanno::pseudo6_N2E2:Pf6N2E2_2194
         (649 letters)



>FitnessBrowser__Cup4G11:RR42_RS32735
          Length = 674

 Score =  541 bits (1395), Expect = e-158
 Identities = 318/664 (47%), Positives = 409/664 (61%), Gaps = 33/664 (4%)

Query: 8   TLLVANRGEIACRVMRTAKAMGLTTVAVHSATDRDARHSREADIRVDLGGSKAADSYLQI 67
           TLLVANRGEIA R+MRTA+ +GL TVAV+S  DR   H   AD  V +G +    SYL I
Sbjct: 10  TLLVANRGEIAMRIMRTARRLGLATVAVYSEADRHGPHVAYADRAVRIGDAAPRASYLNI 69

Query: 68  DKLIAAAKASGAQAIHPGYGFLSENAGFARAIENAGLIFLGPPASAIDAMGSKSAAKALM 127
             +I AA+ SGA A+HPGYGFL+ENA FA A+  AGL+F+GPPA+AI AMG+K+ AK LM
Sbjct: 70  AAIIEAARRSGADAVHPGYGFLAENAEFADAVAQAGLVFVGPPAAAIRAMGNKAEAKRLM 129

Query: 128 ETAGVPLVPGYHGEAQDLETFRDAAERIGYPVLLKATAGGGGKGMKVVEDVSQLAEALAS 187
             A +P +PGY GEAQD      AA  IG+P+++KA AGGGG+GM++V DV  L  ALAS
Sbjct: 130 LAADMPCIPGYQGEAQDDAALLQAAAPIGFPLMVKAAAGGGGRGMRLVHDVHALPGALAS 189

Query: 188 AQREAQSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEEAP 247
           A+ EA ++FG  ++++E+ ++ PRHVEIQVFAD  G+ ++L ERDCS+QRRHQKVVEEAP
Sbjct: 190 ARSEAMAAFGSGQLILERAVIAPRHVEIQVFADTQGHVIHLGERDCSVQRRHQKVVEEAP 249

Query: 248 APGLTAQLRQAMGEAAVRAAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVTEAI 307
           +P ++  LR+ MG AAVRAAQAIGYVGAGT+EFLLD  G F+FMEMNTRLQVEH VTEAI
Sbjct: 250 SPAVSPALRERMGGAAVRAAQAIGYVGAGTMEFLLDGDGNFYFMEMNTRLQVEHAVTEAI 309

Query: 308 TGLDLVAWQIRVAQGEPLPITQAQVPLLGHAIEVRLYAEDPVNDFLPATGRLALYRESAK 367
           TG DLV WQ+RVA GEPLP+TQ QV L GHAIEVRL AED    FLP  G +  +R    
Sbjct: 310 TGFDLVEWQLRVAAGEPLPVTQEQVALRGHAIEVRLTAEDVAAGFLPQGGPVLRWRAPGA 369

Query: 368 GPGRRVDSGVEEGDEISPFYDPMLGKLIAWGENREQARLRLLSMLDEFAIGGLKTNIGFL 427
           G   RVD  ++EG EI   YD M+ KL+  G  RE+AR +LL  +++  + G+ +N GFL
Sbjct: 370 GHDVRVDHALQEGGEIPVHYDSMVAKLVTHGATREEARRKLLRAVEQTVLLGVASNQGFL 429

Query: 428 RRIVAHPAFAAAELDTGFIPRYQAQLL----PEPGELDDAFWLAAAQGFALSLAPHIRGD 483
              +AH AFA  ++ TGF+  +    L    P   ++  A  LAAA   A S  P +   
Sbjct: 430 ADCLAHEAFAGNQVHTGFVDTHMQAALRTTQPAAAQVACAA-LAAAGLLAASECPALVAP 488

Query: 484 DAGSPWASTTGMRLGLSR-ETTLHLSCEGQDRAL-------------------TLDVTAH 523
                 A + G++ G  +    L    +G + A+                    + V   
Sbjct: 489 ------ACSLGLQAGEQQWRVDLRAVAQGWEVAVRGGEGEGEGEGEGDGTSAEIVSVRVL 542

Query: 524 CAELKGERLTIEHHGVRRSHRAIRQGDSLYLHWAGDLHRIDLYDPLAAAE--ASHSHQGG 581
            A+L+     +E +G+         GD+++L  AG   R    DP             G 
Sbjct: 543 RADLEQGSALVECNGMALPLVFATGGDAVHLFSAGRAWRFARLDPRQKKRNPGDAGRAGE 602

Query: 582 LAAPMNGSIVRVLVSVGQPVDAGAQLVVLEAMKMEHSIRAPKAGVIKALYCQEGEMVSEG 641
           L AP+   IV V  + G+ V AG  LVVLEAMKMEH+I AP  GVI  L+ +EG     G
Sbjct: 603 LLAPLTARIVAVKAAAGEAVLAGQVLVVLEAMKMEHAIVAPFDGVIAQLHAREGGQARAG 662

Query: 642 SALV 645
           S LV
Sbjct: 663 SLLV 666


Lambda     K      H
   0.319    0.134    0.389 

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: 1195
Number of extensions: 50
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 649
Length of database: 674
Length adjustment: 38
Effective length of query: 611
Effective length of database: 636
Effective search space:   388596
Effective search space used:   388596
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 (21.7 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