Alignments for a candidate for liuB in Mycolicibacterium vanbaalenii PYR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuB in Mycolicibacterium vanbaalenii PYR-1

Align Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4) (characterized)
to candidate WP_011781245.1 MVAN_RS20500 ATP-grasp domain-containing protein

Query= reanno::pseudo1_N1B4:Pf1N1B4_3984
         (651 letters)



>NCBI__GCF_000015305.1:WP_011781245.1
          Length = 660

 Score =  534 bits (1375), Expect = e-156
 Identities = 305/659 (46%), Positives = 406/659 (61%), Gaps = 28/659 (4%)

Query: 8   TLLVANRGEIACRVMRTAKALGLTTVAVHSATDRDARHSREADIRVDLGGSKAADSYLQI 67
           T+LVANRGEIA RV+RT +A+G+ +VAV S  D  ARH  EAD+ V +G + A  SYL +
Sbjct: 4   TVLVANRGEIAVRVIRTLRAMGIRSVAVFSDADAGARHVAEADVAVRIGPAPARQSYLSV 63

Query: 68  DKLIAAAKASGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPASAIDAMGSKSAAKALM 127
           + L+AA + +GAQA+HPGYGFLSENA FA A++AAG+ F+GPP +AI  MG K +AKA +
Sbjct: 64  EALLAAVRRTGAQAVHPGYGFLSENAQFAEALDAAGIAFIGPPVAAIQTMGDKISAKAAV 123

Query: 128 ETAGVPLVPGYHGEAQDLETFRDACERIGYPVLLKATAGGGGKGMKVVEDVSQLAEALAS 187
              GVP+VPG        +        +G+PVL+K +AGGGGKGM+VV+D S+L  AL S
Sbjct: 124 SEFGVPVVPGISRPGLTDQDLIAGAADVGFPVLVKPSAGGGGKGMRVVQDASELRAALVS 183

Query: 188 AQREALSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEEAP 247
           A+REA S+FGD  + +E+++L PRH+E+QV AD HGN ++L ER+CS+QRRHQKV+EEAP
Sbjct: 184 ARREAASAFGDDTLFLERFVLNPRHIEVQVLADAHGNVVHLGERECSLQRRHQKVIEEAP 243

Query: 248 APGLSPELRRAMGEAAVRSAQAIGYVGAGTVEFLL--DARGEFFFMEMNTRLQVEHPVTE 305
           +P L P+ R  +G AA  +A+++ Y GAGTVEF++  D   EFFFMEMNTRLQVEHPVTE
Sbjct: 244 SPLLDPQTRARIGAAACDTARSVDYTGAGTVEFIVSADRPDEFFFMEMNTRLQVEHPVTE 303

Query: 306 AITGLDLVAWQIRVARGEALPMTQDQVPLIGHAIEVRLYAEDPGNDFLPATGRLALYRES 365
            +TGLDLV  Q+R+A GE LP+ QD + L GHA+E R+YAEDP   FLP  G +   RE 
Sbjct: 304 MVTGLDLVELQVRIAAGEKLPIAQDDIRLDGHAVEARVYAEDPARGFLPTGGDVLALRE- 362

Query: 366 AAGPGRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFAIGGLKTNIN 425
            AG G RVDSG+  G  +   YDPML K+I    DR  A   L + L + A+ GL TN+ 
Sbjct: 363 PAGAGVRVDSGLTRGTAVGSDYDPMLAKVIVHAGDRPTALRALDAALADTAVLGLTTNVE 422

Query: 426 FLRRIIGHPAFAAAELDTGFIPRYQEQLLPAPSDLSDEFWQAAAQAFAQSQSSTTRADDL 485
           FLR ++  P  AA  LDTG + R      PAP+   DE   AAA  + +S          
Sbjct: 423 FLRFLLADPDVAAGNLDTGLLDRRLPDFAPAPA-TDDELIAAAAYRWLRSWPVAP----- 476

Query: 486 SSPWGIGNGFRAG--LPTEITLHLSCEEQDRAL---TLGDADAHT---------AQLKGE 531
           SSPW + +G+R      T   LH   E  D      T GDA A           A L  +
Sbjct: 477 SSPWEVPSGWRIAGRAATPFRLHAG-ERTDHVWLTGTPGDATATVEGGRTRTLRASLVAD 535

Query: 532 YLLTEHNGLRRQHRAIRRGDTLYLQWDGELRRIESY--DPISAVEASHSHQGGLTAPMNG 589
            L    +G+R ++     G  ++L     +  +E     P+   +A HS    LT+PM G
Sbjct: 536 RLAVTVDGMRAEYLVAGAGGQVWLAGPDRVTMVEEVREAPVRPDDA-HSGDAELTSPMPG 594

Query: 590 SIVRVLVEAGQTVEAGAQLVVLEAMKMEHSIRAPHAGIIKALYCQEGEMVSEGSALVEL 648
           ++V V V+ G TV AG  +V +EAMKMEH++ AP  G+++ L    GE V  G  L  +
Sbjct: 595 AVVAVGVDDGATVTAGTVVVTVEAMKMEHALAAPVDGVVE-LLVSAGEQVKVGQVLARI 652


Lambda     K      H
   0.318    0.134    0.386 

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: 1081
Number of extensions: 37
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: 651
Length of database: 660
Length adjustment: 38
Effective length of query: 613
Effective length of database: 622
Effective search space:   381286
Effective search space used:   381286
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 24 2021. The underlying query database was built on Sep 17 2021.

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Rules (tab-delimited)
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