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 methylcrotonoyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.4) (characterized)
to candidate WP_011777666.1 MVAN_RS01755 ATP-grasp domain-containing protein

Query= BRENDA::Q9I299
         (655 letters)



>NCBI__GCF_000015305.1:WP_011777666.1
          Length = 665

 Score =  528 bits (1360), Expect = e-154
 Identities = 305/666 (45%), Positives = 407/666 (61%), Gaps = 24/666 (3%)

Query: 7   SIQRLLVANRGEIACRVMRSARALGIGSVAVHSDIDRHARHVAEADIAVDLGGAKPADSY 66
           +I +LL+ANRGEIA R++R+ARA+ + +VA++SD DR A +V  AD +V L G  PAD+Y
Sbjct: 5   TITKLLIANRGEIAARIIRTARAMDVATVALYSDADRDAPYVTLADESVHLPGTAPADTY 64

Query: 67  LRGDRIIAAALASGAQAIHPGYGFLSENADFARACEEAGLLFLGPPAAAIDAMGSKSAAK 126
           LR D ++AAA  +GA A+HPGYGFLSENADFARAC +AG++F+GP   AI AMGSK AAK
Sbjct: 65  LRADLVLAAAARTGADAVHPGYGFLSENADFARACAQAGVIFVGPSPEAIVAMGSKIAAK 124

Query: 127 ALMEEAGVPLVPGYHGEA---QDLETFRREAGRIGYPVLLKAAAGGGGKGMKVVEREAEL 183
            +M  AGVP++PG   E+   QD E  R  A  IG+P+L+KAA GGGG+GM++V  E EL
Sbjct: 125 DMMRAAGVPVLPGTTVESEEDQDPERLRTAAADIGFPILVKAAFGGGGRGMRIVRGEHEL 184

Query: 184 AEALSSAQREAKAAFGDARMLVEKYLLKPRHVEIQVFADRHGHCLYLNERDCSIQRRHQK 243
            EA++SA+REA +AFGD  + +EK++  PRH+E+Q+F D HG  ++L ER+CSIQRR+QK
Sbjct: 185 VEAVASARREAASAFGDGTVFLEKFVESPRHIEVQIFGDSHGTVVHLGERECSIQRRYQK 244

Query: 244 VVEEAPAPGLGAELRRAMGEAAVRAAQAIGYVGAGTVEFLLDERGQFFFMEMNTRLQVEH 303
           ++EEAP+  +   LR  +G AAV A +A+ Y GAGTVEF++   G F+F+E+NTRLQVEH
Sbjct: 245 IIEEAPSTAVDERLRDELGRAAVAAGKALSYEGAGTVEFVMAPDGSFYFLEVNTRLQVEH 304

Query: 304 PVTEAITGLDLVAWQIRVARGEALPLTQEQVPLNGHAIEVRLYAEDPEGDFLPASGRLML 363
           PVTE +TG+DLV  Q+ VA G  +P         GHA+EVRLYAED    F+P SG L  
Sbjct: 305 PVTELVTGIDLVRAQLLVAAGHPIPSEMLHATPRGHAVEVRLYAEDVAAGFVPVSGTLTT 364

Query: 364 YREAAAGPGRRVDSGVREGDEVSPFYDPMLAKLIAWGETREEARQRLLAMLAETSVGGLR 423
             E     G R+D+G   G +VS FYDPMLAK+I +G TR +A   +   L ET V G+ 
Sbjct: 365 L-EFPTFDGIRIDAGFTSGSKVSTFYDPMLAKVIGFGATRADACALVARALTETRVHGVT 423

Query: 424 TNLAFLRRILGHPAFAAAELDTGFIARHQDDLLPAPQALPEHFWQAAAEAWLQSEPGHRR 483
           TN   L  IL    F A  +DTG++ RH    L    +        A  A L ++ G R 
Sbjct: 424 TNRDLLVGILREQEFLAGAIDTGYLERHDPAELTGASSSVSTLRTHALAAALAAQAGRRT 483

Query: 484 DDD--PHSPWSRNDGWRSALARESDLMLRCRDERRCVRLRHASPSQYRLDGD-------- 533
           D    P  P     GWR+  +++  +     D    VR R    +     GD        
Sbjct: 484 DTSILPGLP----SGWRTLRSQDQVVAFTAGDHTVEVRYRFGRATVSVRIGDWEPEVQIV 539

Query: 534 -----DLVSRVDGVTRRSAALRRGRQLFLEWEGELLAIEAVDPIAEAEAAHAHQGGLSAP 588
                 L + +DGV R+      G   +++      A+  VD   +  +A+   G L AP
Sbjct: 540 AASASCLDAVIDGVRRQYHLTISGATHYVDSGLGSSALTEVDRFPD-PSANQEPGSLLAP 598

Query: 589 MNGSIVRVLVEPGQTVEAGATLVVLEAMKMEHSIRAPHAGVVKALYCSEGELVEEGTPLV 648
           M GS+VRV V+ G  V AG T+VVLEAMKMEHS+RAP  GVV +L  + G  VE G  L 
Sbjct: 599 MPGSVVRVEVDEGAEVAAGTTIVVLEAMKMEHSVRAPAGGVVASLSVAVGTQVESGQVLA 658

Query: 649 ELDENQ 654
            + E Q
Sbjct: 659 VVAEAQ 664


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: 1036
Number of extensions: 38
Number of successful extensions: 4
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 24 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