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_011781995.1 MVAN_RS24365 acetyl/propionyl-CoA carboxylase subunit alpha

Query= BRENDA::Q9I299
         (655 letters)



>NCBI__GCF_000015305.1:WP_011781995.1
          Length = 656

 Score =  453 bits (1165), Expect = e-131
 Identities = 296/669 (44%), Positives = 384/669 (57%), Gaps = 40/669 (5%)

Query: 8   IQRLLVANRGEIACRVMRSARALGIGSVAVHSDIDRHARHVAEADIAVDLGGAKPADSYL 67
           I R+LVANRGEIA RV  + R LGIG+VAV++D D  A HVAEAD  V L G +    YL
Sbjct: 2   ITRVLVANRGEIARRVFATCRRLGIGTVAVYTDADAGAPHVAEADARVRLTGTR---GYL 58

Query: 68  RGDRIIAAALASGAQAIHPGYGFLSENADFARACEEAGLLFLGPPAAAIDAMGSKSAAKA 127
              ++IAAA +SGA AIHPGYGFLSEN DFA A ++AGL ++GPP AA+ AMGSK  AK 
Sbjct: 59  DAAQLIAAARSSGADAIHPGYGFLSENPDFAAAVQDAGLRWIGPPVAAVAAMGSKIEAKK 118

Query: 128 LMEEAGVPLVPGYHGEAQDLETFRREAGRIGYPVLLKAAAGGGGKGMKVVEREAELAEAL 187
           LM  AGVP++     +  D +T   +      PVL+KA+AGGGG+GM+VV   AEL   +
Sbjct: 119 LMAAAGVPVL-----DELDPDTVTADM----LPVLVKASAGGGGRGMRVVRDLAELPAQV 169

Query: 188 SSAQREAKAAFGDARMLVEKYLLKPRHVEIQVFADRHGHCLYLNERDCSIQRRHQKVVEE 247
            +A+REA++AFGD  +  E+YL    HVE+QV AD HG    + ER+CSIQRRHQK++EE
Sbjct: 170 EAARREAQSAFGDPTVFCERYLDAGHHVEVQVMADVHGTVWAVGERECSIQRRHQKIIEE 229

Query: 248 APAPGLG--AELRRAMGEAAVRAAQAIGYVGAGTVEFLLDERGQFFFMEMNTRLQVEHPV 305
           AP+P +   A +R  + EAA  AA AIGY GAGTVEF+ D++G FFF+EMNTRLQVEHPV
Sbjct: 230 APSPLVERVAGMRDKLFEAARLAATAIGYSGAGTVEFMADDQGAFFFLEMNTRLQVEHPV 289

Query: 306 TEAITGLDLVAWQIRVARGEALPLTQEQVPLNGHAIEVRLYAEDPEGDFLPASGRLMLYR 365
           TE  +G+DLV  Q+ VA G  L  +       G +IE RLYAEDP  ++ P  G +  + 
Sbjct: 290 TELTSGVDLVELQLAVADGATLDPSPPAP--RGASIEARLYAEDPANNWQPQPGAVHHFD 347

Query: 366 EAAAG--------PGRRVDSGVREGDEVSPFYDPMLAKLIAWGETREEARQRLLAMLAET 417
              AG         G R+DSG+ +G  +S FYDPM+AK+I++  TR +A   L   L   
Sbjct: 348 VPTAGVEFGPLDRTGVRLDSGITDGAVISVFYDPMIAKVISYAPTRRQAAALLADALTRA 407

Query: 418 SVGGLRTNLAFLRRILGHPAFAAAELDTGFIARHQDDLLPAPQALPEHFWQAAAEAWLQS 477
            + G+RTN   L  +L HPAF     DT F   H    L AP A       +A  A L +
Sbjct: 408 RIHGVRTNRDLLVNVLRHPAFGDGATDTAFFDTHGLAELAAPVADDRTVALSAVAAAL-A 466

Query: 478 EPGHRRD-----DDPHSPWS------RNDGWRSALARESDLMLRCRDERRCVRL-RHASP 525
           +  H R      +D  S W       ++  ++    R  D  +R R  R  V +  H   
Sbjct: 467 DAAHNRSTATVFEDIPSGWRNLPAGFQHKSYQDHAGRAHD--VRYRFTRDGVMIDGHDDV 524

Query: 526 SQYRLDGDDLVSRVDGVTRRSAALRRGRQLFLEWEGELLAIEAVDPIAEAEAAHAHQGGL 585
           S        +V  V GV R     R G  +F++         A+    +  AA AH G L
Sbjct: 525 SVVSAGQRQVVLTVSGVDRPFDVTRYGDSVFVDSPCGCTHFVALPRFPDPAAALAH-GSL 583

Query: 586 SAPMNGSIVRVLVEPGQTVEAGATLVVLEAMKMEHSIRAPHAGVVKALYCSEGELVEEGT 645
            APM GS++RV   PG TV AG  L+ LEAMKMEH+I AP  GV+  L    G  VE G 
Sbjct: 584 LAPMPGSVLRVGAAPGDTVTAGQPLLWLEAMKMEHTITAPTDGVLVELNVEPGRQVEVGA 643

Query: 646 PLVELDENQ 654
            L  ++  +
Sbjct: 644 VLARVESQE 652


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: 1013
Number of extensions: 47
Number of successful extensions: 8
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: 656
Length adjustment: 38
Effective length of query: 617
Effective length of database: 618
Effective search space:   381306
Effective search space used:   381306
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)
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Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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