Alignments for a candidate for liuB in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuB in Acidovorax sp. GW101-3H11

Align Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4) (characterized)
to candidate Ac3H11_1927 Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_1927
          Length = 670

 Score =  510 bits (1314), Expect = e-149
 Identities = 308/681 (45%), Positives = 401/681 (58%), Gaps = 58/681 (8%)

Query: 9   LLVANRGEIACRVMRTAKALGLTTVAVHSATDRDARHSREADIRVDLGGSKAADSYLQID 68
           +L+ANR EIA R++ TA  +G+ TVAV+S  D  A H REA   V LGG+ +AD+YL+ D
Sbjct: 4   ILIANRSEIARRIIHTAHRMGIETVAVYSDPDASALHVREATQAVALGGAASADTYLRTD 63

Query: 69  KLIAAAKASGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPASAIDAMGSKSAAKALME 128
           KL+AAA+A+GA A+HPGYGFLSENA FA+A+  AGL ++GPP +AI A+GSK+ AKAL  
Sbjct: 64  KLLAAARATGADAVHPGYGFLSENADFAQAVVDAGLTWIGPPPAAIRALGSKAGAKALAV 123

Query: 129 TAGVPLVPGYHGEAQDLETFRDACERIGYPVLLKATAGGGGKGMKVVEDVSQLAEALASA 188
              VP +PGY G+ Q  E F     RIG P+++KA AGGGG+GM++V D++QL  ALASA
Sbjct: 124 AHCVPCLPGYAGDDQSDERFAAEAARIGTPLMVKAVAGGGGRGMRLVTDLAQLPAALASA 183

Query: 189 QREALSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEEAPA 248
           + EAL+ FG   +L+E+ LL+PRHVE+Q+FAD HG C++L ERDCS+QRRHQK++EEAP+
Sbjct: 184 RSEALAGFGCGDLLIERALLQPRHVEVQIFADAHGACIHLGERDCSVQRRHQKIIEEAPS 243

Query: 249 PGLSPELRRAMGEAAVRSAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVTEAIT 308
           P +   LR  MG  AV  AQA GYVGAGTVEFLLD   +F+ MEMNTRLQVEHPVTEA+T
Sbjct: 244 PAVDAALRERMGACAVALAQAAGYVGAGTVEFLLDG-PDFYLMEMNTRLQVEHPVTEALT 302

Query: 309 GLDLVAWQIRVARGEALPMTQDQVPLIGHAIEVRLYAEDPGNDFLPATGRLALYR----- 363
           GLDLV WQIRVARGE LP+TQDQV L GHAIEVRL AED    F P TGR+  +      
Sbjct: 303 GLDLVEWQIRVARGEPLPLTQDQVHLQGHAIEVRLCAEDA--HFRPHTGRVLQFSAPPAT 360

Query: 364 --ESAAGPGRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFAIGGLK 421
             E AA    R D  +EEG E++P YD MLGKLI     R +A   L+  L    + GL 
Sbjct: 361 AFERAAPGALRFDHALEEGAEVTPHYDAMLGKLIVHAPTRAEAIAALVRALHSTRVLGLP 420

Query: 422 TNINFLRRIIGHPAFAAAELDTGFIPRYQEQLLPAPSDLSDEFWQAAAQAFAQSQSSTTR 481
           TN  FL   + HP F A      F+  +  QL    S++  +    +A A   S +S+  
Sbjct: 421 TNRAFLAACLQHPVFGAGHALVPFLAEHAAQLQGLLSNIELKVLVQSAVAVIFSSNSSGA 480

Query: 482 ADDLSSPWGIGNGFRAGLPTEITLHLSCEEQDRALTLGDADAHTAQLKGEYL-LTEHNGL 540
           A              A LP  +   L    Q + + L   +    +L  E+   T H  L
Sbjct: 481 AS-------------AQLPCALARPLRLRHQGQVVPLAVRELGAGRLWVEHAGGTTHLQL 527

Query: 541 RRQHRAIRRGDTLYLQWDGELRRIE---------------------------SYDPISAV 573
             Q   + R  T+     GE+   +                           S++P +  
Sbjct: 528 APQAAGMVRITTMQTGAVGEVHHADHTVRAVPVGPRRWHWQTGGVDGWVEDASWEPAARA 587

Query: 574 EASHSHQGGLT---APMNGSIVRVLVEAGQTVEAGAQLVVLEAMKMEHSIRAPHAGIIKA 630
            A+    GG T   AP NG +V + V AGQ + AG  +VV+E+MK+EHS+ +P A  +  
Sbjct: 588 GAA----GGATELRAPFNGKVVALPVAAGQALSAGDTVVVIESMKLEHSLASPVAATVAE 643

Query: 631 LYCQEGEMVSEGSALVELEHA 651
           L    G+ VS G  L     A
Sbjct: 644 LLVAPGQQVSPGQVLARFAPA 664


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: 1139
Number of extensions: 46
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 651
Length of database: 670
Length adjustment: 38
Effective length of query: 613
Effective length of database: 632
Effective search space:   387416
Effective search space used:   387416
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 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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