Alignments for a candidate for liuB in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuB in Burkholderia phytofirmans PsJN

Align methylcrotonoyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.4) (characterized)
to candidate BPHYT_RS25975 BPHYT_RS25975 urea carboxylase

Query= BRENDA::Q9I299
         (655 letters)



>FitnessBrowser__BFirm:BPHYT_RS25975
          Length = 1203

 Score =  406 bits (1043), Expect = e-117
 Identities = 226/443 (51%), Positives = 285/443 (64%), Gaps = 5/443 (1%)

Query: 9   QRLLVANRGEIACRVMRSARALGIGSVAVHSDIDRHARHVAEADIAVDLGGAKPADSYLR 68
           +++L+ANRGEIACRV+R+ + LGI SVAV+S+ DRHA HV  AD AV +G A  A SYL 
Sbjct: 4   RKVLIANRGEIACRVIRTLKRLGIASVAVYSEADRHAMHVMLADEAVCIGPALAAQSYLN 63

Query: 69  GDRIIAAALASGAQAIHPGYGFLSENADFARACEEAGLLFLGPPAAAIDAMGSKSAAKAL 128
              I+ AA A GA A+HPGYGFLSENA FA+AC++AG+ F+GP    +   G K  A+ L
Sbjct: 64  SAAILDAARACGADAVHPGYGFLSENAAFAQACDDAGIRFIGPTPQHMREFGLKHTAREL 123

Query: 129 MEEAGVPLVPGYHGEAQDLETFRREAGRIGYPVLLKAAAGGGGKGMKVVEREAELAEALS 188
            +   V L+PG  G   D+    REA  IGYPV+LK+ AGGGG GM +    A+L    +
Sbjct: 124 AQANDVALLPG-TGLLPDVSAALREAESIGYPVMLKSTAGGGGIGMSLCRDAAQLEGVFA 182

Query: 189 SAQREAKAAFGDARMLVEKYLLKPRHVEIQVFADRHGHCLYLNERDCSIQRRHQKVVEEA 248
           S  R  +A F +A + VEK++   RH+E+QVF D  G  + L ERDCS+QRR+QKV+EE 
Sbjct: 183 SVARLGEANFANAGVYVEKFVENARHIEVQVFGDGKGGVISLGERDCSVQRRNQKVIEET 242

Query: 249 PAPGLGAELRRAMGEAAVRAAQAIGYVGAGTVEFLLD-ERGQFFFMEMNTRLQVEHPVTE 307
           PAPGL    R A+  +AVR AQA+ Y  AGTVEF+ D +  +F+F+E+NTRLQVEH VTE
Sbjct: 243 PAPGLTHAERSALHASAVRLAQAVKYKSAGTVEFVFDADTRRFYFLEVNTRLQVEHCVTE 302

Query: 308 AITGLDLVAWQIRVARGEALPLTQEQVPLNGHAIEVRLYAEDPEGDFLPASGRLMLYREA 367
            ITG+DLV W IR A GE  PL        G +I+VRLYAEDP   F P++G L      
Sbjct: 303 EITGIDLVEWMIREAEGELAPLDTLATVPQGASIQVRLYAEDPHKQFQPSAGVL---THV 359

Query: 368 AAGPGRRVDSGVREGDEVSPFYDPMLAKLIAWGETREEARQRLLAMLAETSVGGLRTNLA 427
           A     RVD+ V  G EVS FYDP+LAKLI  GETRE     L A L +T + G+ TNL 
Sbjct: 360 AFAADARVDTWVDSGTEVSAFYDPLLAKLIVKGETREAGLAALRAALEQTQLYGIETNLD 419

Query: 428 FLRRILGHPAFAAAELDTGFIAR 450
           +LR I G   FA  E  T F+ R
Sbjct: 420 YLRAIAGSATFARGEQTTAFLGR 442



 Score = 51.2 bits (121), Expect = 3e-10
 Identities = 25/67 (37%), Positives = 43/67 (64%)

Query: 582  QGGLSAPMNGSIVRVLVEPGQTVEAGATLVVLEAMKMEHSIRAPHAGVVKALYCSEGELV 641
            Q G+ A ++GS+ ++LV+ G+ V  G  + ++E+MKME S+ A   GV++ + C+EG  V
Sbjct: 1120 QQGIVADVSGSVWKLLVKEGERVGDGQVVAIVESMKMEISVTASGDGVIETIDCAEGAAV 1179

Query: 642  EEGTPLV 648
              G  L+
Sbjct: 1180 VAGQRLM 1186


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: 1706
Number of extensions: 76
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 655
Length of database: 1203
Length adjustment: 43
Effective length of query: 612
Effective length of database: 1160
Effective search space:   709920
Effective search space used:   709920
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: 56 (26.2 bits)

This GapMind analysis is from Sep 17 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