Alignments for a candidate for liuB in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuB in Escherichia coli BW25113

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate 17326 b3256 acetyl-CoA carboxylase (NCBI)

Query= reanno::pseudo5_N2C3_1:AO356_01595
         (649 letters)



>FitnessBrowser__Keio:17326
          Length = 449

 Score =  435 bits (1118), Expect = e-126
 Identities = 222/427 (51%), Positives = 303/427 (70%), Gaps = 4/427 (0%)

Query: 6   LTTLLVANRGEIACRVMRTARAMGLTTVAVHSATDRDARHSREADIRVDLGGSKAADSYL 65
           L  +++ANRGEIA R++R  + +G+ TVAVHS+ DRD +H   AD  V +G + +  SYL
Sbjct: 2   LDKIVIANRGEIALRILRACKELGIKTVAVHSSADRDLKHVLLADETVCIGPAPSVKSYL 61

Query: 66  QIDKLIAAAKASGAQAIHPGYGFLSENAGFARAIENAGLIFLGPPASAIDAMGSKSAAKT 125
            I  +I+AA+ +GA AIHPGYGFLSENA FA  +E +G IF+GP A  I  MG K +A  
Sbjct: 62  NIPAIISAAEITGAVAIHPGYGFLSENANFAEQVERSGFIFIGPKAETIRLMGDKVSAIA 121

Query: 126 LMETAGVPLVPGYHGE-AQDLETFRDAAERIGYPVLLKATAGGGGKGMKVVEDVSQLAEA 184
            M+ AGVP VPG  G    D++  R  A+RIGYPV++KA+ GGGG+GM+VV   ++LA++
Sbjct: 122 AMKKAGVPCVPGSDGPLGDDMDKNRAIAKRIGYPVIIKASGGGGGRGMRVVRGDAELAQS 181

Query: 185 LASAQREAQSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVE 244
           ++  + EA+++F +  + +EKYL  PRHVEIQV AD  GN +YL ERDCS+QRRHQKVVE
Sbjct: 182 ISMTRAEAKAAFSNDMVYMEKYLENPRHVEIQVLADGQGNAIYLAERDCSMQRRHQKVVE 241

Query: 245 EAPAPGLTPQLRRAMGEAAVRAAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVT 304
           EAPAPG+TP+LRR +GE   +A   IGY GAGT EFL +  GEF+F+EMNTR+QVEHPVT
Sbjct: 242 EAPAPGITPELRRYIGERCAKACVDIGYRGAGTFEFLFE-NGEFYFIEMNTRIQVEHPVT 300

Query: 305 EAITGLDLVAWQIRVAQGEPLPITQAQVPLLGHAIEVRLYAEDPGNDFLPATGRLALYRE 364
           E ITG+DL+  Q+R+A G+PL I Q +V + GHA+E R+ AEDP N FLP+ G++  +  
Sbjct: 301 EMITGVDLIKEQLRIAAGQPLSIKQEEVHVRGHAVECRINAEDP-NTFLPSPGKITRF-H 358

Query: 365 SAEGPGRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFVIGGLKTNI 424
           +  G G R +S +  G  + P+YD M+GKLI +GE+R+ A  R+ + L E +I G+KTN+
Sbjct: 359 APGGFGVRWESHIYAGYTVPPYYDSMIGKLICYGENRDVAIARMKNALQELIIDGIKTNV 418

Query: 425 GFLRRIV 431
               RI+
Sbjct: 419 DLQIRIM 425


Lambda     K      H
   0.319    0.134    0.390 

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: 705
Number of extensions: 28
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: 649
Length of database: 449
Length adjustment: 35
Effective length of query: 614
Effective length of database: 414
Effective search space:   254196
Effective search space used:   254196
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 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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 2024 update 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