Alignments for a candidate for liuD in Pedobacter sp. GW460-11-11-14-LB5

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuD in Pedobacter sp. GW460-11-11-14-LB5

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate CA265_RS10640 CA265_RS10640 methylcrotonoyl-CoA carboxylase

Query= reanno::SB2B:6937191
         (535 letters)



>FitnessBrowser__Pedo557:CA265_RS10640
          Length = 542

 Score =  504 bits (1298), Expect = e-147
 Identities = 258/528 (48%), Positives = 348/528 (65%), Gaps = 16/528 (3%)

Query: 14  EFKQKHDAMAALVADLKDKLAHIEQGGGLVAMERHLSRGKLAPRARVEKLLDPGSPFLEL 73
           EF +  D    LV +LK +L  I  GGG     +   +GKL  R R+  L+D  S FLE+
Sbjct: 4   EFNKNEDVNKQLVYELKTRLKKIYLGGGEKNAAKQKEKGKLLARERIAYLIDKDSNFLEV 63

Query: 74  SQFAAFEVYDED--VPAAGIIAGIGRVSGVECMIIANDATVKGGTYYPITVKKHLRAQAI 131
             F A  +Y E    P+AG++ GIG VSG +CMI+ANDATVK G ++P+T KK+LRAQ I
Sbjct: 64  GAFTADGMYAEQGGCPSAGVVCGIGYVSGRQCMIVANDATVKAGAWFPMTAKKNLRAQEI 123

Query: 132 AERCHLPCIYLVDSGGANLPRQDEVFPDRDHFGRIFFNQARMSAKGIPQIAVVMGLCTAG 191
           A    LP IYLVDS G  LP QDE+FPD++HFGR+F N A MS++GI QI+ +MG C AG
Sbjct: 124 AMENRLPVIYLVDSAGVYLPMQDEIFPDKEHFGRMFRNNAIMSSEGIVQISAIMGACVAG 183

Query: 192 GAYVPAMADESIIVREQGTIFLAGPPLVKAATGEEVSAEELGGGDVHTKISGVADHLAQN 251
           GAY+P M+DE++IV + G++FLAG  LVK+A GEEV  E LGG   H +ISGV D+   N
Sbjct: 184 GAYLPIMSDEAMIVDKTGSVFLAGSYLVKSAIGEEVDNETLGGATTHCEISGVTDYKHLN 243

Query: 252 DEHALELARKAVSRLNHQKQVELQLSKVKPPKYDINELYGIVGTDLKKPFDVKEVIARIV 311
           D+  L+  R  +S L   +       K   PK    ELYGI+  +  KP+++ ++I R+V
Sbjct: 244 DQACLDSIRNIMSMLGAPQNAGFDRIKPAKPKEKEEELYGILPENRDKPYEIMDIINRLV 303

Query: 312 DDSDFDEFKANYGTTLVCGFARIHGYPVGIVAN--------------NGILFSESAQKGA 357
           D S+F+E+K  YG ++VCG  RI G+ VGIVAN               G+++S+SA K  
Sbjct: 304 DGSEFEEYKKGYGQSIVCGLGRIDGWAVGIVANQRKVVKSKKGEMQFGGVIYSDSADKAT 363

Query: 358 HFIELCCQRKIPLVFLQNITGFMVGKKYEHEGIAKHGAKMVTAVSCATVPKFTVLIGGSY 417
            FI  C Q+KIPLVFLQ++TGFMVG + EH GI K GAKMV AV+ + VPKFT+++G SY
Sbjct: 364 RFIMNCNQKKIPLVFLQDVTGFMVGSRSEHGGIIKDGAKMVNAVANSVVPKFTIVLGNSY 423

Query: 418 GAGNYGMCGRAFEPTLMWMWPNARISVMGGEQAAGVLATVRKDGLARKGETMSAEEEAKF 477
           GAGNY MCG+A++P L++ WP A+I+VMGG QAA  L  +++  L  KGE ++ E+EA+ 
Sbjct: 424 GAGNYAMCGKAYDPRLIYAWPTAKIAVMGGSQAAKTLLQIQEASLKAKGEVITPEKEAEL 483

Query: 478 KAPIIAQYDKEGHPYHASARLWDDGIIDPAQTRDVLGLAISAALNAPI 525
              I  +YD +  PY+A++RLW DGIIDP +TR V+ + I AA  +PI
Sbjct: 484 LKEITDRYDSQTTPYYAASRLWVDGIIDPLETRKVISMGIEAANQSPI 531


Lambda     K      H
   0.320    0.137    0.405 

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: 761
Number of extensions: 30
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: 535
Length of database: 542
Length adjustment: 35
Effective length of query: 500
Effective length of database: 507
Effective search space:   253500
Effective search space used:   253500
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: 52 (24.6 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