Aligments for a candidate for liuB in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Aligments for a candidate for liuB in Phaeobacter inhibens BS107

Align methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate GFF1244 PGA1_c12600 biotin carboxylase AccA

Query= BRENDA::Q42523
         (734 letters)



>lcl|FitnessBrowser__Phaeo:GFF1244 PGA1_c12600 biotin carboxylase
           AccA
          Length = 450

 Score =  425 bits (1093), Expect = e-123
 Identities = 218/443 (49%), Positives = 289/443 (65%), Gaps = 4/443 (0%)

Query: 39  EKILVANRGEIACRIMRTAKRLGIQTVAVYSDADRDSLHVKSADEAVRIGPPSARLSYLS 98
           +KIL+ANRGEIA R++R  + +GIQ+VAV+S AD D++HV+ ADE+V IGPPS   SYLS
Sbjct: 3   DKILIANRGEIALRVIRACREMGIQSVAVHSTADADAMHVRMADESVCIGPPSGTHSYLS 62

Query: 99  GVTIMEAAARTGAQAIHPGYGFLSESSDFAQLCEDSGLTFIGPPASAIRDMGDKSASKRI 158
              I+ A   TGAQAIHPGYGFLSE+++F Q+ ED GLTFIGP A  IR MGDK  +K  
Sbjct: 63  IPAIISACEITGAQAIHPGYGFLSENANFVQIVEDHGLTFIGPTAEHIRVMGDKITAKDT 122

Query: 159 MGAAGVPLVPGYHGHEQDIDHMKSEAEKIGYPIIIKPTHGGGGKGMRIVQSGKDFADSFL 218
           M   GVP VPG  G   D++  K   E IGYP+IIK T GGGG+GM++ ++  D   +F+
Sbjct: 123 MKDLGVPCVPGSDGGVPDLETAKKIGEDIGYPVIIKATAGGGGRGMKVAKTAADMEQAFM 182

Query: 219 GAQREAAASFGVNTILLEKYITRPRHIEVQIFGDKHGNVLHLYERDCSVQRRHQKIIEEA 278
            A+ E  A+FG + + +EKY+T PRHIE+Q+FGD  G  +HL ERDCS+QRRHQK+ EEA
Sbjct: 183 TARAEGKAAFGNDEVYIEKYLTTPRHIEIQVFGDGKGKAVHLGERDCSLQRRHQKVFEEA 242

Query: 279 PAPNISEKFRANLGQAAVSAARAVGYYNAGTVEFIVDTESDQFYFMEMNTRLQVEHPVTE 338
           P P I+ + RA +G+    A   + Y  AGT+EF+   E  +FYF+EMNTRLQVEHPVTE
Sbjct: 243 PGPCITPEERARIGKTCAEAVAKINYIGAGTIEFLY--EKGEFYFIEMNTRLQVEHPVTE 300

Query: 339 MIVGQDLVEWQIRVANGEPLPLSQSEVPMSGHAFEARIYAENVPKGFLPATGVLNHYRPV 398
            I G DLV  QIRVA G P+  SQ ++ ++GH+ E RI AE +P  F P  G +  Y   
Sbjct: 301 SIFGVDLVREQIRVAEGLPMSFSQDDLEINGHSIEVRINAEKLP-NFSPCPGRITQYHAP 359

Query: 399 AVSPSVRVETGVEQGDTVSMHYDPMIAKLVVWGGNRGEALVKLKDCLSNFQVAGVPTNIN 458
                VR+++ +  G ++  +YD +I KL+V G +R EAL +L   L    V GV T + 
Sbjct: 360 G-GLGVRMDSALYDGYSIPPYYDSLIGKLIVHGRDRPEALARLSRALGELIVDGVDTTVP 418

Query: 459 FLQKLASHKEFAVGNVETHFIEH 481
               L   K+   G    H++EH
Sbjct: 419 LFHALLEEKDIRTGEYNIHWLEH 441


Lambda     K      H
   0.316    0.132    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: 863
Number of extensions: 35
Number of successful extensions: 3
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: 734
Length of database: 450
Length adjustment: 36
Effective length of query: 698
Effective length of database: 414
Effective search space:   288972
Effective search space used:   288972
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 (21.6 bits)
S2: 53 (25.0 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 preprint on GapMind for carbon sources, or view the source code.

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