Aligments for a candidate for acs in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Aligments for a candidate for acs in Pseudomonas simiae WCS417

Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate GFF3324 PS417_17010 AMP-binding protein

Query= metacyc::MONOMER-20125
         (556 letters)



>FitnessBrowser__WCS417:GFF3324
          Length = 544

 Score =  148 bits (374), Expect = 5e-40
 Identities = 146/542 (26%), Positives = 232/542 (42%), Gaps = 69/542 (12%)

Query: 28  GDCTSVVYDAVSYTWSQTHRRCLCLASSIASLGIENGHVVSVLAPNVPQMYELHFAVPMA 87
           G+   V +    YTW Q        A +  +LG++ G  + + APN  +      A    
Sbjct: 36  GEALVVRHQQRRYTWRQLAETVDLHARAFLALGMQTGDRLGIWAPNCAEWCISQIASAKL 95

Query: 88  GAILNAVNLRLDARTISILLHHSESKLI-------------FVDHLSRDLILEAIALFPK 134
           G IL  +N    +  +  +L  S  + +              +  L+ DL    I+L P 
Sbjct: 96  GVILVNINPAYRSSELEYVLKQSGCQWLVCAGSFKTSDYHAMLQALNPDL-RGMISLDP- 153

Query: 135 QAPVPRLVFMADESESGNSSELGKEFFCSYKDLIDRGDPDFKWVMPKSEWDPMI-LNYTS 193
            +P P  +  A  +  G    L        + L  R             +D  + + YTS
Sbjct: 154 -SPPPGFLPWAQLAALGTGIPL--------EQLHSR--------QTSLHFDQAVNIQYTS 196

Query: 194 GTTSSPKGVVHCHRGIF---IMTVDSLIDWGVPKQPVYLWTLPMFHANGWSYPWGMAAVG 250
           GTT  PKG    H  I     M  +SL   G+  Q   +  +P++H  G           
Sbjct: 197 GTTGFPKGATLSHHNILNNGYMVGESL---GLTAQDRLVIPVPLYHCFGMVMGNLGCITH 253

Query: 251 GTNICLRK--FDSEIIYDMIKRHGVTHMCGAPVVLNMLSNAP--GSEPLKTTVQIMTAGA 306
           GT +      FD  +    +     T + G P +   + + P  G   L +    + AGA
Sbjct: 254 GTTMIYPNDGFDPLLTLTAVAEEHATGLYGVPTMFIAMLDHPQLGGFDLSSLRTGIMAGA 313

Query: 307 PPPSAVLFR--TESLGFAVSHGYGLTETAGLVVSCAWKKEWNHLPATERARLKSRQGVGT 364
             P  V+ R  +E     V   YG+TET+ + +      +           L+ R  V T
Sbjct: 314 TCPIEVMRRVISEMHMSEVQIAYGMTETSPVSLQTGADDD-----------LERR--VTT 360

Query: 365 VMQTKIDVVDPVTGAAVKRDGST-----LGEVVLRGGSVMLGYLKDPEGTAKSMTADGWF 419
           V +T+  + + +  A    DG+T     +GE+  RG SVMLGY  +P+ T +++   GW 
Sbjct: 361 VGRTQPQLENKIIDA----DGNTVARGEIGELCTRGYSVMLGYWNNPDATREAIDDAGWM 416

Query: 420 YTGDVGVMHPDGYLEIKDRSKDVIISGGENLSSVEVESILYSHPDILEAAVVARPDEFWG 479
           +TGD+  M   GY+ I  R+KD+II GGEN+   E+E   ++HP + +  V+  PDE +G
Sbjct: 417 HTGDLASMDAHGYVCIAGRNKDMIIRGGENVYPRELEEFFFTHPAVADVQVIGIPDERYG 476

Query: 480 ETPCAFVSLKKGLTKKPTEKEIVEYCRSKLPRYMVPKTVVFKEELPKTSTGKVQKFILRD 539
           E   A+V    G      E E+  +C+ ++  +  PK   F EE P T TGK+QKF +R+
Sbjct: 477 EAIVAWVKFHPG--HVANELELQTWCKGRIAHFKTPKHFKFVEEFPMTVTGKIQKFRMRE 534

Query: 540 MA 541
           ++
Sbjct: 535 IS 536


Lambda     K      H
   0.319    0.135    0.412 

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: 755
Number of extensions: 40
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: 556
Length of database: 544
Length adjustment: 36
Effective length of query: 520
Effective length of database: 508
Effective search space:   264160
Effective search space used:   264160
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: 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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Steps (tab-delimited)
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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, 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