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)



>lcl|FitnessBrowser__WCS417:GFF3324 PS417_17010 AMP-binding protein
          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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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

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:

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. Gaps may be due to:

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