GapMind for catabolism of small carbon sources

 

Alignments 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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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:

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. 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:

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:

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