GapMind for catabolism of small carbon sources

 

Aligments for a candidate for paaK in Pseudomonas simiae WCS417

Align medium-chain acyl-CoA ligase (EC 6.2.1.2); phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate GFF4309 PS417_22070 long-chain fatty acid--CoA ligase

Query= BRENDA::O74725
         (578 letters)



>lcl|FitnessBrowser__WCS417:GFF4309 PS417_22070 long-chain fatty
           acid--CoA ligase
          Length = 562

 Score =  173 bits (439), Expect = 1e-47
 Identities = 149/484 (30%), Positives = 229/484 (47%), Gaps = 42/484 (8%)

Query: 104 RLGGVLTPANASYSAAELTHQLLDSKAKALVTCVPLLSISLEAAAKAGLPKNRIYLLDVP 163
           R G ++   N  Y+  E+ HQ  D+  +ALV      S   E  +   +     YL+   
Sbjct: 97  RAGLIVVNTNPLYTPREMRHQFKDAGVRALVYLNLFGSRVQEVCSDTEID----YLI--- 149

Query: 164 EQLLGGVKPPAGYKSVSELTQAGKSLPPVDEL----------RWSAGEGARR-------T 206
           E  +G   P A    V+ L    K + P   L             AG G  R        
Sbjct: 150 EARMGDFMPTAKGWLVNTLVDKVKKMVPAYSLPRAVAFKRALHMGAGLGVTRHPVTLDDI 209

Query: 207 AFVCYSSGTSGLPKGVMISHRNVIANTLQIKA-FEQNYRDGGGTKPASTEVALGLLPQSH 265
           A + Y+ GT+GL KG M++H N++AN  Q++A   Q   DG        EV +  LP  H
Sbjct: 210 AVLQYTGGTTGLAKGAMLTHGNLVANMQQVRACMSQTGDDGHPLIKEGQEVMIAPLPLYH 269

Query: 266 IYALVVIGHAGAYRGDQTIVLPK-FELKSYLNAIQQYKISALFLVPPIIIHMLGTQDVCS 324
           IYA           G+  +++    ++  ++  +++++ + L  +  + + ++   D  S
Sbjct: 270 IYAFTANCMCMMVSGNHNVLITNPRDIGGFIKELKKWRFTGLLGLNTLFVALMDHPDFKS 329

Query: 325 KYDLSSVTSLFTGAAPLGMETAADFLKLYPNILIRQGYGLTETCTVVSSTHPHD--IWLG 382
             D S +    +G   L   TA  + ++     I +GYGLTET + V+ST+P+     LG
Sbjct: 330 -LDFSHLKLTNSGGTALIKATAERWQQI-TGCAIGEGYGLTET-SPVASTNPYGNKSRLG 386

Query: 383 SSGALLPGVEARIVTPENKEITTYDSPGELVVRSPSVVLGYLNNEKATAETF-VDGWMRT 441
           + G  +P    +++     E+   +  GEL ++ P V+ GY    +ATAE    +GW++T
Sbjct: 387 TVGIPVPATAMKVIDDHGVELPLGER-GELCIKGPQVMKGYWQQPEATAEALDAEGWLKT 445

Query: 442 GDEAVIRRSPKGIEHVFIVDRIKELIKVKGLQVAPAELEAHILAHPDVSDCAVIAIPDDR 501
           GD AVI         V IVDR K+LI V G  V P E+E  ++AHP V++CAVI +PD+R
Sbjct: 446 GDIAVIDEEG----FVSIVDRKKDLIIVSGFNVYPNEIEDVVMAHPAVANCAVIGVPDER 501

Query: 502 AGEVPKAIVVKSASAGSDESVSQALVKYVEDHKARHKWLKGGIRFVDAIPKSPSGKILRR 561
            GE  K  VV  A   S E     L  Y + +   +K  K  I   D++P +P GKILRR
Sbjct: 502 TGEAVKLFVVARAEGVSLEE----LKAYCKTNFTGYKVPK-HIVLRDSLPMTPVGKILRR 556

Query: 562 LIRD 565
            +RD
Sbjct: 557 ELRD 560


Lambda     K      H
   0.316    0.134    0.392 

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: 712
Number of extensions: 36
Number of successful extensions: 7
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: 578
Length of database: 562
Length adjustment: 36
Effective length of query: 542
Effective length of database: 526
Effective search space:   285092
Effective search space used:   285092
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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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