GapMind for catabolism of small carbon sources

 

Aligments for a candidate for paaK in Burkholderia phytofirmans PsJN

Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate BPHYT_RS21775 BPHYT_RS21775 long-chain fatty acid--CoA ligase

Query= BRENDA::A7KUK6
         (562 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS21775 BPHYT_RS21775 long-chain
           fatty acid--CoA ligase
          Length = 553

 Score =  213 bits (542), Expect = 2e-59
 Identities = 160/530 (30%), Positives = 256/530 (48%), Gaps = 57/530 (10%)

Query: 46  TYKSLRDASLDFGKGLKALYE---WRKGDVLALFTPNSIDTPVVMWGTLWAGGTISPANP 102
           T++ LRD      + L+A +     + G+V+++F  N I T  ++   +++G   +P N 
Sbjct: 44  TFRELRDDC----RALEARFREAGLQPGEVISVFMGNGIQTARLLLAAMYSGLVANPLNL 99

Query: 103 GYTVDELAFQLKNSHAKGLVTQA---SVLPVAREAAKKVGMPEDRIILIG---DQRDPDA 156
                ++ + + +S  + +   +   +V+  A    +  G+  + I LI    D  +P +
Sbjct: 100 LCQPSQVRYIVDHSDTRMIFAASDTHAVIGAAVAELRAAGLTRE-IALIQTEPDDAEPPS 158

Query: 157 RVKHFTSV-----RNISGATR----YRKQKITP-------------AKDVAFLVYSSGTT 194
             KH  ++        SGAT       K+ + P             A DVA L+Y+SGTT
Sbjct: 159 LAKHEPALVEAAAHGASGATAPAPALAKRSVAPRPVTSRATAYEPTADDVALLMYTSGTT 218

Query: 195 GVPKGVMISHRNIVANIRQQFIAEGEMLSWNGGPDGKGDRVLAFLPFYHIYGLTCLITQA 254
           G PKGV+++HRN+VAN R    AE  + S         DRVLA LP YHI GL   +   
Sbjct: 219 GTPKGVLLTHRNLVANARN-ISAEHRLAS--------DDRVLASLPLYHINGLVVTLLAP 269

Query: 255 LYKGYHLIVMSKFDIEKWCAHVQNYRCSFSYIVPPVVLLLGKHPVVDKYDLSSLRMMNSG 314
           L+ G   ++ S+F    +   V  + C++  +VP +V  L        YDLS+L+   S 
Sbjct: 270 LFHGGSAVMTSRFSARTFWRDVALHACTWINVVPTIVAYLLNADEACTYDLSALKFCRSA 329

Query: 315 AAPLTQELVEAVYSRIKVGIKQGYGLSETSPTTHSQRWEDWREAMGSVGRLMPNMQAKYM 374
           +A L  +   A  +R  +G+ +  G++ET+    S  +E  R  +GS+G L    +AK +
Sbjct: 330 SAALPADHHRAFEARFGIGVIETMGMTETAAPVFSNPYEMERRRVGSIG-LPSGGEAKVI 388

Query: 375 TMPEDGSEPKEVGEGEVGELYLKGPNVFLGYHENPEATKGCLSEDGWFQTGDVGYQDAKG 434
                  E +E    E GEL L+G  V  GY++ PE T    + DGW +TGD+GY+DA G
Sbjct: 389 DR-----EGRECAANECGELVLRGEQVMGGYYKRPEETAAAFTSDGWLRTGDLGYRDADG 443

Query: 435 NFYITDRVKELIKYKGFQVPPAELEGYLVDNDAIDDVAVIGIESETHGSEVPMACVVRSA 494
            FYI  R KELI   G  + P E++  L+ +  + D A +G+    +G ++ +A VV   
Sbjct: 444 YFYINGRAKELIIKGGENIAPREIDEALLRHPDVLDAAAVGVPDPAYGQDI-VAFVVPRM 502

Query: 495 KSKSSGTSEKDEAARIIKWLDSKVASHKRLRGGVHFVDEIPKNPSGKILR 544
                     D     ++ L  +  + K  R    FVDE+P+ PSGK+ R
Sbjct: 503 SDGRGAPDPADLREHCLREL-GRYKTPKEFR----FVDELPRGPSGKVQR 547


Lambda     K      H
   0.317    0.136    0.410 

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: 687
Number of extensions: 26
Number of successful extensions: 5
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: 562
Length of database: 553
Length adjustment: 36
Effective length of query: 526
Effective length of database: 517
Effective search space:   271942
Effective search space used:   271942
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 (21.7 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