GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaK in Kocuria flava HO-9041

Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_058858514.1 AS188_RS08645 long-chain fatty acid--CoA ligase

Query= BRENDA::A7KUK6
         (562 letters)



>NCBI__GCF_001482365.1:WP_058858514.1
          Length = 506

 Score =  199 bits (507), Expect = 2e-55
 Identities = 154/503 (30%), Positives = 240/503 (47%), Gaps = 46/503 (9%)

Query: 49  SLRDASLDFGKGLKALYEWRKGDVLALFTPNSIDTPVVMWGTLWAGGTISPANPGYTVDE 108
           S R ASL   +G++A      GD +AL  PN    PV  +G L  GG + P NP  +  E
Sbjct: 37  SARVASLLTSRGVRA------GDRVALILPNVPHMPVAYYGVLRTGGVVVPLNPLLSPRE 90

Query: 109 LAFQLKNSHAKGLVTQASVLPVAREAAKKVGMPEDRIILIGDQRDPDAR-VKHFTSVRNI 167
           L +  +++    ++   +V   AR AA ++G     + +      P+ R V     V   
Sbjct: 91  LGYHFQDAEVSLVLVWETVAGAARAAAAELGRDVPVVEITAAGTLPELRRVPPLPEVAER 150

Query: 168 SGATRYRKQKITPAKDVAFLVYSSGTTGVPKGVMISHRNIVANIRQQFIAEGEMLSWNGG 227
           +G            +D A L+Y+SGTTG PKG +++H N+ +N R       E+ S    
Sbjct: 151 AG------------EDPAVLLYTSGTTGRPKGAVLTHANLTSNAR----LSAELFSL--- 191

Query: 228 PDGKGDRVLAFLPFYHIYGLTCLITQALYKGYHLIVMSKFDIEKWCAHVQNYRCSFSYIV 287
               GD +   LPF+H++G T  +  AL  G  + ++ +FD  +    +     +    V
Sbjct: 192 --APGDVMFGGLPFFHVFGQTVALNGALGAGATVTLLPRFDPARALEILVRDEVTVFAGV 249

Query: 288 PPVVLLLGKHPVVDKYDLSSLRMMNSGAAPLTQELVEAVYSRIKVGIKQGYGLSETSPTT 347
           P + + L +    +      LR   SG +PL  E++E   +     + +GYGLSETSP  
Sbjct: 250 PSMYVALLRAAGGEPVRAPHLRAGVSGGSPLPVEVLERFEALFGAPVYEGYGLSETSPVV 309

Query: 348 HSQRWEDWREAMGSVGRLMPNMQAKYMTMPEDGSEPKEVGEGEVGELYLKGPNVFLGYHE 407
              + ED     GS+G ++   Q + +   +D     EV  GE+GEL + G  V  GY  
Sbjct: 310 CFNQ-EDRGRRPGSIGTVVRGAQLRVL---DDAGA--EVPVGEIGELAVAGEYVMAGYWR 363

Query: 408 NPEATKGCLSEDGWFQTGDVGYQDAKGNFYITDRVKELIKYKGFQVPPAELEGYLVDNDA 467
           NPEAT   + +DGWF+TGD+   D  G ++I DR K+++   G+ V P E+E  L     
Sbjct: 364 NPEATAAAI-QDGWFRTGDLARVDEDGFYWIVDRKKDMVLRGGYNVYPREIEEVLYQYPG 422

Query: 468 IDDVAVIGIESETHGSEVPMACVVRSAKSKSSGTSEKDEAARIIK---WLDSKVASHKRL 524
           I + AV+G+  E  G EV      R          E +  AR+ +   ++  ++A +K  
Sbjct: 423 IAEAAVVGVPDEAMGEEVAAVVAFRD-------VPEPERPARLDELDAFVRERLARYKHP 475

Query: 525 RGGVHFVDEIPKNPSGKILRRIL 547
           R     V+E+PK P+GKIL+R L
Sbjct: 476 R-WYKVVEELPKGPTGKILKRSL 497


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: 683
Number of extensions: 37
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: 562
Length of database: 506
Length adjustment: 35
Effective length of query: 527
Effective length of database: 471
Effective search space:   248217
Effective search space used:   248217
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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