GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaK in Corynebacterium deserti GIMN1.010

Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_053544053.1 CDES_RS02115 long-chain fatty acid--CoA ligase

Query= BRENDA::A7KUK6
         (562 letters)



>NCBI__GCF_001277995.1:WP_053544053.1
          Length = 568

 Score =  165 bits (417), Expect = 5e-45
 Identities = 159/533 (29%), Positives = 241/533 (45%), Gaps = 62/533 (11%)

Query: 46  TYKSLRDASLDFGKGLKALYEWRKGDVLALFTPNSIDTPVVMWGTLWAGGTISPANPGYT 105
           TY  L         GL+AL   R GD +A+  PN        +  L  G T+   NP YT
Sbjct: 53  TYAELDKEVRRTAAGLRALGV-RPGDRVAIILPNCPQHIAAFYAVLKLGATVIEHNPLYT 111

Query: 106 VDELAFQLKNSHAK-------------------GLVTQASV-----LPVAREAAKKVGMP 141
             EL    K+  A+                    L T  SV     +P  +  A K+ +P
Sbjct: 112 AHELLEPFKDHGARVAIVWDKASPVVEKLRGETNLETIVSVNMINAMPTVQRLALKLPIP 171

Query: 142 ---EDRIILIGDQRDPDARVKHFTSVRNISGATRYRKQKITPAKD-VAFLVYSSGTTGVP 197
              + R  L G   +        ++     G     +  +T  KD VA ++Y+SGTTG P
Sbjct: 172 ALRKSREALSGSAPNTVPFETLASAAMGGEGEDIVSEPSVT--KDTVALILYTSGTTGTP 229

Query: 198 KGVMISHRNIVANIRQQFIAEGEMLSWNGGPDGKGDRVLAFLPFYHIYGLTCLITQALYK 257
           KG  ++H N+ +N+ Q          W  G   K +R+LA LP +H YGLT + T +++ 
Sbjct: 230 KGAQLTHGNLFSNLLQG-------KHWVPGLGDKPERMLAALPMFHAYGLTMVGTLSVFI 282

Query: 258 GYHLIVMSKFDIEKWCAHVQNYRCSFSYIVPPVVLLLGKHPVVDKYD-----LSSLRMMN 312
           G  ++++    I+     ++ +  ++   +P V  L  K  +VD  D     +  +R   
Sbjct: 283 GGEMVLLPTPRIDLIMNIMKKHTPTW---LPGVPTLYEK--IVDASDKEGIPIKGVRNAF 337

Query: 313 SGAAPLTQELVEAVYSRIKVGIKQGYGLSETSPTTHSQRWEDWREAMGSVGRLMPNMQAK 372
           SGA+ L+   VE   +     + +GYGL+ETSP        D R+  G VG   P+   +
Sbjct: 338 SGASTLSTRTVERWENHTGGRLVEGYGLTETSPIIVGNPMSDHRK-QGYVGIPFPDTIVR 396

Query: 373 YMTMPEDGSEPKEVGEGEVGELYLKGPNVFLGYHENPEATKGCLSEDGWFQTGDVGYQDA 432
            +  PE+  E   V +GE GE+ +KGP VF GY    EATK     + W++TGDVG  + 
Sbjct: 397 -IANPENLDET--VPDGEEGEVLVKGPQVFKGYLNQEEATKNSFHGE-WYRTGDVGVMEE 452

Query: 433 KGNFYITDRVKELIKYKGFQVPPAELEGYLVDNDAIDDVAVIGIESETHGSEVPMACVVR 492
            G   +  R+KE+I   GF V PAE+E  +  +  ++D AV+GI  E  GSE  +A +  
Sbjct: 453 DGFIRLVARIKEVIITGGFNVYPAEVEDVITAHPDVEDAAVVGIPRE-DGSENVVAAITL 511

Query: 493 SAKSKSSGTSEKDEAARIIKWLDSKVASHKRLRGGVHFVDEIPKNPSGKILRR 545
              +       KD A          +  +K  R   HF +E+P++  GKI RR
Sbjct: 512 VEGAALDPEGLKDFAR-------ENLTRYKVPRTFYHF-EEMPRDQMGKIRRR 556


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: 729
Number of extensions: 32
Number of successful extensions: 6
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: 562
Length of database: 568
Length adjustment: 36
Effective length of query: 526
Effective length of database: 532
Effective search space:   279832
Effective search space used:   279832
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 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