GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaK in Methanobacterium lacus AL-21

Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_013645675.1 METBO_RS10410 AMP-binding protein

Query= BRENDA::A7KUK6
         (562 letters)



>NCBI__GCF_000191585.1:WP_013645675.1
          Length = 552

 Score =  182 bits (462), Expect = 3e-50
 Identities = 159/556 (28%), Positives = 261/556 (46%), Gaps = 59/556 (10%)

Query: 22  FERKDRAYPD-DKIIYQDADTQRHYTYKSLRDASLDFGKGLKALYEWRKGDVLALFTPNS 80
           FE++    P  D ++Y D D +  +TYK   +      KGL ++   +KGD + ++  N 
Sbjct: 12  FEKQVEKDPSRDFLVYPDRDLR--FTYKQFDERVNMLAKGLLSIGV-KKGDHVGIWAKNV 68

Query: 81  IDTPVVMWGTLWAGGTISPANPGYTVDELAFQLKNSHAKGLVT-----QASVLPVAREAA 135
            D    M+ T   G  +   N  Y   EL + LK S  K L           L +  +  
Sbjct: 69  PDWLTFMFATAKIGVVLVTMNTAYKSHELEYVLKQSDMKALAIIDGFRDVDYLKILYDLV 128

Query: 136 KKVGMPE------------DRIILIGDQRDPDARVKHFTSVRNISGA----TRY-RKQKI 178
            ++   E             ++I +G ++    R  + T+   + G     T + R +K 
Sbjct: 129 PELRTHERGELKSERFPYLKQVIYVGQEKH---RGMYNTNELMLLGKHTDDTEFLRVKKT 185

Query: 179 TPAKDVAFLVYSSGTTGVPKGVMISHRNIVANIRQQFIAEGEMLSWNGGPDGKGDRVLAF 238
               DV  + Y+SGTTG PKGVM++HRNI+ N    +I E +  +       + D++   
Sbjct: 186 LDNHDVINMQYTSGTTGFPKGVMLTHRNILNN--GYYIGECQKFT-------EEDKLCLP 236

Query: 239 LPFYHIYGLTCLITQALYKGYHLIVMSKFDIEKWCAHVQNYRCSFSYIVPPVVLLLGKHP 298
           +P +H +G+   +   L     L+++ +FD     A VQ   C+  Y VP + +    HP
Sbjct: 237 VPLFHCFGIVLGVLAILTHRGTLVMLEEFDPLLALAAVQKESCTALYGVPTMFIAEFNHP 296

Query: 299 VVDKYDLSSLRMMNSGAAPLTQELVEAVYSRIKV-GIKQGYGLSETSPT-THSQRWEDWR 356
           + + +DL+SLR      +P   E ++ V S + +  I   YGL+E SP  T +   +   
Sbjct: 297 MFEMFDLTSLRTGIMAGSPCPIEAMKKVISDMHMEDITIAYGLTEASPVFTQTSVDDSVE 356

Query: 357 EAMGSVGRLMPNMQAKYMTMPEDGSEPKEVGEGEVGELYLKGPNVFLGYHENPEATKGCL 416
           + + +VGR  PN++ K +  PE G   + +G G+ GE+  +G NV  GY++ P+ TK  +
Sbjct: 357 KRVNTVGRARPNIEVKLID-PETG---ETLGPGQPGEICCRGYNVMKGYYKMPDKTKEAI 412

Query: 417 SEDGWFQTGDVGYQDAKGNFYITDRVKELIKYKGFQVPPAELEGYLVDNDAIDDVAVIGI 476
            EDGW  +GD+   D  G + I  R+K++I   G  + P E+E ++     + DV V+GI
Sbjct: 413 EEDGWLHSGDLATVDKDGYYTIVGRIKDMIIRGGENIYPREIEEFIHTMPEVQDVQVVGI 472

Query: 477 ESETHGSEVPMACVVRSAKSKSSGTSEKDEAARIIKWLDSKVASHKRLRGGVHFVDEIPK 536
             E +G E+  A V+     K     E+D    +  +   K+A +K +   V  V+E P 
Sbjct: 473 PDEKYG-EIVGAFVI---PEKDVDLEEED----VRDYALQKIARYK-VPKHVFIVEEFPL 523

Query: 537 NPSGKILRRILKQKFK 552
             SGKI      QKFK
Sbjct: 524 TTSGKI------QKFK 533


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: 667
Number of extensions: 32
Number of successful extensions: 3
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: 552
Length adjustment: 36
Effective length of query: 526
Effective length of database: 516
Effective search space:   271416
Effective search space used:   271416
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 Apr 09 2024. 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