GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaK in Methylocapsa aurea KYG

Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_036258835.1 DL86_RS04845 malonyl-CoA synthase

Query= BRENDA::A7KUK6
         (562 letters)



>NCBI__GCF_000746085.1:WP_036258835.1
          Length = 507

 Score =  180 bits (457), Expect = 1e-49
 Identities = 159/536 (29%), Positives = 250/536 (46%), Gaps = 37/536 (6%)

Query: 20  FLFER-KDRAYPDDKIIYQDADTQRHYTYKSLRDASLDFGKGLKALYEWRKGDVLALFTP 78
           +LF+  +DR  P D  I+        ++Y     AS      L AL   + GD +A    
Sbjct: 4   YLFQMIRDRIGPPDDRIFLQTPGGPDFSYGDAVAASARSAAALSALGV-KPGDRVAAQVE 62

Query: 79  NSIDTPVVMWGTLWAGGTISPANPGYTVDELAFQLKNSHAKGLVTQASVLPVAREAAKKV 138
            S    ++  G + AG    P NP YT+ E+A+ L ++    ++              K 
Sbjct: 63  KSAAAVMLYLGAVRAGAIFLPLNPAYTLAEIAYFLSDAEPAVVICDPDRRGELASLVAKA 122

Query: 139 GMPEDRIILIGDQRDPDARVKHFTSVRNISGATRYRKQKITPAKDVAFLVYSSGTTGVPK 198
           G P     L  D R   A +   T   + S A R          D+A ++Y+SGTTG  K
Sbjct: 123 GAPLLET-LGADGRGSFADLCA-TQSGDFSDAAR-------GPDDLAAILYTSGTTGRSK 173

Query: 199 GVMISHRNIVANIRQQFIAEGEMLSWNGGPDGKGDRVLAFLPFYHIYGLTCLITQALYKG 258
           G M++H N+ +N      A   + +W   P    D +L  LP YH +GL   I   L+  
Sbjct: 174 GAMLTHANLASN------AATLVEAWRFTP---ADVLLHALPIYHTHGLFVAINTILFSA 224

Query: 259 YHLIVMSKFDIEKWCAHVQNYRCSFSYIVPPVVLLLGKHPVVDKYDLSSLRMMNSGAAPL 318
             ++ +++FD ++  A +   + S    VP     L + P V +   + +R+  SG+APL
Sbjct: 225 GRILFLARFDADECLALMP--QASAMMGVPTFYTRLLRRPDVLRRASAHMRLFISGSAPL 282

Query: 319 TQELVEAVYSRIKVGIKQGYGLSETSPTTHSQRWEDWREAMGSVGRLMPNMQAKYMTMPE 378
             E       R    I + YG++ET+    +    D     G+VG  +P +  + +  PE
Sbjct: 283 LAETHREWVERTGHAILERYGMTETNMIASNPY--DGERIAGTVGPPLPGVAVR-IADPE 339

Query: 379 DGSEPKEVGEGEVGELYLKGPNVFLGYHENPEATKGCLSEDGWFQTGDVGYQDAKGNFYI 438
            G++   +G  ++G + +KGPNVF GY  NPE T      DG+F TGD+G  DA G  +I
Sbjct: 340 TGAD---LGRDKIGVIEVKGPNVFKGYWRNPEKTAAEFRADGFFITGDLGKIDANGYVHI 396

Query: 439 TDRVKELIKYKGFQVPPAELEGYLVDNDAIDDVAVIGIESETHGSEVPMACVVRSAKSKS 498
             R K+LI   GF V P E+E  +     + + AV+G+  E  G  +  A VVR   +  
Sbjct: 397 IGRAKDLIITGGFNVYPKEVEAEIDAIAGVVESAVVGLPHEDFGEGI-AAIVVR---TPG 452

Query: 499 SGTSEKDEAARIIKWLDSKVASHKRLRGGVHFVDEIPKNPSGKILRRILKQKFKGA 554
           SG  E    A +   L++++A  K L   V FV+E+P+N  GK+ +  L++ +KG+
Sbjct: 453 SGLDE----AGVRSALENRLAKFK-LPKRVIFVEELPRNAMGKVQKNALRETYKGS 503


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: 657
Number of extensions: 31
Number of successful extensions: 6
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: 507
Length adjustment: 35
Effective length of query: 527
Effective length of database: 472
Effective search space:   248744
Effective search space used:   248744
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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