GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Methylocapsa aurea KYG

Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_036261146.1 DL86_RS10295 acetyl-CoA C-acyltransferase

Query= uniprot:A0A2Z5MFE9
         (400 letters)



>NCBI__GCF_000746085.1:WP_036261146.1
          Length = 395

 Score =  242 bits (618), Expect = 1e-68
 Identities = 154/393 (39%), Positives = 221/393 (56%), Gaps = 8/393 (2%)

Query: 6   ICDAIRTPIGRYGGALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQAGEDNR 65
           I  A RTPIG + G  K + A DLGA  IKA + R+ G+    +D+VI GC   AG+  +
Sbjct: 9   IVAAARTPIGGFQGDFKGLAATDLGAAAIKAAVARS-GLRPEDIDEVILGCVLSAGQ-GQ 66

Query: 66  NVARMSALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESMTRAPF 125
             AR +AL AGLP  A   TIN++CGSGM A+      ++A  A +++AGG+ESMT AP+
Sbjct: 67  APARQAALKAGLPEAAGCVTINKMCGSGMKAIMFGHDLLRADSAAIVLAGGMESMTNAPY 126

Query: 126 VMGKAASAFTRQAEIHDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGISRADQDAFA 185
           ++ +A + +      H   I   F++ L         M   AE+ AE F  +RA QDAFA
Sbjct: 127 LLDRARAGYRMG---HGRIIDHMFLDGLEDAYGQRLPMGAFAEDCAEAFQFTRAAQDAFA 183

Query: 186 LASQQKAARAQRDGTLAQEIVGVEIAQKKGDAIRVTLDEHPRETSLESLARLKGVVRPDG 245
           L S ++A +A  DG+   EI  V     K D + +  DE P +  ++ ++ LK   R  G
Sbjct: 184 LCSLERAQKAIADGSFEAEIAQVSAPAGKIDRM-IAEDEQPLKARIDKISTLKPAFRDGG 242

Query: 246 TVTAGNASGVNDGACALLIASQQAAEQYGLRRRARVVGMATAGVEPRIMGIGPAPATQKL 305
           TVTA N+S ++DGA AL++  +  AE+ G    A +   AT    P      P  A +KL
Sbjct: 243 TVTAANSSSISDGAAALVLMRRSDAERRGASALAIIRAHATHAQAPDQFATAPIGALRKL 302

Query: 306 LRQLGMTLDQLDVIELNEAFASQGLAVLRMLGLRDDDPRVNPNGGAIALGHPLGASGARL 365
           + + G +L  +D+ E+NEAFA   +A +R L L  +  +VN +GGA ALGHP+GASGAR+
Sbjct: 303 MDKTGWSLPDVDLFEINEAFAVVTMAAMRELALPHE--KVNVHGGACALGHPIGASGARI 360

Query: 366 VTTALHQLERSNGRFALCTMCIGVGQGIALVIE 398
           V T L  L++   +     +CIG G+  AL IE
Sbjct: 361 VATLLAALKKYGLKRGAAALCIGGGEATALAIE 393


Lambda     K      H
   0.319    0.134    0.386 

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: 413
Number of extensions: 23
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: 400
Length of database: 395
Length adjustment: 31
Effective length of query: 369
Effective length of database: 364
Effective search space:   134316
Effective search space used:   134316
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 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