GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Rhodobacter viridis JA737

Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_110806646.1 C8J30_RS14960 acetyl-CoA C-acyltransferase

Query= uniprot:A0A2Z5MFE9
         (400 letters)



>NCBI__GCF_003217355.1:WP_110806646.1
          Length = 395

 Score =  264 bits (675), Expect = 3e-75
 Identities = 162/390 (41%), Positives = 225/390 (57%), Gaps = 9/390 (2%)

Query: 11  RTPIGRYGGALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQAGEDNRNVARM 70
           RTP+G + GA  D+ A DLGAV ++A + R  G+   AVD+VI GC   AG+  +  AR 
Sbjct: 13  RTPMGGFQGAFADLAAADLGAVALRAALSR-AGLPAEAVDEVILGCVLPAGQ-GQAPARQ 70

Query: 71  SALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESMTRAPFVMGKA 130
           +AL AGLP  A   TIN++CGSGM A       + AG AQ+++AGG+ESMT AP+++ KA
Sbjct: 71  AALKAGLPLAAGATTINKMCGSGMKAAMFGHDLLLAGSAQVVLAGGMESMTNAPYLLPKA 130

Query: 131 ASAFTRQAEIHDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGISRADQDAFALASQQ 190
                     H   +   F++ L         M   AE+ AE+FG +RA QD +A+ S  
Sbjct: 131 RGGLRLG---HGQVMDHMFLDGLEDAYDRGRLMGTFAEDCAEEFGFTRAAQDGYAITSLT 187

Query: 191 KAARAQRDGTLAQEIVGVEIAQKKGDAIRVTLDEHPRETSLESLARLKGVVRPDGTVTAG 250
           +A  A   G  A EI  V I+ K    + V  DE P +  ++ +A LK   RP GTVTA 
Sbjct: 188 RAQAAIASGAFAAEIAPVVISGKT--EVTVNTDEQPGKARMDKIATLKPAFRPGGTVTAA 245

Query: 251 NASGVNDGACALLIASQQAAEQYGLRRRARVVGMATAGVEPRIMGIGPAPATQKLLRQLG 310
           N+S ++DGA AL++     AE  GL   ARV+G AT   +P +    P  A  KL  +L 
Sbjct: 246 NSSSISDGAAALVLMRASEAEARGLTPLARVLGHATHADKPNLFPTAPIGALSKLSEKLD 305

Query: 311 MTLDQLDVIELNEAFASQGLAVLRMLGLRDDDPRVNPNGGAIALGHPLGASGARLVTTAL 370
           + L  +D+ E+NEAFA   +A + +L L  +  RVN +GGA ALGHP+GASGAR++ T L
Sbjct: 306 LDLRAVDLFEVNEAFAVVAMAAMTVLNLPHE--RVNVHGGACALGHPIGASGARVLVTLL 363

Query: 371 HQLERSNGRFALCTMCIGVGQGIALVIERL 400
             L+R   R  + T+CIG G+  A+ IER+
Sbjct: 364 AALQRHGLRTGVATLCIGGGEATAMAIERI 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: 375
Number of extensions: 18
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 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