GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Sinorhizobium meliloti 1021

Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate SMa1450 SMa1450 thiolase

Query= uniprot:A0A2Z5MFE9
         (400 letters)



>FitnessBrowser__Smeli:SMa1450
          Length = 396

 Score =  265 bits (677), Expect = 2e-75
 Identities = 155/388 (39%), Positives = 232/388 (59%), Gaps = 8/388 (2%)

Query: 11  RTPIGRYGGALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQAGEDNRNVARM 70
           RTP+G + G LKD+ A DLGA  I   ++R  G+   AVD+V++GC   AG+  +  AR 
Sbjct: 14  RTPLGSFQGELKDLSAADLGAAAIVDALKR-AGLAPDAVDEVMFGCVLTAGQ-GQAPARQ 71

Query: 71  SALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESMTRAPFVMGKA 130
           +AL AGLP      T+N++CGSGM A   A   IKA  A +++AGG+ESMT AP+++ +A
Sbjct: 72  AALGAGLPPGVGATTVNKMCGSGMKAAMLAHDLIKAESASIVVAGGMESMTNAPYLLDRA 131

Query: 131 ASAFTRQAEIHDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGISRADQDAFALASQQ 190
              +      H   +   F++ L         M   AE+ AE +  +R+ QD +A+AS +
Sbjct: 132 RQGYRIG---HQKVLDHMFLDGLEDAYDKGRLMGSFAEDCAEAYQFTRSAQDEYAIASLE 188

Query: 191 KAARAQRDGTLAQEIVGVEIAQKKGDAIRVTLDEHPRETSLESLARLKGVVRPDGTVTAG 250
           KA +A  DG+ A+EIV + IA  KG+   V LDE P++  L+ +  LK   R  GT+TA 
Sbjct: 189 KAQKASADGSFAEEIVPLSIASGKGERT-VNLDEQPQKARLDKIPLLKPAFRDGGTITAA 247

Query: 251 NASGVNDGACALLIASQQAAEQYGLRRRARVVGMATAGVEPRIMGIGPAPATQKLLRQLG 310
           NAS ++DGA AL++  + AA++ G+   A + G AT    P +    P  A + L R++G
Sbjct: 248 NASSISDGAAALVLMRRSAADKQGIGPLAVICGHATHADAPSLFPTAPIGAIKALCRRIG 307

Query: 311 MTLDQLDVIELNEAFASQGLAVLRMLGLRDDDPRVNPNGGAIALGHPLGASGARLVTTAL 370
             + ++D+ E+NEAFA   +A +R LGL  D  +VN +GGA ALGHP+GASGAR++ T +
Sbjct: 308 WDIGEVDLFEINEAFAVVPMAAMRELGL--DAEKVNVHGGACALGHPIGASGARVIVTLV 365

Query: 371 HQLERSNGRFALCTMCIGVGQGIALVIE 398
           + L R   R  + ++CIG G+  A+ +E
Sbjct: 366 NALRRRGLRRGIASVCIGGGEATAVAVE 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: 399
Number of extensions: 26
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: 396
Length adjustment: 31
Effective length of query: 369
Effective length of database: 365
Effective search space:   134685
Effective search space used:   134685
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 17 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