GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Pseudomonas stutzeri RCH2

Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate GFF3012 Psest_3070 3-oxoadipyl-CoA thiolase

Query= uniprot:D8ITH5
         (401 letters)



>FitnessBrowser__psRCH2:GFF3012
          Length = 401

 Score =  555 bits (1429), Expect = e-162
 Identities = 279/399 (69%), Positives = 330/399 (82%), Gaps = 1/399 (0%)

Query: 2   EALICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAGE 61
           +  ICDA+RTP GR+GGAL AVRADDLAA P+R+L+ERNPG+D + V+++  G ANQAGE
Sbjct: 4   DVFICDAVRTPIGRFGGALAAVRADDLAAIPLRALLERNPGLDPAAVDEVFMGSANQAGE 63

Query: 62  DNRNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMTR 121
           DNRNVARMA LLAGLP  VPG T+NRLC S +DAVG A RAI SGE++L IAGGVESM+R
Sbjct: 64  DNRNVARMALLLAGLPETVPGVTLNRLCASGMDAVGTAFRAISSGELELAIAGGVESMSR 123

Query: 122 APFVMGKAESAFARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQD 181
           AP+VMGKA++AF R   I DTTIGWRF+NP MK  YG+D+MP+TA+NVA ++Q+ RADQD
Sbjct: 124 APYVMGKADTAFGRIQKIEDTTIGWRFINPKMKELYGVDAMPQTADNVADEWQVGRADQD 183

Query: 182 AFALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHPRPDTTLATLAKLKGVV 241
           AFALRSQQR AAAQ AGFFA EI P+ I  KKG+  VV TDEHPR DTT   LAKLK V 
Sbjct: 184 AFALRSQQRAAAAQQAGFFAEEIVPVVIRGKKGE-TVVDTDEHPRADTTAEALAKLKPVN 242

Query: 242 RPDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAPA 301
            PD TVTAGNASGVNDGA A++LAS +A   Y LKPRA+VLGMA+AGVAPRIMG+GP PA
Sbjct: 243 GPDKTVTAGNASGVNDGAAAMILASAEAVQKYGLKPRAKVLGMASAGVAPRIMGYGPVPA 302

Query: 302 VRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGAS 361
           VRK+  ++ + ++  DVIELNEAFAAQGLAV RDLG+PDD+  VNPNGGAIA+GHPLG S
Sbjct: 303 VRKLCERLNIAVSDFDVIELNEAFAAQGLAVTRDLGVPDDSPKVNPNGGAIALGHPLGMS 362

Query: 362 GARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIERV 400
           GARLV TA++QLE++GGR  L TMC+GVGQG+ALV+ERV
Sbjct: 363 GARLVLTAVHQLEKTGGRLGLATMCVGVGQGLALVVERV 401


Lambda     K      H
   0.320    0.135    0.394 

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: 578
Number of extensions: 28
Number of successful extensions: 2
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: 401
Length of database: 401
Length adjustment: 31
Effective length of query: 370
Effective length of database: 370
Effective search space:   136900
Effective search space used:   136900
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