GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Sphingopyxis indica DS15

Align 3-ketoacyl-CoA thiolase, peroxisomal; Acetyl-CoA acyltransferase; Beta-ketothiolase; Peroxisomal 3-oxoacyl-CoA thiolase; EC 2.3.1.16 (characterized)
to candidate WP_089216969.1 CHB69_RS16130 acetyl-CoA C-acyltransferase

Query= SwissProt::P09110
         (424 letters)



>NCBI__GCF_900188185.1:WP_089216969.1
          Length = 393

 Score =  266 bits (680), Expect = 8e-76
 Identities = 162/390 (41%), Positives = 229/390 (58%), Gaps = 7/390 (1%)

Query: 37  DVVVVHGRRTAICRAGRGGFKDTTPDELLSAVMTAVLKDVNLRPEQLGDICVGNVLQPGA 96
           D V+V   RT + +A RG F +T    L +  + A ++   L   ++ D+  G  +Q G+
Sbjct: 3   DAVIVSTARTPLTKAARGSFNNTPSPTLGAFSVKAAVERAGLEGGEIDDVVFGAAMQQGS 62

Query: 97  GAI-MARIAQFLSDIPETVPLSTVNRQCSSGLQAVASIAGGIRNGSYDIGMACGVESMSL 155
            +  +AR+    + +P TVP  +++RQCSSGL  +A+ A  I     DI +A GVES+S 
Sbjct: 63  QSPNVARLIALRAGLPVTVPGMSIDRQCSSGLMTIATAAKQIIVDRQDICVAGGVESISK 122

Query: 156 ADRGNPGNITSRLMEKEKARDCLIPMGITSENVAERFGISREKQDTFALASQQKAARAQS 215
                   I          +D  +PM  T+E VA+R+ I RE QD ++L SQQ+ A AQ+
Sbjct: 123 VSGSGKVFIEPDAELLAMHKDTYMPMIGTAEVVAKRYNIGREAQDEYSLQSQQRTAAAQA 182

Query: 216 KGCFQAEIVPVTTTVHD-DKGTK----RSITVTQDEGIRPSTTMEGLAKLKPAFKKDGST 270
            G F  EI+P   T+   DK TK    + +T  +DE  RP TT+EGLA LKP   +  + 
Sbjct: 183 AGKFADEIIPCKATMAIVDKETKEVSYKDVTADRDECNRPDTTLEGLASLKPVMGEGHTI 242

Query: 271 TAGNSSQVSDGAAAILLARRSKAEELGLPILGVLRSYAVVGVPPDIMGIGPAYAIPVALQ 330
           TAGN+SQ+SDG++A ++     AE+ GL  LG     AV G  PD MGIGP +AIP  L+
Sbjct: 243 TAGNASQLSDGSSACVVMEAKVAEKRGLQPLGRYVGMAVAGTEPDEMGIGPVFAIPKLLE 302

Query: 331 KAGLTVSDVDIFEINEAFASQAAYCVEKLRLPPEKVNPLGGAVALGHPLGCTGARQVITL 390
           +  L + D+ ++E+NEAFA Q  YC +KL +P E +N  GG++++GHP G TGAR V   
Sbjct: 303 RFELKMDDIGLWELNEAFAVQVLYCRDKLGIPNELLNVNGGSISIGHPFGMTGARCVGHA 362

Query: 391 LNELKRRGKRAYGVVSMCIGTGMGAAAVFE 420
           L E KRRG + Y VV+MCIG G GAA +FE
Sbjct: 363 LIEGKRRGVK-YAVVTMCIGGGQGAAGLFE 391


Lambda     K      H
   0.317    0.134    0.385 

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: 421
Number of extensions: 20
Number of successful extensions: 5
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: 424
Length of database: 393
Length adjustment: 31
Effective length of query: 393
Effective length of database: 362
Effective search space:   142266
Effective search space used:   142266
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: 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