GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Novosphingobium aromaticivorans DSM 12444

Align 3-oxo-acyl CoA thiolase (EC 2.3.1.16) (characterized)
to candidate WP_011444728.1 SARO_RS05335 acetyl-CoA C-acetyltransferase

Query= metacyc::G185E-7833-MONOMER
         (386 letters)



>NCBI__GCF_000013325.1:WP_011444728.1
          Length = 390

 Score =  383 bits (984), Expect = e-111
 Identities = 212/395 (53%), Positives = 271/395 (68%), Gaps = 14/395 (3%)

Query: 1   MTEAYVIDAVRTAVGKRGGALAGIHPVDLGALAWRGLLDRTDIDPAAVDDVIAGCVDAIG 60
           M  AY++DAVRTA G+RGG LAG+HPVDL A +   ++ RT IDP AVDDVI GCV   G
Sbjct: 1   MATAYIVDAVRTAGGRRGGRLAGVHPVDLAARSLDAIVARTGIDPTAVDDVIMGCVTQAG 60

Query: 61  GQAGNIARLSWLAAGY-PEEVPGVTVDRQCGSSQQAISFGAQAIMSGTADVIVAGGVQNM 119
            QA  + R + LA+   P+  P VT+DRQCGSSQQAI F AQA+MSG  D+++A GV++M
Sbjct: 61  QQAMQVGRNAVLASKLLPQSTPAVTIDRQCGSSQQAIQFAAQAVMSGVQDMVIAAGVESM 120

Query: 120 SQIPISSAMTVGEQFG---FTSPTNESKQWLHRYGDQEISQFRGSELIAEKWNLSREEME 176
           S++P+ S  T   + G   + SP  E K     Y     SQF G+E+I +K   ++++++
Sbjct: 121 SRVPMGSNATFHMKEGLGHYKSPGLEEK-----YPGVMFSQFMGAEMIVKKHGFTKDDLD 175

Query: 177 RYSLTSHERAFAAIRAGHFENEIITVETES--GP--FRVDEGPR-ESSLEKMAGLQPLVE 231
           R+SL SH +A AA  A  F NEI+ VE E+  GP    VDEG R +++LE +AG++ L  
Sbjct: 176 RFSLDSHRKAIAATNAQAFANEIVPVEIETPEGPAMHTVDEGIRFDATLEGIAGVKLLSP 235

Query: 232 GGRLTAAMASQISDGASAVLLASERAVKDHGLRPRARIHHISARAADPVFMLTGPIPATR 291
            G LTAA +SQI DG+SAVL+ SE A+K HGL P ARIH+++  A DPV ML  P+ AT 
Sbjct: 236 EGSLTAASSSQICDGSSAVLVVSEAALKAHGLTPLARIHNLTVTAGDPVIMLEEPLFATD 295

Query: 292 YALDKTGLAIDDIDTVEINEAFAPVVMAWLKEIKADPAKVNPNGGAIALGHPLGATGAKL 351
            AL + G+ I DID  E+NEAFA V MAWLK   ADP K+N NGGAIALGHPLGA+G+KL
Sbjct: 296 RALQRAGMKISDIDLYEVNEAFASVPMAWLKHTGADPEKLNVNGGAIALGHPLGASGSKL 355

Query: 352 FTTMLGELERIGGRYGLQTMCEGGGTANVTIIERL 386
             T++  L   GG+YGLQTMCEGGG ANVTIIE L
Sbjct: 356 MATLVHALRARGGKYGLQTMCEGGGVANVTIIEAL 390


Lambda     K      H
   0.317    0.134    0.389 

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: 433
Number of extensions: 19
Number of successful extensions: 4
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: 386
Length of database: 390
Length adjustment: 30
Effective length of query: 356
Effective length of database: 360
Effective search space:   128160
Effective search space used:   128160
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 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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