GapMind for catabolism of small carbon sources

 

Aligments for a candidate for patA in Pseudomonas fluorescens FW300-N1B4

Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate Pf1N1B4_2377 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (EC 2.6.1.62)

Query= BRENDA::Q9I6J2
         (456 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2377
           Adenosylmethionine-8-amino-7-oxononanoate
           aminotransferase (EC 2.6.1.62)
          Length = 468

 Score =  229 bits (583), Expect = 2e-64
 Identities = 138/431 (32%), Positives = 217/431 (50%), Gaps = 9/431 (2%)

Query: 24  PFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAATRQMR 83
           P T  K   +     I + EGV++ D EG + LDA++  W    G+    + Q    Q+ 
Sbjct: 18  PCTQMKDHEQLPLIPIKRGEGVWLEDFEGKRYLDAVSSWWVNVFGHANPRINQRIKDQVD 77

Query: 84  ELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYWATKGQ 143
           +L  + +    +H PV+EL++ +  + PEG+   F+  +GS   +  L+M  HYW  +GQ
Sbjct: 78  QLE-HVILAGFSHQPVIELSERLVKMTPEGLTRCFYADNGSSCIEVALKMSFHYWLNRGQ 136

Query: 144 PQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHIAQPYWYGEGGDMSPDEF 203
           P KK  +   NGYHG T+A +++G +    E     +   + +  P  Y     MS +E 
Sbjct: 137 PNKKRFVTLTNGYHGETMAAMAVGDVPLFTETYKALLMDTIKVPSPDCYLRPEGMSWEEH 196

Query: 204 GVWAAEQLEKKILEVGEENVAAFIAEP-IQGAGGVIVPPDTYWPKIREILAKYDILFIAD 262
                  +E+ + +   + VAA I EP IQGAGG+ +    Y   +R+   +Y +  I D
Sbjct: 197 SRNMFAAMEQTLAD-NHDTVAAVILEPLIQGAGGMRMYHPVYLKLLRDACDRYGVHLIHD 255

Query: 263 EVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVLNQG----GE 318
           E+  GFGRTG  F  +  G  PD + ++K LT GY+P+  V+  DE+             
Sbjct: 256 EIAVGFGRTGTMFACEQAGIRPDFLCLSKALTGGYLPLAAVLTTDEVYGAFYDDYPTLRA 315

Query: 319 FYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELADHPLVGEARGV 378
           F H  +Y+G+P+A A AL  + I  E+ +IE  K   A  +      LADHP V E R  
Sbjct: 316 FLHSHSYTGNPLACAAALATLDIFEEDNVIENNKV-LAQRMASSTAHLADHPNVAEVRQT 374

Query: 379 GMVAALELVKNKKTRERFT-DKGVGMLCREHCFRNGLIMRAVGDTMIISPPLVIDPSQID 437
           GMV A+E+VK+K ++  +   +  G+   +H    G ++R +G  +   PP VI P QID
Sbjct: 375 GMVLAIEMVKDKASKTAYPWQERRGLRVFQHALERGALLRPLGSVVYFLPPYVITPEQID 434

Query: 438 ELITLARKCLD 448
            L  +A + +D
Sbjct: 435 FLAEVASEGID 445


Lambda     K      H
   0.320    0.138    0.425 

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: 589
Number of extensions: 38
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: 456
Length of database: 468
Length adjustment: 33
Effective length of query: 423
Effective length of database: 435
Effective search space:   184005
Effective search space used:   184005
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: 51 (24.3 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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