GapMind for catabolism of small carbon sources

 

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

Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate Pf1N1B4_1109 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26)

Query= uniprot:Q88CC3
         (496 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1109 2-ketoglutaric
           semialdehyde dehydrogenase (EC 1.2.1.26)
          Length = 481

 Score =  213 bits (541), Expect = 2e-59
 Identities = 146/445 (32%), Positives = 227/445 (51%), Gaps = 12/445 (2%)

Query: 41  AETIARIDQAQSAFEAWRSVPAPRRGELVRLFGEVLREHKADLGELVSIEAGKITQEGLG 100
           A+  A ID A++AF AW +     R + +   G  +   + +LG L++ E GK   E +G
Sbjct: 43  AQVHAAIDAARAAFPAWSTSGIQARHDSLDKVGTEILARREELGTLLAREEGKTLPEAIG 102

Query: 101 EVQEMIDICDFAVGLSRQLYGLTIASERPGHHMRETWHPLGVVGVISAFNFPVAVWAWNT 160
           EV    +I  F  G   +L G  + S RPG ++  T   LGVVG+I+ +NFP+A+ AW  
Sbjct: 103 EVTRAGNIFKFFAGECLRLSGDYLPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKI 162

Query: 161 ALALVAGNSVVWKPSEKTPLTALACQALFEKALKAFGDAPAGLAQLVIG-GREAGEAMVD 219
           A AL  GN VV KP++  P  A A   +  +A       PAG+  LV+G GR  G+A+V 
Sbjct: 163 APALAYGNCVVLKPADLVPGCAWALAEIISRA-----GFPAGVFNLVMGSGRVVGDALVQ 217

Query: 220 DPRVPLVSATGSTRMGREVGPRVAARFGRSILELGGNNAMILAPSADLDLAVRGILFSAV 279
            P+V  +S TGS  +GR++     +R  +  LE+GG N  I+   ADL  AV   + SA 
Sbjct: 218 SPKVDGISFTGSVGVGRQIAVSCVSRQAKVQLEMGGKNPQIILDDADLKQAVELSVQSAF 277

Query: 280 GTAGQRCTTLRRLIVHRSIKDEVVARVKAAYGKVRIGDPRKDNL-VGPLIDKQSFDAMQG 338
            + GQRCT   R IV   I D+ V  +      +++G   K    +GP++ +   +    
Sbjct: 278 YSTGQRCTASSRFIVTAGIHDKFVEAMAERMKSIKVGHALKTGTDIGPVVSQAQLEQDLK 337

Query: 339 ALAKARDEGGQVFGGERQLADQYPNAYYVSPAI-AEMPAQSDVVRHETFAPILYVLAYDD 397
            +   + EG ++  G   +A      Y+++P + A+  A   + R E F P+  ++   D
Sbjct: 338 YIDIGQSEGARLVSGGGLVACD-TEGYFLAPTLFADSTAAMRISREEIFGPVANIVRVAD 396

Query: 398 FEEALRLNNEVPQGLSSCIFTTDIREAERFQSASGSDCGIANVNIGTSGAEIGGAFGGEK 457
           +E AL + N+   GLS+ I TT ++ A  F+    S  G+  VN+ T+G +    FGG K
Sbjct: 397 YEAALAMANDTEFGLSAGIATTSLKYANHFK--RHSQAGMVMVNLPTAGVDYHVPFGGRK 454

Query: 458 ETG-GGRESGSDAWKGYMRRQTNTV 481
            +  G RE G  A + Y   +T+ +
Sbjct: 455 GSSYGSREQGRYAQEFYTVVKTSYI 479


Lambda     K      H
   0.318    0.135    0.396 

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: 519
Number of extensions: 26
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: 496
Length of database: 481
Length adjustment: 34
Effective length of query: 462
Effective length of database: 447
Effective search space:   206514
Effective search space used:   206514
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: 52 (24.6 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, 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