GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1109
          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 (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