Aligments for a candidate for davT in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Aligments for a candidate for davT in Pseudomonas fluorescens FW300-N2C3

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate AO356_27515 AO356_27515 4-aminobutyrate aminotransferase

Query= BRENDA::Q88RB9
         (425 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27515 AO356_27515
           4-aminobutyrate aminotransferase
          Length = 457

 Score =  234 bits (598), Expect = 3e-66
 Identities = 151/430 (35%), Positives = 230/430 (53%), Gaps = 23/430 (5%)

Query: 3   KTNESL-MQRRVAAVPRGVGQIHPIFVDTAKNSTVIDVEGRELIDFAGGIAVLNTGHLHP 61
           +T E+L +  R  ++ RG G++ P+ +D A  +T  D +    ID + G+ V + G  HP
Sbjct: 25  RTTEALALSARTESMARGGGRM-PVAMDRAFGATFKDADDNTYIDLSAGVGVSSVGRCHP 83

Query: 62  KVVAAVQEQLTKVSHTCFQVLAYEPYVELCEKINKLVPGDF--DKKTLLVTTGSEAVENA 119
           KVV A++EQ   + H     +      EL  K++++ P     D  T    +GS+A+E A
Sbjct: 84  KVVQAIREQSEVLMHAL--EVNSTRRTELAAKLSEIAPDGLRGDCITFFTQSGSDALEAA 141

Query: 120 VKIARAATGRAGVIAFTGGYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALFPSELHGI 179
           +K A+  TGR  +IAF GGYHG    +  LT     Y  G G   GG+  A +P   +  
Sbjct: 142 IKFAKRVTGRHQIIAFHGGYHGVWNASGALTTGTA-YRKGYGAQMGGVIHAPYPYA-YRF 199

Query: 180 SVDDAIASVERIFKNDAE---------PRDIAAIILEPVQGEGGFLPAPKELMKRLRALC 230
             D    S E+I     +           D+AA+I+EPVQGEGG++P   E ++ LR  C
Sbjct: 200 PFDTTHKSAEQIAGEYVDYLLNTPYTAADDVAAVIVEPVQGEGGYVPPSPEFLQLLRKAC 259

Query: 231 DQHGILLIADEVQTGAGRTGTFFAMEQMGVAPDLTTFAKSIAGGFPLAGVCGKAEYMDAI 290
           D+ G LLI DEVQ+GAGRTG  +A+E  GV PD+ TF K I    P+AG+  +++   AI
Sbjct: 260 DRSGTLLIVDEVQSGAGRTGKMWAVEHSGVKPDMLTFGKGIGSDLPMAGLIMRSDLAAAI 319

Query: 291 APGGLGGTYAGSPIACAAALAVIEVFEEEK--LLDRSKAVGERLTAGLREIQKKYPIIGD 348
             G +  T+A + ++ A AL  I + ++ +  LL+R+  +G      +R      P++G+
Sbjct: 320 PDGSMPNTFAANSLSAAVALTNISILQDPELDLLNRAHTLGLEAQERIRGFGS--PLVGE 377

Query: 349 VRGLGSMIAVE-VFEKGTHTPNA-AAVGQVVAKAREKGLILLSCGTYGNVLRILVPLTAE 406
           VRG G MI +E V +  T  P A   +GQ++      G++++ CG Y NV+R++  LT  
Sbjct: 378 VRGRGLMIGIELVSDPTTKAPLAPEKIGQLMGYLLSHGVLMIPCGRYSNVMRVMPSLTIS 437

Query: 407 DALLDKGLAI 416
            AL  K L I
Sbjct: 438 RALFFKALDI 447


Lambda     K      H
   0.320    0.138    0.395 

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: 528
Number of extensions: 35
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: 425
Length of database: 457
Length adjustment: 32
Effective length of query: 393
Effective length of database: 425
Effective search space:   167025
Effective search space used:   167025
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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Steps (tab-delimited)
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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources