GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo5_N2C3_1:AO356_27515
          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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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