GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gabT in Phaeobacter inhibens BS107

Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate GFF3387 PGA1_c34400 aminotransferase class-III

Query= reanno::WCS417:GFF5299
         (454 letters)



>lcl|FitnessBrowser__Phaeo:GFF3387 PGA1_c34400 aminotransferase
           class-III
          Length = 464

 Score =  597 bits (1540), Expect = e-175
 Identities = 295/453 (65%), Positives = 347/453 (76%), Gaps = 3/453 (0%)

Query: 3   SNNPQTREWQALSSDHHLAPFSDFKQLKEKGPRIITKAHGVYLWDSEGNKILDGMAGLWC 62
           +N+  T E QAL + HH+ PF+   +L EKG RIIT+A GV L DSEGN+ILD MAGLWC
Sbjct: 5   TNHLPTAELQALDAAHHMHPFTANGELAEKGARIITRARGVTLTDSEGNEILDAMAGLWC 64

Query: 63  VAIGYGRDELADAAAKQMKELPYYNLFFQTAHPPVLELAKAISDIAPAGMNHVFFTGSGS 122
           V IGYGRDELAD AA+QM+ELPYYN FFQT H P + LA  I+++AP G+NHVFF GSGS
Sbjct: 65  VNIGYGRDELADVAARQMRELPYYNTFFQTTHAPAIALAAKIAELAPDGLNHVFFAGSGS 124

Query: 123 EGNDTMLRMVRHYWAIKGQPNKKTIISRKNGYHGSTVAGASLGGMTYMHEQGDLPIPGIT 182
           E NDT +RMVRHYWA+K +P K  IISRKNGYHGS+V   SLGGMT MHEQG LPIP I 
Sbjct: 125 EANDTNIRMVRHYWAMKAKPTKSVIISRKNGYHGSSVGSGSLGGMTAMHEQGGLPIPDIH 184

Query: 183 HIAQPYWFGEGGDMSPEEFGVWAANQLEEKILELGVDNVGAFIAEPIQGAGGVIVPPATY 242
           HI QP W+ EGGDMS E+FG+  A +LE+ ILELG D V AFIAEP+QGAGGVIVPPATY
Sbjct: 185 HINQPNWWAEGGDMSAEDFGLARAQELEQAILELGEDRVAAFIAEPVQGAGGVIVPPATY 244

Query: 243 WPRIKEILAKYDILFIADEVICGFGRTGEWFGSDFYDLKPHMMTIAKGLTSGYIPMGGLI 302
           WP I+ I  KY+IL IADEVICGFGRTG WFGS    ++P +MTIAKGL+SGY P+GG I
Sbjct: 245 WPEIQRICDKYEILLIADEVICGFGRTGNWFGSQSVGIRPDIMTIAKGLSSGYAPIGGSI 304

Query: 303 VRDEVVEVLNEGGDFNHGFTYSGHPVAAAVALENIRIMRDEKIVNRVHDETAPYLQKRLR 362
           V DE+  V+   G+FNHG+TYSGHPVAAAVALEN+RI+ +E I+  V D  APYL+++  
Sbjct: 305 VSDEIASVIG-SGEFNHGYTYSGHPVAAAVALENLRILEEENIIGHVRDVAAPYLKEKWE 363

Query: 363 ELADHPLVGEVRGVGMLGAIELVQDKATRKRY--EGKGVGMICRTFCFENGLIMRAVGDT 420
            LADHPLVGE + VGM+G+I L  +KATR  +  EG  VG ICR  CF N L+MR VGD 
Sbjct: 364 ALADHPLVGEAKIVGMMGSIALTPNKATRAGFAAEGGTVGYICRERCFANNLVMRHVGDR 423

Query: 421 MIISPPLVISKAEIDELVTKARQCLDLTLAALQ 453
           MIISPPLVI+  EID L+ +ARQ LD   AALQ
Sbjct: 424 MIISPPLVITPEEIDTLIARARQSLDECYAALQ 456


Lambda     K      H
   0.320    0.139    0.426 

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: 751
Number of extensions: 26
Number of successful extensions: 3
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: 454
Length of database: 464
Length adjustment: 33
Effective length of query: 421
Effective length of database: 431
Effective search space:   181451
Effective search space used:   181451
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, 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