GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Phaeo:GFF3387
          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 (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