GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dadA in Pseudomonas fluorescens FW300-N2E3

Align D-arginine dehydrogenase (EC 1.4.99.6) (characterized)
to candidate AO353_08065 AO353_08065 amino acid dehydrogenase

Query= BRENDA::Q9HTQ0
         (432 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_08065 AO353_08065 amino acid
           dehydrogenase
          Length = 413

 Score =  288 bits (738), Expect = 2e-82
 Identities = 159/411 (38%), Positives = 231/411 (56%), Gaps = 9/411 (2%)

Query: 2   RVLVLGSGVIGTASAYYLARAGFEVVVVDRQDGPALETSFANAGQVSPGYASPWAAPGIP 61
           RV ++G GVIG  +AY L R GFEV VV+ +D    ETSFAN GQ+S  Y +P A  G+P
Sbjct: 4   RVCIIGGGVIGLTTAYALVRDGFEVTVVEARDSLGSETSFANGGQLSYRYVAPLADAGVP 63

Query: 62  LKAMKWLLEKHAPLAIKLTSDPSQYAWMLQMLRNCTAERYAVNKERMVRLSEYSRDCLDE 121
           L+A+ W+L   +PL +++  DP+Q+ WM   L  C       N   ++RL+  S+  L  
Sbjct: 64  LQAIGWMLRGDSPLKLRMRFDPAQWRWMASFLGACRTSVNRQNAAHLLRLALLSQTTLQG 123

Query: 122 LRAETGI-AYEGRTLGTTQLFRTQAQLDAAGKDIAVLERSGVPYEVLDRDGIARVEPALA 180
            R E  +  +  R  G    FR  A  + A   +   ++     +VL     AR+EPALA
Sbjct: 124 WREEDSLDGFNWRRNGKLVTFRQAASFEHARNSLVDPQQQ----QVLSPTESARLEPALA 179

Query: 181 KVADKLVGALRLPNDQTGDCQLFTTRLAEMAKGLGV-EFRFGQNIERLDFAGDRINGVLV 239
             A   VGA+  P+++ GDC  F  +L +  K  G+ EFR G+ +  +      ++ + +
Sbjct: 180 DAA--FVGAIYTPDEEVGDCHAFCQQLMKRLKASGLCEFRLGRAVTGIRHVDGAVSAIEL 237

Query: 240 NGELLTADHYVLALGSYSPQLLKPLGIKAPVYPLKGYSLTVPITNPEMAPTSTILDETYK 299
             E+L  +  V+A G  SP L  P G+  P+YPLKGYSLTVPI     AP  +I D   K
Sbjct: 238 ADEVLPVEQLVIAAGHRSPLLALP-GVHLPLYPLKGYSLTVPIGAEHRAPDLSITDYDRK 296

Query: 300 VAITRFDQRIRVGGMAEIAGFDLSLNPRRRETLEMITTDLYPEGGDISQATFWTGLRPAT 359
           +   R  +++RV  M +I GFD + +P+R   ++    D +P  G    A  W G+RPAT
Sbjct: 297 IVYARIGEQLRVAAMVDIVGFDPAPDPKRLALIKRQACDTFPNAGTYDAAVEWAGMRPAT 356

Query: 360 PDGTPIVGATRYRNLFLNTGHGTLGWTMACGSGRYLADLMAKKRPQISTEG 410
           P G P++GAT YRNL+LN GHG LG+T+ACGS R L++L+ ++ P I  +G
Sbjct: 357 PSGVPLLGATAYRNLWLNLGHGALGFTLACGSARVLSELIGQRNPSIDLQG 407


Lambda     K      H
   0.318    0.135    0.401 

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: 450
Number of extensions: 20
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: 432
Length of database: 413
Length adjustment: 32
Effective length of query: 400
Effective length of database: 381
Effective search space:   152400
Effective search space used:   152400
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: 50 (23.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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