GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Phaeobacter inhibens BS107

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate GFF2392 PGA1_c24230 acetylornithine aminotransferase ArgD

Query= BRENDA::P42588
         (459 letters)



>FitnessBrowser__Phaeo:GFF2392
          Length = 394

 Score =  219 bits (558), Expect = 1e-61
 Identities = 129/365 (35%), Positives = 201/365 (55%), Gaps = 20/365 (5%)

Query: 76  LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLD-PLRAMLAKTLA 134
           L++  G+ F+D   G  +  +GH +P +V A+ +Q A+   H   L   P +  LA  L 
Sbjct: 24  LIEADGRRFLDLAAGIAVNALGHAHPALVKALTDQ-AETLWHVSNLYHIPQQQALADRLV 82

Query: 135 ALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRG---KFTFIATSGAFHGKSLGALSAT 191
             +       FF NSGTES E A+K+A+ Y   +G   +   +  SG+FHG+S   +SA 
Sbjct: 83  EHSFADTV--FFTNSGTESCELAVKMARKYFHDKGQPERVEILTFSGSFHGRSSAGISAA 140

Query: 192 AKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPP 251
                   F P+LPGF+H+ FG+++ +  A+       D  AA+++EP+QGEGG+   P 
Sbjct: 141 GSEKMTAGFGPMLPGFKHLMFGDLDGVTDAIT------DQTAAILIEPVQGEGGIRPVPD 194

Query: 252 GYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGA 311
             L A+R++CDE G L+ILDEVQ G+GRTGK+FA E   + PDI+ +AK +GGG  P+GA
Sbjct: 195 AELKALRQICDEHGLLLILDEVQCGVGRTGKLFAHEWAGITPDIMMVAKGIGGG-FPLGA 253

Query: 312 TIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFR 371
            +ATEE  S +      H +T+GGNPL CA   A ++ + +    A+  +K  +L     
Sbjct: 254 VLATEEAASGM--TAGTHGSTYGGNPLGCAVGCAVMDHVTDPEFLAEVSRKAGLLRQKLE 311

Query: 372 QLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAKTIRIEPPL 431
            L   +P + +  RG G+++ ++ V      +  +  +   V+     +N   +R+ PPL
Sbjct: 312 GLVASHPQVFEAVRGSGLMLGLKCV--AANTDVVAAGYEAEVVTVPAADN--VVRLLPPL 367

Query: 432 TLTIE 436
           TLT E
Sbjct: 368 TLTDE 372


Lambda     K      H
   0.320    0.135    0.393 

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: 394
Number of extensions: 24
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 459
Length of database: 394
Length adjustment: 32
Effective length of query: 427
Effective length of database: 362
Effective search space:   154574
Effective search space used:   154574
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