GapMind for catabolism of small carbon sources

 

Aligments for a candidate for astC in Pseudomonas fluorescens GW456-L13

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate PfGW456L13_494 5-aminovalerate aminotransferase (EC 2.6.1.48) / Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)

Query= reanno::Koxy:BWI76_RS11670
         (406 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_494
           5-aminovalerate aminotransferase (EC 2.6.1.48) /
           Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase
           (EC 2.6.1.19)
          Length = 425

 Score =  211 bits (538), Expect = 2e-59
 Identities = 135/403 (33%), Positives = 213/403 (52%), Gaps = 40/403 (9%)

Query: 16  PVYAPAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWHTG 75
           P++A +A      + + + D +G+E+IDFAGGIAV   GH HP+++ A+TEQ  K  HT 
Sbjct: 25  PIFADSA------KNATVTDVEGREFIDFAGGIAVLNTGHVHPKVIAAVTEQLNKLTHTC 78

Query: 76  -NGYTNEPVLRLAKQL---IDATFADRVFFCNSGAEANEAALKLARKYAHDRFGSEKSGI 131
                 EP + + +++   +   FA +     +G+EA E ++K+AR        + ++G+
Sbjct: 79  FQVLAYEPYVEVCEKINAKVPGDFAKKTLLVTTGSEAVENSIKIARA------ATGRAGV 132

Query: 132 VAFKNAFHGRTLFTVSAGGQPA-YSQDFAPLPPQIQHAIYND------LDSAKALID--- 181
           +AF  A+HGRT+ T+   G+   YS     +P  I  A+Y +      +D + A I+   
Sbjct: 133 IAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVSIDDSIASIERIF 192

Query: 182 ------DNTCAVIVEPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGEL 235
                  +  A+I+EP+QGEGG   A  +F++ LR LCD H  LLI DEVQTG GRTG  
Sbjct: 193 KNDAEPKDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTGTF 252

Query: 236 YAYMHYGVTPDLLSTAKALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLACAVAGEV 295
           +A    GV  DL + AK++ GGFP+  +         +  G  G TY G+P+ACA A  V
Sbjct: 253 FAMEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAV 312

Query: 296 FATINTREVLNGVKQRHQWFCERLNAINARYGLFKEIRGLGLLIGCVL---KDEYAGKAK 352
                   +L+  K   +     L AI A+Y +  E+R LG +I   L    D +   A 
Sbjct: 313 MEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVELFENGDSHKPNAA 372

Query: 353 AISN---QAAEEGLMILIAG--ANVVRFAPALIISEDEVNSGL 390
           A+++   +A ++GL++L  G   NV+R    L   +++++ GL
Sbjct: 373 AVASVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDEQLDKGL 415


Lambda     K      H
   0.321    0.137    0.412 

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: 447
Number of extensions: 22
Number of successful extensions: 4
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: 406
Length of database: 425
Length adjustment: 31
Effective length of query: 375
Effective length of database: 394
Effective search space:   147750
Effective search space used:   147750
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: 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