GapMind for catabolism of small carbon sources

 

Aligments for a candidate for astC in Pseudomonas fluorescens FW300-N1B4

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate Pf1N1B4_1733 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__pseudo1_N1B4:Pf1N1B4_1733 5-aminovalerate
           aminotransferase (EC 2.6.1.48) /
           Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase
           (EC 2.6.1.19)
          Length = 425

 Score =  212 bits (539), Expect = 2e-59
 Identities = 137/405 (33%), Positives = 212/405 (52%), Gaps = 44/405 (10%)

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

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

Query: 132 VAFKNAFHGRTLFTVSAGGQPA-YSQDFAPLPPQIQHAIY-NDLDSAKALIDDNTC---- 185
           +AF  A+HGRT+ T+   G+   YS     +P  I  A+Y N+L      IDD+      
Sbjct: 133 IAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVS--IDDSIASIER 190

Query: 186 ------------AVIVEPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTG 233
                       A+I+EP+QGEGG   A  +F++ LR LCD H  LLI DEVQTG GRTG
Sbjct: 191 IFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTG 250

Query: 234 ELYAYMHYGVTPDLLSTAKALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLACAVAG 293
             +A    GV  DL + AK++ GGFP+  +         +  G  G TY G+P+ACA A 
Sbjct: 251 TFFAMEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAAL 310

Query: 294 EVFATINTREVLNGVKQRHQWFCERLNAINARYGLFKEIRGLGLLIGCVL---KDEYAGK 350
            V        +L+  K   +     L AI A+Y +  E+R LG +I   L    D +   
Sbjct: 311 AVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVELFVDGDSHKPN 370

Query: 351 AKAISN---QAAEEGLMILIAG--ANVVRFAPALIISEDEVNSGL 390
           A A+++   +A ++GL++L  G   NV+R    L   +++++ GL
Sbjct: 371 AAAVASVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDEQLDKGL 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: 445
Number of extensions: 23
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 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