GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Stutzerimonas stutzeri A1501

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_011911296.1 PST_RS00235 aspartate aminotransferase family protein

Query= reanno::pseudo1_N1B4:Pf1N1B4_3440
         (406 letters)



>NCBI__GCF_000013785.1:WP_011911296.1
          Length = 439

 Score =  151 bits (382), Expect = 3e-41
 Identities = 115/397 (28%), Positives = 181/397 (45%), Gaps = 38/397 (9%)

Query: 30  RGAGSRVWDQSGRELIDFAGGIAVNVLGHAHPALVAALTEQANKLWHVSNVFTNEPA-LR 88
           R  G       GR+++D   G+     GH    +  A+++Q  ++          P    
Sbjct: 31  RAEGMYYTASDGRQVLDGTAGLWCCNAGHGRREISEAVSKQIARMDFAPTFQMGHPLPFE 90

Query: 89  LAHKL--VDATFAERVFFCNSGAEANEAAFKLARRVAHDRFGTEKYEIVAALNSFHGRTL 146
           LA KL  +      RVFF NSG+E+ + A K+A           +  ++    ++HG   
Sbjct: 91  LAEKLAAISPEGLNRVFFTNSGSESADTALKIALAYQRAIGQGSRTRLIGRELAYHGVGF 150

Query: 147 FTVNVGGQSKYSDGFGPKITGITHVPYN-DLA-----------------ALKAAV----S 184
             ++VGG +     FGP + G+ H+P+  DL                   L+  V    +
Sbjct: 151 GGMSVGGMANNRRAFGPMLPGVDHLPHTLDLQRNAFSKGLPQHGVERADELERLVTLHGA 210

Query: 185 DKTCAVVLEPIQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFAYQHY 244
           +   AV++EP+ G  GV+   + YLQ  RE+   H  LL+FDEV TG GR G+ FA Q +
Sbjct: 211 ENIAAVIVEPMSGSAGVILPPVGYLQRLREITAKHGILLIFDEVITGFGRVGEAFAAQRW 270

Query: 245 GVTPDILTSAKSL-GGGFPIAAMLTTEDLAKHLVVGT-------HGTTYGGNPLACAVAE 296
           GVTPDILT AK L  G  P+ A+   + L    + G        HG TY G+P+ACA A 
Sbjct: 271 GVTPDILTCAKGLTNGAIPMGAVFVADRLYDAFMQGPESVIEFFHGYTYSGHPVACAAAL 330

Query: 297 AVIDVINTPEVLNGVNAKHDKFKTRLEQIGEKYGLFTEVRGLGLLLGCVLSDAWKGKAK- 355
           A   +     +          ++  L  + +   +  ++R +GL+ G   +    G  K 
Sbjct: 331 ATQQIYQQENLFQKAIDLEPYWQEALFSLRDLPNVI-DIRTVGLVAGIQFAAHADGVGKR 389

Query: 356 --DIFNAAEREGLMILQAGPDVIRFAPSLVVEDADID 390
             ++F      GL++  +G D I  +P+L+VE A+ID
Sbjct: 390 GYEVFRECFENGLLVRASG-DTIALSPALIVEKAEID 425


Lambda     K      H
   0.320    0.136    0.400 

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: 428
Number of extensions: 23
Number of successful extensions: 6
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: 406
Length of database: 439
Length adjustment: 32
Effective length of query: 374
Effective length of database: 407
Effective search space:   152218
Effective search space used:   152218
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 Apr 09 2024. 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