GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argE in Klebsiella michiganensis M5al

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate BWI76_RS14620 BWI76_RS14620 acetylornithine deacetylase or succinyl-diaminopimelate desuccinylase

Query= ecocyc::ACETYLORNDEACET-MONOMER
         (383 letters)



>FitnessBrowser__Koxy:BWI76_RS14620
          Length = 370

 Score =  127 bits (318), Expect = 7e-34
 Identities = 105/360 (29%), Positives = 155/360 (43%), Gaps = 29/360 (8%)

Query: 31  SNADLITLLADWFKDLGFNVEVQPVPGTRNKFNMLASIGQGAGGLLLA--GHTDTVPFDD 88
           S AD +   ADW    GF V +     +R+  N++A +     G  LA  GH DTVP  +
Sbjct: 22  SEADCMRYFADWLNANGFAVSLSSFGESRS--NLIAWLPGATPGKPLAFTGHLDTVPLGN 79

Query: 89  GRWTRDPFTLTEHDGKLYGLGTADMK-GFFAFILDALRDVDVTKLKKPLYILATADEETS 147
            RW  DPF     DG+LYG G++DMK    AF +  ++  +     +   +L T  EET 
Sbjct: 80  ARWRYDPFGSQMEDGRLYGRGSSDMKAAIAAFAVACVQQRETILAGRGAVLLITGGEETG 139

Query: 148 MAGARYFAETTAL-RPDCAIIGEPTSLQPVRAHKGHISNAIRIQGQSGHSSDPARGVNAI 206
             GAR    +  L      I+GEPT+  PV  HKG +      +G++ H + P  G+NAI
Sbjct: 140 CDGARALIASAPLPEVGALIVGEPTANYPVIGHKGALWLRCETRGKTAHGAMPELGINAI 199

Query: 207 ELMHDAIGHILQLRDNLKERYHYEAFTVPYPTLNLGHIHGGDASNRICACCELHMDIRPL 266
            L  DA+  I                 +  PT+N+G I GG   N +       +DIR  
Sbjct: 200 YLAADALAKIQHFSPGAPHP------LMKQPTVNVGRIEGGLNINSVPDRTRFDVDIRSA 253

Query: 267 PGMTLNELNGLLNDALAPVSERWPGRLTVDELHPPIPGYECPPNHQLVEVVEKLL----- 321
           P +    +   L   L          +TV  L   +P      +H  ++ V +       
Sbjct: 254 PDLQHATIRQRLTTLLGE-------SVTVSTL-VDLPAVLSEQDHAWIKQVYQRCQPLHD 305

Query: 322 -GAKTEVVNYCTEAPFIQTLC---PTLVLGPGSINQAHQPDEYLETRFIKPTRELITQVI 377
              +  VV Y T+A  +       P ++LGPG  + AHQ DEY     ++   +L   +I
Sbjct: 306 RPLEPRVVPYFTDASLLLPALGNPPCIILGPGEPSMAHQTDEYCLLSRLEEAEQLYGNLI 365


Lambda     K      H
   0.320    0.139    0.430 

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: 375
Number of extensions: 15
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: 383
Length of database: 370
Length adjustment: 30
Effective length of query: 353
Effective length of database: 340
Effective search space:   120020
Effective search space used:   120020
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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

Related tools

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