GapMind for Amino acid biosynthesis

 

Aligments for a candidate for dapC in Pseudomonas fluorescens FW300-N2E3

Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate AO353_03025 AO353_03025 acetylornithine aminotransferase

Query= SwissProt::P18335
         (406 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_03025 AO353_03025
           acetylornithine aminotransferase
          Length = 406

 Score =  536 bits (1381), Expect = e-157
 Identities = 262/406 (64%), Positives = 314/406 (77%)

Query: 1   MAIEQTAITRATFDEVILPIYAPAEFIPVKGQGSRIWDQQGKEYVDFAGGIAVTALGHCH 60
           M++E  A+ RA FD+V++P YAPA FIPV+G GSR+WDQ G+E +DFAGGIAV  LGH H
Sbjct: 1   MSVEHAAVQRADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAH 60

Query: 61  PALVNALKTQGETLWHISNVFTNEPALRLGRKLIEATFAERVVFMNSGTEANETAFKLAR 120
           PALV AL  Q   LWH+SNVFTNEPALRL  KLI+ATFA+RV F NSG EANE AFKLAR
Sbjct: 61  PALVGALTEQANKLWHVSNVFTNEPALRLAHKLIDATFADRVFFCNSGAEANEAAFKLAR 120

Query: 121 HYACVRHSPFKTKIIAFHNAFHGRSLFTVSVGGQPKYSDGFGPKPADIIHVPFNDLHAVK 180
             A  R    K +IIA  N+FHGR+LFTV+VGGQ KYSDGFGPK   I HV FNDL A+K
Sbjct: 121 RVAHDRFGSEKYEIIAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVKFNDLDALK 180

Query: 181 AVMDDHTCAVVVEPIQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGDLFA 240
           A + D TCAVV+EPIQGEGGV  A   +LQG RELC QH ALL+FDEVQ GMGR+G+LFA
Sbjct: 181 AAISDKTCAVVLEPIQGEGGVLPADLAYLQGARELCTQHNALLIFDEVQTGMGRSGELFA 240

Query: 241 YMHYGVTPDILTSAKALGGGFPISAMLTTAEIASAFHPGSHGSTYGGNPLACAVAGAAFD 300
           Y HYGVTPDILTSAK+LGGGFPI+AMLTT ++A     G+HG+TYGGNPLACAVA A  D
Sbjct: 241 YQHYGVTPDILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVID 300

Query: 301 IINTPEVLEGIQAKRQRFVDHLQKIDQQYDVFSDIRGMGLLIGAELKPQYKGRARDFLYA 360
           ++NTPEVL G++AK   F   L++I  +Y +F+ +RG+GLL+G  L   +KG+A+D   A
Sbjct: 301 VVNTPEVLNGVKAKHDLFKTRLEQIGAKYGLFTQVRGLGLLLGCVLSEAWKGKAKDVFNA 360

Query: 361 GAEAGVMVLNAGPDVMRFAPSLVVEDADIDEGMQRFAHAVAKVVGA 406
               G+M+L AGPDV+RFAPSLVVEDADI+EG++RF  AVAK+  A
Sbjct: 361 AEREGLMILQAGPDVIRFAPSLVVEDADIEEGLERFERAVAKLTQA 406


Lambda     K      H
   0.322    0.138    0.415 

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: 560
Number of extensions: 15
Number of successful extensions: 1
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: 406
Length adjustment: 31
Effective length of query: 375
Effective length of database: 375
Effective search space:   140625
Effective search space used:   140625
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 (21.9 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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 paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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