Alignments for a candidate for argD'B in Pseudomonas fluorescens FW300-N2E3

GapMind for Amino acid biosynthesis

Alignments for a candidate for argD'B in Pseudomonas fluorescens FW300-N2E3

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate AO353_03025 AO353_03025 acetylornithine aminotransferase

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



>FitnessBrowser__pseudo3_N2E3:AO353_03025
          Length = 406

 Score =  768 bits (1984), Expect = 0.0
 Identities = 379/406 (93%), Positives = 396/406 (97%)

Query: 1   MSVEHAAVERADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAH 60
           MSVEHAAV+RADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAH
Sbjct: 1   MSVEHAAVQRADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAH 60

Query: 61  PALVAALTEQANKLWHVSNVFTNEPALRLAHKLVDATFAERVFFCNSGAEANEAAFKLAR 120
           PALV ALTEQANKLWHVSNVFTNEPALRLAHKL+DATFA+RVFFCNSGAEANEAAFKLAR
Sbjct: 61  PALVGALTEQANKLWHVSNVFTNEPALRLAHKLIDATFADRVFFCNSGAEANEAAFKLAR 120

Query: 121 RVAHDRFGTEKYEIVAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALK 180
           RVAHDRFG+EKYEI+AALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHV +NDL ALK
Sbjct: 121 RVAHDRFGSEKYEIIAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVKFNDLDALK 180

Query: 181 AAVSDKTCAVVLEPIQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFA 240
           AA+SDKTCAVVLEPIQGEGGVLPA+L+YLQGARELC  HNALL+FDEVQTGMGRSG+LFA
Sbjct: 181 AAISDKTCAVVLEPIQGEGGVLPADLAYLQGARELCTQHNALLIFDEVQTGMGRSGELFA 240

Query: 241 YQHYGVTPDILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVID 300
           YQHYGVTPDILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVID
Sbjct: 241 YQHYGVTPDILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVID 300

Query: 301 VINTPEVLNGVNAKHDKFKTRLEQIGEKYGLFTEVRGLGLLLGCVLSDAWKGKAKDIFNA 360
           V+NTPEVLNGV AKHD FKTRLEQIG KYGLFT+VRGLGLLLGCVLS+AWKGKAKD+FNA
Sbjct: 301 VVNTPEVLNGVKAKHDLFKTRLEQIGAKYGLFTQVRGLGLLLGCVLSEAWKGKAKDVFNA 360

Query: 361 AEREGLMILQAGPDVIRFAPSLVVEDADIDAGLDRFERAAAKLTQA 406
           AEREGLMILQAGPDVIRFAPSLVVEDADI+ GL+RFERA AKLTQA
Sbjct: 361 AEREGLMILQAGPDVIRFAPSLVVEDADIEEGLERFERAVAKLTQA 406


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: 666
Number of extensions: 8
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 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate AO353_03025 AO353_03025 (acetylornithine aminotransferase)
to HMM TIGR03246 (astC: succinylornithine transaminase family (EC 2.6.1.81))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR03246.hmm
# target sequence database:        /tmp/gapView.3048.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03246  [M=397]
Accession:   TIGR03246
Description: arg_catab_astC: succinylornithine transaminase family
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   8.2e-223  725.5   1.0   9.3e-223  725.3   1.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03025  AO353_03025 acetylornithine amin


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_03025  AO353_03025 acetylornithine aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  725.3   1.0  9.3e-223  9.3e-223       1     396 [.       8     403 ..       8     404 .. 1.00

  Alignments for each domain:
  == domain 1  score: 725.3 bits;  conditional E-value: 9.3e-223
                                     TIGR03246   1 veresfdevmvpvyapakfipvrgeGsrvwdqegkeyidfaGGiavnalGhahpelvealkeqae 65 
                                                   v+r++fd+vmvp+yapa+fipvrg Gsrvwdq+g+e+idfaGGiavn lGhahp+lv al+eqa+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03025   8 VQRADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAHPALVGALTEQAN 72 
                                                   79*************************************************************** PP

                                     TIGR03246  66 klwhlgngytnepvlrlakklvdatfadkvffcnsGaeaneaalklarkvaldkygaekseivaf 130
                                                   klwh++n++tnep+lrla+kl+datfad+vffcnsGaeaneaa+klar+va+d++g+ek+ei+a 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03025  73 KLWHVSNVFTNEPALRLAHKLIDATFADRVFFCNSGAEANEAAFKLARRVAHDRFGSEKYEIIAA 137
                                                   ***************************************************************** PP

                                     TIGR03246 131 knsfhGrtlftvsvGGqakysedfaplpegikhaayndlealkalisdktcavivepiqGegGvv 195
                                                    nsfhGrtlftv vGGq+kys++f+p+++gi+h+++ndl+alka+isdktcav++epiqGegGv+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03025 138 LNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVKFNDLDALKAAISDKTCAVVLEPIQGEGGVL 202
                                                   ***************************************************************** PP

                                     TIGR03246 196 padkaflkglrelcdrhnallifdevqtGvGrtGelyaymeyGvtpdiltsakalGgGfpiGall 260
                                                   pad a+l+g+relc +hnallifdevqtG+Gr Gel+ay++yGvtpdiltsak+lGgGfpi a+l
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03025 203 PADLAYLQGARELCTQHNALLIFDEVQTGMGRSGELFAYQHYGVTPDILTSAKSLGGGFPIAAML 267
                                                   ***************************************************************** PP

                                     TIGR03246 261 tteelakvlkvGthGttyGGnplacavaekvldlvntaelleGvkqrhelfvdelekinarykvf 325
                                                   tte+lak+l vGthGttyGGnplacavae+v+d+vnt+e+l+Gvk++h+lf ++le+i+a+y +f
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03025 268 TTEDLAKHLVVGTHGTTYGGNPLACAVAEAVIDVVNTPEVLNGVKAKHDLFKTRLEQIGAKYGLF 332
                                                   ***************************************************************** PP

                                     TIGR03246 326 seirGkGlliGavlteeyaGkakdlvnaaaeeGvlvliaGpdvvrfapslvieeeeikeGlarle 390
                                                   +++rG Gll+G+vl+e+++Gkakd+ naa++eG+++l+aGpdv+rfapslv+e+++i+eGl+r+e
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03025 333 TQVRGLGLLLGCVLSEAWKGKAKDVFNAAEREGLMILQAGPDVIRFAPSLVVEDADIEEGLERFE 397
                                                   ***************************************************************** PP

                                     TIGR03246 391 kavekl 396
                                                   +av+kl
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03025 398 RAVAKL 403
                                                   ***987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (397 nodes)
Target sequences:                          1  (406 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.37
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer
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

GapMind for Amino acid biosynthesis