Alignments for a candidate for argD'B in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for argD'B in Pseudomonas stutzeri RCH2

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate GFF2666 Psest_2719 acetylornithine and succinylornithine aminotransferases/succinylornithine transaminase family

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



>FitnessBrowser__psRCH2:GFF2666
          Length = 406

 Score =  672 bits (1733), Expect = 0.0
 Identities = 321/406 (79%), Positives = 362/406 (89%)

Query: 1   MSVEHAAVERADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAH 60
           MS  H  VERADFDQV+VP +APAAF+PVRG GSRVWDQSGREL+DFAGGIAVN LGHAH
Sbjct: 1   MSAPHTPVERADFDQVIVPTFAPAAFVPVRGLGSRVWDQSGRELVDFAGGIAVNALGHAH 60

Query: 61  PALVAALTEQANKLWHVSNVFTNEPALRLAHKLVDATFAERVFFCNSGAEANEAAFKLAR 120
           PA+VAALTEQA KLWH+SN++TNEPALRLA KLV ATFA+R FFCNSGAEANEAAFKLAR
Sbjct: 61  PAMVAALTEQAGKLWHISNIYTNEPALRLAKKLVAATFADRAFFCNSGAEANEAAFKLAR 120

Query: 121 RVAHDRFGTEKYEIVAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALK 180
           R AHD +G +K+EI++ALNSFHGRTLFTV VGGQSKYSDGFGPKI GITHVPYNDL ALK
Sbjct: 121 RYAHDVYGPQKFEIISALNSFHGRTLFTVTVGGQSKYSDGFGPKIEGITHVPYNDLEALK 180

Query: 181 AAVSDKTCAVVLEPIQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFA 240
           AA+SDKTCAVVLEPIQGE G+LP E +YL+GAR+LC+ HNALL+FDEVQTGMGR+G+LFA
Sbjct: 181 AAISDKTCAVVLEPIQGESGILPGEQAYLEGARQLCNEHNALLIFDEVQTGMGRTGELFA 240

Query: 241 YQHYGVTPDILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVID 300
           Y HYG+TPDILT+AKSLGGGFPI AMLTT ++A HL VGTHGTTYGGNPLACAVAEAV+D
Sbjct: 241 YMHYGITPDILTNAKSLGGGFPIGAMLTTNEIAAHLSVGTHGTTYGGNPLACAVAEAVVD 300

Query: 301 VINTPEVLNGVNAKHDKFKTRLEQIGEKYGLFTEVRGLGLLLGCVLSDAWKGKAKDIFNA 360
           ++NTPEVL GV AKH++FK RL QIGE+YG+F+ VRG GLL+GCVLSDAWKGKA     A
Sbjct: 301 IVNTPEVLEGVKAKHERFKARLTQIGERYGVFSLVRGRGLLIGCVLSDAWKGKAGAFCAA 360

Query: 361 AEREGLMILQAGPDVIRFAPSLVVEDADIDAGLDRFERAAAKLTQA 406
           AE+E LM+LQAGPDV+R APSLV++ ADID GLDR ERA A LTQA
Sbjct: 361 AEKEALMVLQAGPDVVRLAPSLVIDQADIDEGLDRLERAVAALTQA 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: 607
Number of extensions: 10
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 GFF2666 Psest_2719 (acetylornithine and succinylornithine aminotransferases/succinylornithine transaminase family)
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.3742811.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.4e-217  708.2   0.7   1.6e-217  708.1   0.7    1.0  1  FitnessBrowser__psRCH2:GFF2666  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__psRCH2:GFF2666  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  708.1   0.7  1.6e-217  1.6e-217       1     396 [.       8     403 ..       8     404 .. 1.00

  Alignments for each domain:
  == domain 1  score: 708.1 bits;  conditional E-value: 1.6e-217
                       TIGR03246   1 veresfdevmvpvyapakfipvrgeGsrvwdqegkeyidfaGGiavnalGhahpelvealkeqaeklwhlgngytnepv 79 
                                     ver++fd+v+vp++apa+f+pvrg Gsrvwdq+g+e++dfaGGiavnalGhahp++v+al+eqa klwh++n ytnep+
  FitnessBrowser__psRCH2:GFF2666   8 VERADFDQVIVPTFAPAAFVPVRGLGSRVWDQSGRELVDFAGGIAVNALGHAHPAMVAALTEQAGKLWHISNIYTNEPA 86 
                                     79***************************************************************************** PP

                       TIGR03246  80 lrlakklvdatfadkvffcnsGaeaneaalklarkvaldkygaekseivafknsfhGrtlftvsvGGqakysedfaplp 158
                                     lrlakklv atfad++ffcnsGaeaneaa+klar++a+d yg++k ei++  nsfhGrtlftv+vGGq+kys++f+p++
  FitnessBrowser__psRCH2:GFF2666  87 LRLAKKLVAATFADRAFFCNSGAEANEAAFKLARRYAHDVYGPQKFEIISALNSFHGRTLFTVTVGGQSKYSDGFGPKI 165
                                     ******************************************************************************* PP

                       TIGR03246 159 egikhaayndlealkalisdktcavivepiqGegGvvpadkaflkglrelcdrhnallifdevqtGvGrtGelyaymey 237
                                     egi+h++yndlealka+isdktcav++epiqGe+G++p ++a+l+g+r+lc++hnallifdevqtG+GrtGel+aym+y
  FitnessBrowser__psRCH2:GFF2666 166 EGITHVPYNDLEALKAAISDKTCAVVLEPIQGESGILPGEQAYLEGARQLCNEHNALLIFDEVQTGMGRTGELFAYMHY 244
                                     ******************************************************************************* PP

                       TIGR03246 238 GvtpdiltsakalGgGfpiGalltteelakvlkvGthGttyGGnplacavaekvldlvntaelleGvkqrhelfvdele 316
                                     G+tpdilt ak+lGgGfpiGa+ltt+e+a++l+vGthGttyGGnplacavae+v+d+vnt+e+leGvk++he+f ++l 
  FitnessBrowser__psRCH2:GFF2666 245 GITPDILTNAKSLGGGFPIGAMLTTNEIAAHLSVGTHGTTYGGNPLACAVAEAVVDIVNTPEVLEGVKAKHERFKARLT 323
                                     ******************************************************************************* PP

                       TIGR03246 317 kinarykvfseirGkGlliGavlteeyaGkakdlvnaaaeeGvlvliaGpdvvrfapslvieeeeikeGlarlekavek 395
                                     +i++ry vfs +rG+GlliG+vl+++++Gka  +  aa++e ++vl+aGpdvvr+apslvi++++i+eGl+rle+av+ 
  FitnessBrowser__psRCH2:GFF2666 324 QIGERYGVFSLVRGRGLLIGCVLSDAWKGKAGAFCAAAEKEALMVLQAGPDVVRLAPSLVIDQADIDEGLDRLERAVAA 402
                                     *****************************************************************************87 PP

                       TIGR03246 396 l 396
                                     l
  FitnessBrowser__psRCH2:GFF2666 403 L 403
                                     6 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 15.26
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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