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.22552.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: 10.46
//
[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:

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