GapMind for catabolism of small carbon sources

 

Aligments for a candidate for astC in Pseudomonas fluorescens FW300-N2C3

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate AO356_18725 AO356_18725 acetylornithine aminotransferase

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



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18725 AO356_18725
           acetylornithine aminotransferase
          Length = 406

 Score =  761 bits (1966), Expect = 0.0
 Identities = 380/406 (93%), Positives = 392/406 (96%)

Query: 1   MSVEHAAVERADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAH 60
           MSVE AAV+RADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAH
Sbjct: 1   MSVEQAAVQRADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAH 60

Query: 61  PALVAALTEQANKLWHVSNVFTNEPALRLAHKLVDATFAERVFFCNSGAEANEAAFKLAR 120
           PALV ALTEQANKLWHVSNVFTNEPALRLAHKLV+ATFAER FFCNSGAEANEAAFKLAR
Sbjct: 61  PALVGALTEQANKLWHVSNVFTNEPALRLAHKLVNATFAERAFFCNSGAEANEAAFKLAR 120

Query: 121 RVAHDRFGTEKYEIVAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALK 180
           RVA DRFG+EKYEI+AALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALK
Sbjct: 121 RVAFDRFGSEKYEIIAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALK 180

Query: 181 AAVSDKTCAVVLEPIQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFA 240
           AAVSDKTCAVVLEPIQGEGGVLPAE +YLQGAR+LCDAH+ALLVFDEVQTGMGRSG LFA
Sbjct: 181 AAVSDKTCAVVLEPIQGEGGVLPAEQAYLQGARDLCDAHDALLVFDEVQTGMGRSGHLFA 240

Query: 241 YQHYGVTPDILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVID 300
           Y HYGV PDILTSAKSLGGGFPIAAMLTTE LAKHLVVGTHGTTYGGNPLACAVAEAVID
Sbjct: 241 YMHYGVVPDILTSAKSLGGGFPIAAMLTTEALAKHLVVGTHGTTYGGNPLACAVAEAVID 300

Query: 301 VINTPEVLNGVNAKHDKFKTRLEQIGEKYGLFTEVRGLGLLLGCVLSDAWKGKAKDIFNA 360
           V+NTPEVL GV  KH KFK RLEQIGEKYGLFT+VRGLGLL+GCVL+DAWKGKAKDIFNA
Sbjct: 301 VVNTPEVLGGVKTKHAKFKARLEQIGEKYGLFTQVRGLGLLIGCVLNDAWKGKAKDIFNA 360

Query: 361 AEREGLMILQAGPDVIRFAPSLVVEDADIDAGLDRFERAAAKLTQA 406
           AE+EGLMILQAGPDVIRFAPSLVVEDADIDAGLDRFERAAAKLTQA
Sbjct: 361 AEQEGLMILQAGPDVIRFAPSLVVEDADIDAGLDRFERAAAKLTQA 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: 661
Number of extensions: 7
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 AO356_18725 AO356_18725 (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.carbon/TIGR03246.hmm
# target sequence database:        /tmp/gapView.6031.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   5.3e-220  716.2   1.9     6e-220  716.1   1.9    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18725  AO356_18725 acetylornithine amin


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18725  AO356_18725 acetylornithine aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  716.1   1.9    6e-220    6e-220       1     396 [.       8     403 ..       8     404 .. 1.00

  Alignments for each domain:
  == domain 1  score: 716.1 bits;  conditional E-value: 6e-220
                                       TIGR03246   1 veresfdevmvpvyapakfipvrgeGsrvwdqegkeyidfaGGiavnalGhahpelvealkeq 63 
                                                     v+r++fd+vmvp+yapa+fipvrg Gsrvwdq+g+e+idfaGGiavn lGhahp+lv al+eq
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18725   8 VQRADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAHPALVGALTEQ 70 
                                                     79************************************************************* PP

                                       TIGR03246  64 aeklwhlgngytnepvlrlakklvdatfadkvffcnsGaeaneaalklarkvaldkygaekse 126
                                                     a+klwh++n++tnep+lrla+klv+atfa+++ffcnsGaeaneaa+klar+va+d++g+ek+e
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18725  71 ANKLWHVSNVFTNEPALRLAHKLVNATFAERAFFCNSGAEANEAAFKLARRVAFDRFGSEKYE 133
                                                     *************************************************************** PP

                                       TIGR03246 127 ivafknsfhGrtlftvsvGGqakysedfaplpegikhaayndlealkalisdktcavivepiq 189
                                                     i+a  nsfhGrtlftv vGGq+kys++f+p+++gi+h++yndl+alka++sdktcav++epiq
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18725 134 IIAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALKAAVSDKTCAVVLEPIQ 196
                                                     *************************************************************** PP

                                       TIGR03246 190 GegGvvpadkaflkglrelcdrhnallifdevqtGvGrtGelyaymeyGvtpdiltsakalGg 252
                                                     GegGv+pa++a+l+g+r+lcd+h+all+fdevqtG+Gr G+l+aym+yGv+pdiltsak+lGg
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18725 197 GEGGVLPAEQAYLQGARDLCDAHDALLVFDEVQTGMGRSGHLFAYMHYGVVPDILTSAKSLGG 259
                                                     *************************************************************** PP

                                       TIGR03246 253 GfpiGalltteelakvlkvGthGttyGGnplacavaekvldlvntaelleGvkqrhelfvdel 315
                                                     Gfpi a+ltte+lak+l vGthGttyGGnplacavae+v+d+vnt+e+l Gvk++h++f ++l
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18725 260 GFPIAAMLTTEALAKHLVVGTHGTTYGGNPLACAVAEAVIDVVNTPEVLGGVKTKHAKFKARL 322
                                                     *************************************************************** PP

                                       TIGR03246 316 ekinarykvfseirGkGlliGavlteeyaGkakdlvnaaaeeGvlvliaGpdvvrfapslvie 378
                                                     e+i+++y +f+++rG GlliG+vl+++++Gkakd+ naa++eG+++l+aGpdv+rfapslv+e
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18725 323 EQIGEKYGLFTQVRGLGLLIGCVLNDAWKGKAKDIFNAAEQEGLMILQAGPDVIRFAPSLVVE 385
                                                     *************************************************************** PP

                                       TIGR03246 379 eeeikeGlarlekavekl 396
                                                     +++i+ Gl+r+e+a +kl
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18725 386 DADIDAGLDRFERAAAKL 403
                                                     **************9886 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: 10.74
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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.

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