GapMind for catabolism of small carbon sources

 

Aligments for a candidate for garD in Pseudomonas putida KT2440

Align Galactarate dehydratase (EC 4.2.1.42) (characterized)
to candidate PP_3601 PP_3601 galactarate dehydratase

Query= reanno::WCS417:GFF829
         (517 letters)



>lcl|FitnessBrowser__Putida:PP_3601 PP_3601 galactarate dehydratase
          Length = 517

 Score =  872 bits (2254), Expect = 0.0
 Identities = 433/517 (83%), Positives = 463/517 (89%)

Query: 1   MQLIEHADSPRSIRLHERDNVVIVVNDQGVPAGTEFPDGLVTVDFIPQSHKVTLEDIPEG 60
           MQLIEH+DSPR +RLH+ DNVV+VVND G+  G  F DGL  ++ +PQSHKV    I +G
Sbjct: 1   MQLIEHSDSPRYVRLHDDDNVVVVVNDGGLGEGARFADGLTLIEGVPQSHKVATVSIAKG 60

Query: 61  GQIIRYGQTIGYALAPIPRGSWVQEDQLRMPTAPPLDSLPLSTEVPEAQAPLEGFTFEGY 120
             + RYGQ IGYAL  + +GSWVQE QL MP AP LDSLP    VP+   PLEGFTFEGY
Sbjct: 61  EPVRRYGQIIGYALEDLRQGSWVQESQLAMPAAPELDSLPRCDAVPQPLPPLEGFTFEGY 120

Query: 121 RNADGTVGTRNILGITTTVQCVTGVLDHAVKRIKDELLPKYPHVDDVVALTHSYGCGVAI 180
           RNADGTVGTRNILGITTTVQCVTGVL+HAVKRI++ELLPKYP+VDDVVA+THSYGCGVAI
Sbjct: 121 RNADGTVGTRNILGITTTVQCVTGVLEHAVKRIRNELLPKYPNVDDVVAITHSYGCGVAI 180

Query: 181 TATDAYIPIRTVRNLARNPNLGGEALVISLGCEKLQAGQVMHDNDSSVDLSEPWLYRLQD 240
            A DAYIPIRTVRNLARNPNLGGEALVISLGCEKLQA QVMHDND SVDLS+PWLYRLQD
Sbjct: 181 NARDAYIPIRTVRNLARNPNLGGEALVISLGCEKLQASQVMHDNDPSVDLSDPWLYRLQD 240

Query: 241 SSHGFTEMIEQIMALAETRLKKLDQRRRETVPASELILGMQCGGSDAFSGITANPALGYA 300
           +S GF EMIEQIM LAETRLKKLDQRRRETVPASELILGMQCGGSDAFSGITANPALGYA
Sbjct: 241 ASLGFVEMIEQIMDLAETRLKKLDQRRRETVPASELILGMQCGGSDAFSGITANPALGYA 300

Query: 301 SDLLLRAGATVMFSEVTEVRDAIYLLTSRAENTQVAQELVREMDWYDRYLAKGEADRSAN 360
           +DLL+RAGATV+FSEVTEVRDAIY+LTSRAEN  VA  LVREMDWYDRYL +G ADRSAN
Sbjct: 301 ADLLVRAGATVLFSEVTEVRDAIYMLTSRAENQDVADALVREMDWYDRYLQQGAADRSAN 360

Query: 361 TTPGNKKGGLSNIVEKSLGSIVKSGSSAINGVLGPGERFKGKGLIFCATPASDFVCGTLQ 420
           TTPGNKKGGLSNIVEKSLGSIVKSGS AI GVLGPGER   KGLIFCATPASDFVCGTLQ
Sbjct: 361 TTPGNKKGGLSNIVEKSLGSIVKSGSGAIQGVLGPGERANRKGLIFCATPASDFVCGTLQ 420

Query: 421 LAAGMNLHVFTTGRGTPYGLAMAPVVKVSTRTELAQRWPDLIDIDAGRIATGRATIEELG 480
           LAAGMNLHVFTTGRGTPYGLAMAPVVKV TR+ELAQRWPDLIDIDAGRIA+GR+TIEELG
Sbjct: 421 LAAGMNLHVFTTGRGTPYGLAMAPVVKVCTRSELAQRWPDLIDIDAGRIASGRSTIEELG 480

Query: 481 WELFHFYLDVASGRKQTWAEHHKLHNDITLFNPAPIT 517
           WELFH+YLDVASGRKQTWAE H+LHNDITLFNPAPIT
Sbjct: 481 WELFHYYLDVASGRKQTWAEQHRLHNDITLFNPAPIT 517


Lambda     K      H
   0.318    0.135    0.401 

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: 910
Number of extensions: 20
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: 517
Length of database: 517
Length adjustment: 35
Effective length of query: 482
Effective length of database: 482
Effective search space:   232324
Effective search space used:   232324
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate PP_3601 PP_3601 (galactarate dehydratase)
to HMM TIGR03248 (garD: galactarate dehydratase (EC 4.2.1.42))

# 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/TIGR03248.hmm
# target sequence database:        /tmp/gapView.8909.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03248  [M=507]
Accession:   TIGR03248
Description: galactar-dH20: galactarate dehydratase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.8e-287  939.6   0.0   2.1e-287  939.4   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_3601  PP_3601 galactarate dehydratase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_3601  PP_3601 galactarate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  939.4   0.0  2.1e-287  2.1e-287       2     507 .]      12     517 .]      11     517 .] 1.00

  Alignments for each domain:
  == domain 1  score: 939.4 bits;  conditional E-value: 2.1e-287
                           TIGR03248   2 yirvneqdnvaivvndkGlpagtefedgltlvekipqghkvalvdlekgdaiirygeviGyavkdiarGswvkee 76 
                                         y+r++++dnv++vvnd Gl +g++f+dgltl+e +pq+hkva+v ++kg+ ++ryg++iGya++d+ +Gswv+e+
  lcl|FitnessBrowser__Putida:PP_3601  12 YVRLHDDDNVVVVVNDGGLGEGARFADGLTLIEGVPQSHKVATVSIAKGEPVRRYGQIIGYALEDLRQGSWVQES 86 
                                         89************************************************************************* PP

                           TIGR03248  77 llelpsapaleelplatkvpeklapleGytfeGyrnadGsvGtknilgittsvqcvagvvdyavkrikkellpky 151
                                         +l +p+ap+l++lp +++vp++l+pleG+tfeGyrnadG+vGt+nilgitt+vqcv+gv+++avkri++ellpky
  lcl|FitnessBrowser__Putida:PP_3601  87 QLAMPAAPELDSLPRCDAVPQPLPPLEGFTFEGYRNADGTVGTRNILGITTTVQCVTGVLEHAVKRIRNELLPKY 161
                                         *************************************************************************** PP

                           TIGR03248 152 pnvddvvalnhsyGcGvaidapdaivpirtlrnlalnpnlGGealvvglGceklqperllpeelsavelkdaavl 226
                                         pnvddvva++hsyGcGvai+a da++pirt+rnla+npnlGGealv++lGceklq++++++++  +v+l+d++++
  lcl|FitnessBrowser__Putida:PP_3601 162 PNVDDVVAITHSYGCGVAINARDAYIPIRTVRNLARNPNLGGEALVISLGCEKLQASQVMHDNDPSVDLSDPWLY 236
                                         *************************************************************************** PP

                           TIGR03248 227 rlqdeklGfaemveailelaeerlkklnarkretvpaselvvGlqcGGsdafsGvtanpavGfaadllvraGatv 301
                                         rlqd++lGf em+e+i++lae+rlkkl++r+retvpasel++G+qcGGsdafsG+tanpa+G+aadllvraGatv
  lcl|FitnessBrowser__Putida:PP_3601 237 RLQDASLGFVEMIEQIMDLAETRLKKLDQRRRETVPASELILGMQCGGSDAFSGITANPALGYAADLLVRAGATV 311
                                         *************************************************************************** PP

                           TIGR03248 302 lfsevtevrdaihlltpraedaevakaliremkwydeylarGeadrsanttpGnkkGGlsnivekalGsivksGs 376
                                         lfsevtevrdai++lt+rae+++va al+rem+wyd+yl++G adrsanttpGnkkGGlsnivek+lGsivksGs
  lcl|FitnessBrowser__Putida:PP_3601 312 LFSEVTEVRDAIYMLTSRAENQDVADALVREMDWYDRYLQQGAADRSANTTPGNKKGGLSNIVEKSLGSIVKSGS 386
                                         *************************************************************************** PP

                           TIGR03248 377 saivevlspGekvkkkGliyaatpasdfvcGtlqlasglnlhvfttGrGtpyGlalvpvikvstrtelaerwadl 451
                                          ai++vl+pGe++++kGli++atpasdfvcGtlqla+g+nlhvfttGrGtpyGla++pv+kv+tr+ela+rw dl
  lcl|FitnessBrowser__Putida:PP_3601 387 GAIQGVLGPGERANRKGLIFCATPASDFVCGTLQLAAGMNLHVFTTGRGTPYGLAMAPVVKVCTRSELAQRWPDL 461
                                         *************************************************************************** PP

                           TIGR03248 452 idldaGriatGeatiedvGwelfrlildvasGrkktwaekyklhndlalfnpapvt 507
                                         id+daGria+G+ tie++Gwelf+ +ldvasGrk+twae+++lhnd++lfnpap+t
  lcl|FitnessBrowser__Putida:PP_3601 462 IDIDAGRIASGRSTIEELGWELFHYYLDVASGRKQTWAEQHRLHNDITLFNPAPIT 517
                                         *******************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (507 nodes)
Target sequences:                          1  (517 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: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.53
//
[ok]

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

Links

Downloads

Related tools

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