GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Putida:PP_3601
          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.8014.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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.57
//
[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:

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