Alignments for a candidate for trpE in Pseudomonas putida KT2440

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Pseudomonas putida KT2440

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate PP_0417 PP_0417 Anthranilate synthase component 1

Query= SwissProt::P20579
         (493 letters)



>FitnessBrowser__Putida:PP_0417
          Length = 493

 Score =  959 bits (2478), Expect = 0.0
 Identities = 482/493 (97%), Positives = 486/493 (98%)

Query: 1   MNREEFLRLAAVGYNRIPLACETLADFDTPLSIYLKLADQPNSYLLESVQGGEKWGRYSM 60
           MNREEFLRLAA GYNRIPLACETLADFDTPLSIYLKLADQPNSYLLESVQGGEKWGRYSM
Sbjct: 1   MNREEFLRLAAAGYNRIPLACETLADFDTPLSIYLKLADQPNSYLLESVQGGEKWGRYSM 60

Query: 61  IGLPSRTVMRVHGYHVSILHDGVEVESHDVEDPLAFVESFKDRYKVADIPGLPRFNGGLV 120
           IGLPSRTVMRVHGY VSILHDGVEVES +VEDPLAFVE+FKDRYKVADIPGLPRFNGGLV
Sbjct: 61  IGLPSRTVMRVHGYRVSILHDGVEVESCEVEDPLAFVETFKDRYKVADIPGLPRFNGGLV 120

Query: 121 GYFGYDCVRYVEKRLGVSPNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVLVDPAEEQA 180
           GYFGYDCVRYVEKRLG SPNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVLVDPAE+QA
Sbjct: 121 GYFGYDCVRYVEKRLGASPNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVLVDPAEDQA 180

Query: 181 FEQGQARLQGLLETLRQPITPRRGLDLSGPQAAEPEFRSSYTREDYENAVGRIKEYILAG 240
           FEQGQARLQGLLETLRQPITPRRGLDLSGPQAAEP FRSSYTREDYENAVGRIKEYILAG
Sbjct: 181 FEQGQARLQGLLETLRQPITPRRGLDLSGPQAAEPAFRSSYTREDYENAVGRIKEYILAG 240

Query: 241 DCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDNL 300
           DCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDNL
Sbjct: 241 DCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDNL 300

Query: 301 VTVRPIAGTRPRGATEEADRALEDDLLSDDKEIAEHLMLIDLGRNDVGRVSSTGSVRLTE 360
           VTVRPIAGTRPRGATEEADRALEDDLLSDDKEIAEHLMLIDLGRNDVGRVSSTGSVRLTE
Sbjct: 301 VTVRPIAGTRPRGATEEADRALEDDLLSDDKEIAEHLMLIDLGRNDVGRVSSTGSVRLTE 360

Query: 361 KMVIERYSNVMHIVSNVAGQLREGLTAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKR 420
           KMVIERYSNVMHIVSNV GQLREGLTAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKR
Sbjct: 361 KMVIERYSNVMHIVSNVTGQLREGLTAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKR 420

Query: 421 GVYGGAVGYFAWNGNMDTAIAIRTAVINDGELHVQAGGGIVADSVPALEWEETINKRRAM 480
           GVYGGAVGYFAWNGNMDTAIAIRTAVI DGELHVQAGGGIVADSVPALEWEETINKRRAM
Sbjct: 421 GVYGGAVGYFAWNGNMDTAIAIRTAVIKDGELHVQAGGGIVADSVPALEWEETINKRRAM 480

Query: 481 FRAVALAEQTSAK 493
           FRAVALAEQTSA+
Sbjct: 481 FRAVALAEQTSAR 493


Lambda     K      H
   0.320    0.138    0.403 

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: 967
Number of extensions: 19
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: 493
Length of database: 493
Length adjustment: 34
Effective length of query: 459
Effective length of database: 459
Effective search space:   210681
Effective search space used:   210681
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: 52 (24.6 bits)

Align candidate PP_0417 PP_0417 (Anthranilate synthase component 1)
to HMM TIGR00564 (trpE: anthranilate synthase component I (EC 4.1.3.27))

# 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/TIGR00564.hmm
# target sequence database:        /tmp/gapView.18232.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00564  [M=455]
Accession:   TIGR00564
Description: trpE_most: anthranilate synthase component I
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.7e-176  573.7   0.0   1.9e-176  573.5   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_0417  PP_0417 Anthranilate synthase co


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_0417  PP_0417 Anthranilate synthase component 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  573.5   0.0  1.9e-176  1.9e-176       2     454 ..      26     484 ..      25     485 .. 0.93

  Alignments for each domain:
  == domain 1  score: 573.5 bits;  conditional E-value: 1.9e-176
                           TIGR00564   2 dtltpisvylklakrkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeak.ieedelkelrkl 75 
                                         d  tp+s+ylkla +++s+llEsv+ +e++gRyS+igl +++++++++ ++ +l+   e ++ ++ed+l  ++++
  lcl|FitnessBrowser__Putida:PP_0417  26 DFDTPLSIYLKLADQPNSYLLESVQGGEKWGRYSMIGLPSRTVMRVHGYRVSILHDGVEVEScEVEDPLAFVETF 100
                                         6679******************************************99866665533333334889999988888 PP

                           TIGR00564  76 leka.eesedeldeplsggavGylgydtvrlveklke..eaedelelpdlllllvetvivfDhvekkvilienar 147
                                          +++   ++++l+  + gg+vGy+gyd+vr+vek     +++d+l +pd+ll++ + v+vfD+ + k++ i  + 
  lcl|FitnessBrowser__Putida:PP_0417 101 KDRYkVADIPGLP-RFNGGLVGYFGYDCVRYVEKRLGasPNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVLVD 174
                                         8887444555555.5******************97653345*********************************8 PP

                           TIGR00564 148 teaersaeeeaaarleellaelqkeleka....vkaleekkesftsnvekeeyeekvakakeyikaGdifqvvlS 218
                                          ++++ a+e+ +arl+ ll++l+++++++     + ++ ++  f s++++e+ye++v ++keyi aGd +qvv+S
  lcl|FitnessBrowser__Putida:PP_0417 175 PAEDQ-AFEQGQARLQGLLETLRQPITPRrgldLSGPQAAEPAFRSSYTREDYENAVGRIKEYILAGDCMQVVPS 248
                                         88888.9*******************99867555556666667******************************** PP

                           TIGR00564 219 qrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvkgkrvetrPiAGtrkRGatkeeDeale 293
                                         qr++ +++a p++lYr+LR  NP py+y++++ df++vgsSPE+lv+v+++ v++rPiAGtr+RGat+e+D+ale
  lcl|FitnessBrowser__Putida:PP_0417 249 QRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDNLVTVRPIAGTRPRGATEEADRALE 323
                                         *************************************************************************** PP

                           TIGR00564 294 eeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellkiekyshvmHivSeVeGelkdeltavDalraalPaG 368
                                         ++Ll+d Ke AEHlmL+DL+RND+g+v+++gsv+ +e + ie+ys vmHivS+V+G+l+++lta+Dalra+lPaG
  lcl|FitnessBrowser__Putida:PP_0417 324 DDLLSDDKEIAEHLMLIDLGRNDVGRVSSTGSVRLTEKMVIERYSNVMHIVSNVTGQLREGLTAMDALRAILPAG 398
                                         *************************************************************************** PP

                           TIGR00564 369 TlsGAPKvrAmelidelEkekRgiYgGavgylsfdgdvdtaiaiRtmvlkdgvayvqAgaGiVaDSdpeaEyeEt 443
                                         TlsGAPK+rAme+idelE++kRg+YgGavgy+  +g++dtaiaiRt+v+kdg ++vqAg+GiVaDS+p  E+eEt
  lcl|FitnessBrowser__Putida:PP_0417 399 TLSGAPKIRAMEIIDELEPVKRGVYGGAVGYFAWNGNMDTAIAIRTAVIKDGELHVQAGGGIVADSVPALEWEET 473
                                         *************************************************************************** PP

                           TIGR00564 444 lnKakallrai 454
                                         +nK +a+ ra+
  lcl|FitnessBrowser__Putida:PP_0417 474 INKRRAMFRAV 484
                                         *******9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (493 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: 7.40
//
[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:

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