Alignments for a candidate for trpE in Pseudomonas simiae WCS417

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Pseudomonas simiae WCS417

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate GFF5021 PS417_25725 anthranilate synthase component I

Query= SwissProt::P20579
         (493 letters)



>FitnessBrowser__WCS417:GFF5021
          Length = 493

 Score =  879 bits (2271), Expect = 0.0
 Identities = 438/490 (89%), Positives = 458/490 (93%)

Query: 1   MNREEFLRLAAVGYNRIPLACETLADFDTPLSIYLKLADQPNSYLLESVQGGEKWGRYSM 60
           M REEFLRLAA GYNRIPLACETLADFDTPLSIYLKLAD+PNSYLLESVQGGEKWGRYS+
Sbjct: 1   MTREEFLRLAAAGYNRIPLACETLADFDTPLSIYLKLADEPNSYLLESVQGGEKWGRYSI 60

Query: 61  IGLPSRTVMRVHGYHVSILHDGVEVESHDVEDPLAFVESFKDRYKVADIPGLPRFNGGLV 120
           IGLP RTV+RVH +HVSI  DGVE+ESHDV+DPLAFVE+FK RY V  I GLPRFNGGLV
Sbjct: 61  IGLPCRTVLRVHDHHVSITQDGVEIESHDVDDPLAFVEAFKARYNVPTIAGLPRFNGGLV 120

Query: 121 GYFGYDCVRYVEKRLGVSPNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVLVDPAEEQA 180
           GYFGYDCVRYVEKRLG  PNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVL DP++  A
Sbjct: 121 GYFGYDCVRYVEKRLGKCPNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVLADPSQADA 180

Query: 181 FEQGQARLQGLLETLRQPITPRRGLDLSGPQAAEPEFRSSYTREDYENAVGRIKEYILAG 240
           FEQGQA L+ LLE LRQPITPRRGLDLS P AA+P FRSS+T++DYE AV  IKEYILAG
Sbjct: 181 FEQGQASLEALLEKLRQPITPRRGLDLSRPPAADPVFRSSFTQDDYERAVDTIKEYILAG 240

Query: 241 DCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDNL 300
           DCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDNL
Sbjct: 241 DCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDNL 300

Query: 301 VTVRPIAGTRPRGATEEADRALEDDLLSDDKEIAEHLMLIDLGRNDVGRVSSTGSVRLTE 360
           +TVRPIAGTRPRGATEEAD ALE+DLLSDDKEIAEHLMLIDLGRND GRVS  GSV+LTE
Sbjct: 301 ITVRPIAGTRPRGATEEADLALEEDLLSDDKEIAEHLMLIDLGRNDTGRVSEIGSVKLTE 360

Query: 361 KMVIERYSNVMHIVSNVAGQLREGLTAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKR 420
           KMVIERYSNVMHIVSNV G+L+ GLTAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKR
Sbjct: 361 KMVIERYSNVMHIVSNVTGELKAGLTAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKR 420

Query: 421 GVYGGAVGYFAWNGNMDTAIAIRTAVINDGELHVQAGGGIVADSVPALEWEETINKRRAM 480
           GVYGGAVGYFAWNGNMDTAIAIRTAVI DGELHVQAGGGIVADSVPALEWEET+NKRRAM
Sbjct: 421 GVYGGAVGYFAWNGNMDTAIAIRTAVIKDGELHVQAGGGIVADSVPALEWEETLNKRRAM 480

Query: 481 FRAVALAEQT 490
           FRAVALAEQT
Sbjct: 481 FRAVALAEQT 490


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: 913
Number of extensions: 23
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 GFF5021 PS417_25725 (anthranilate synthase component I)
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.750.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   6.2e-176  571.8   0.0   7.1e-176  571.6   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF5021  PS417_25725 anthranilate synthas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF5021  PS417_25725 anthranilate synthase component I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  571.6   0.0  7.1e-176  7.1e-176       2     454 ..      26     484 ..      25     485 .. 0.91

  Alignments for each domain:
  == domain 1  score: 571.6 bits;  conditional E-value: 7.1e-176
                           TIGR00564   2 dtltpisvylklakrkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeak..ieedelkelrk 74 
                                         d  tp+s+ylkla +++s+llEsv+ +e++gRyS+igl  +++++++d+++ + + d+ e++   ++d+l  +++
  lcl|FitnessBrowser__WCS417:GFF5021  26 DFDTPLSIYLKLADEPNSYLLESVQGGEKWGRYSIIGLPCRTVLRVHDHHVSITQ-DGVEIEshDVDDPLAFVEA 99 
                                         6679*******************************************98444333.3333331245555555555 PP

                           TIGR00564  75 llekaeesedeld..eplsggavGylgydtvrlveklke..eaedelelpdlllllvetvivfDhvekkvilien 145
                                         + +++  + + +   + + gg+vGy+gyd+vr+vek     +++d+l +pd+ll++ + v+vfD+ + k++ i  
  lcl|FitnessBrowser__WCS417:GFF5021 100 FKARY--NVPTIAglPRFNGGLVGYFGYDCVRYVEKRLGkcPNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVL 172
                                         55554..3444435566******************97653466*******************************9 PP

                           TIGR00564 146 arteaersaeeeaaarleellaelqkeleka....vkaleekkesftsnvekeeyeekvakakeyikaGdifqvv 216
                                         a   ++ +a+e+ +a le+ll++l+++++++     ++++ +   f s++++++ye +v+++keyi aGd +qvv
  lcl|FitnessBrowser__WCS417:GFF5021 173 AD-PSQADAFEQGQASLEALLEKLRQPITPRrgldLSRPPAADPVFRSSFTQDDYERAVDTIKEYILAGDCMQVV 246
                                         95.556669*******************99877555666666666****************************** PP

                           TIGR00564 217 lSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvkgkrvetrPiAGtrkRGatkeeDea 291
                                         +Sqr++ +++a p++lYr+LR  NP py+y++++ df++vgsSPE+lv+v+++ +++rPiAGtr+RGat+e+D a
  lcl|FitnessBrowser__WCS417:GFF5021 247 PSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDNLITVRPIAGTRPRGATEEADLA 321
                                         *************************************************************************** PP

                           TIGR00564 292 leeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellkiekyshvmHivSeVeGelkdeltavDalraalP 366
                                         lee+Ll+d Ke AEHlmL+DL+RND g+v+++gsv+ +e + ie+ys vmHivS+V+Gelk +lta+Dalra+lP
  lcl|FitnessBrowser__WCS417:GFF5021 322 LEEDLLSDDKEIAEHLMLIDLGRNDTGRVSEIGSVKLTEKMVIERYSNVMHIVSNVTGELKAGLTAMDALRAILP 396
                                         *************************************************************************** PP

                           TIGR00564 367 aGTlsGAPKvrAmelidelEkekRgiYgGavgylsfdgdvdtaiaiRtmvlkdgvayvqAgaGiVaDSdpeaEye 441
                                         aGTlsGAPK+rAme+idelE++kRg+YgGavgy+  +g++dtaiaiRt+v+kdg ++vqAg+GiVaDS+p  E+e
  lcl|FitnessBrowser__WCS417:GFF5021 397 AGTLSGAPKIRAMEIIDELEPVKRGVYGGAVGYFAWNGNMDTAIAIRTAVIKDGELHVQAGGGIVADSVPALEWE 471
                                         *************************************************************************** PP

                           TIGR00564 442 EtlnKakallrai 454
                                         EtlnK +a+ ra+
  lcl|FitnessBrowser__WCS417:GFF5021 472 ETLNKRRAMFRAV 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 11.06
//
[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