Alignments for a candidate for trpE in Pseudomonas fluorescens FW300-N2E3

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Pseudomonas fluorescens FW300-N2E3

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate AO353_07230 AO353_07230 anthranilate synthase

Query= SwissProt::P20579
         (493 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_07230
          Length = 491

 Score =  875 bits (2261), Expect = 0.0
 Identities = 437/490 (89%), Positives = 458/490 (93%)

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

Query: 61  IGLPSRTVMRVHGYHVSILHDGVEVESHDVEDPLAFVESFKDRYKVADIPGLPRFNGGLV 120
           IGLP RTV+RVH +HVS+  DG EVESH+VEDPLAFVE+FK RY V  I GLPRFNGGLV
Sbjct: 61  IGLPCRTVLRVHDHHVSVTVDGAEVESHEVEDPLAFVETFKARYNVPTIAGLPRFNGGLV 120

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

Query: 181 FEQGQARLQGLLETLRQPITPRRGLDLSGPQAAEPEFRSSYTREDYENAVGRIKEYILAG 240
           FEQGQARL+ LLE LRQPITPRRGLD S  QAA+P FRSS+T++DYE AV  IKEYILAG
Sbjct: 181 FEQGQARLEELLEKLRQPITPRRGLDFSKQQAADPVFRSSFTQDDYERAVDTIKEYILAG 240

Query: 241 DCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDNL 300
           DCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDNL
Sbjct: 241 DCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDNL 300

Query: 301 VTVRPIAGTRPRGATEEADRALEDDLLSDDKEIAEHLMLIDLGRNDVGRVSSTGSVRLTE 360
           +TVRPIAGTRPRGA EEADRALE+DLLSDDKEIAEHLMLIDLGRND GRVS  GSV+LTE
Sbjct: 301 ITVRPIAGTRPRGANEEADRALEEDLLSDDKEIAEHLMLIDLGRNDTGRVSEIGSVKLTE 360

Query: 361 KMVIERYSNVMHIVSNVAGQLREGLTAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKR 420
           KMVIERYSNVMHIVSNV GQL+ GLTAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKR
Sbjct: 361 KMVIERYSNVMHIVSNVTGQLKAGLTAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKR 420

Query: 421 GVYGGAVGYFAWNGNMDTAIAIRTAVINDGELHVQAGGGIVADSVPALEWEETINKRRAM 480
           GVYGGAVGYFAWNGNMDTAIAIRTAVI +GELHVQAGGGIVADSVPALEWEET+NKRRAM
Sbjct: 421 GVYGGAVGYFAWNGNMDTAIAIRTAVIKNGELHVQAGGGIVADSVPALEWEETLNKRRAM 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: 916
Number of extensions: 22
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: 491
Length adjustment: 34
Effective length of query: 459
Effective length of database: 457
Effective search space:   209763
Effective search space used:   209763
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 AO353_07230 AO353_07230 (anthranilate synthase)
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.23664.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
     6e-177  575.1   0.0   6.9e-177  574.9   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_07230  AO353_07230 anthranilate synthas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_07230  AO353_07230 anthranilate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  574.9   0.0  6.9e-177  6.9e-177       2     454 ..      26     484 ..      25     485 .. 0.92

  Alignments for each domain:
  == domain 1  score: 574.9 bits;  conditional E-value: 6.9e-177
                                     TIGR00564   2 dtltpisvylklakrkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeak..i 64 
                                                   d  tp+s+ylkla +++s+llEsv+ +e++gRyS+igl  +++++++d+  v +++d+ e +  +
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_07230  26 DFDTPLSIYLKLADEPNSYLLESVQGGEKWGRYSIIGLPCRTVLRVHDH-HVSVTVDGAEVEshE 89 
                                                   6679******************************************998.444444444443226 PP

                                     TIGR00564  65 eedelkelrkllekaeesedeld..eplsggavGylgydtvrlveklke..eaedelelpdllll 125
                                                   +ed+l  ++++ +++  + + +   + + gg+vGy+gyd+vr+vek     +++d+l +pd+ll+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_07230  90 VEDPLAFVETFKARY--NVPTIAglPRFNGGLVGYFGYDCVRYVEKRLGkcPNPDPLGVPDILLM 152
                                                   666666666665554..3333335466******************97653466************ PP

                                     TIGR00564 126 lvetvivfDhvekkvilienarteaersaeeeaaarleellaelqkelekavkaleekkes.... 186
                                                   + + v+vfD+ + k++ i  a  ++++ a+e+ +arleell++l+++++++    + k++     
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_07230 153 VSDAVVVFDNLAGKMHAIVLADPSQDN-AFEQGQARLEELLEKLRQPITPRRGLDFSKQQAadpv 216
                                                   *********************888887.9********************9965555555545577 PP

                                     TIGR00564 187 ftsnvekeeyeekvakakeyikaGdifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldle 251
                                                   f s++++++ye +v+++keyi aGd +qvv+Sqr++ +++a p++lYr+LR  NP py+y++++ 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_07230 217 FRSSFTQDDYERAVDTIKEYILAGDCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFG 281
                                                   ***************************************************************** PP

                                     TIGR00564 252 dfelvgsSPEllvkvkgkrvetrPiAGtrkRGatkeeDealeeeLladeKerAEHlmLvDLaRND 316
                                                   df++vgsSPE+lv+v+++ +++rPiAGtr+RGa++e+D+alee+Ll+d Ke AEHlmL+DL+RND
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_07230 282 DFHVVGSSPEVLVRVEDNLITVRPIAGTRPRGANEEADRALEEDLLSDDKEIAEHLMLIDLGRND 346
                                                   ***************************************************************** PP

                                     TIGR00564 317 igkvaklgsvevkellkiekyshvmHivSeVeGelkdeltavDalraalPaGTlsGAPKvrAmel 381
                                                    g+v+++gsv+ +e + ie+ys vmHivS+V+G+lk +lta+Dalra+lPaGTlsGAPK+rAme+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_07230 347 TGRVSEIGSVKLTEKMVIERYSNVMHIVSNVTGQLKAGLTAMDALRAILPAGTLSGAPKIRAMEI 411
                                                   ***************************************************************** PP

                                     TIGR00564 382 idelEkekRgiYgGavgylsfdgdvdtaiaiRtmvlkdgvayvqAgaGiVaDSdpeaEyeEtlnK 446
                                                   idelE++kRg+YgGavgy+  +g++dtaiaiRt+v+k+g ++vqAg+GiVaDS+p  E+eEtlnK
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_07230 412 IDELEPVKRGVYGGAVGYFAWNGNMDTAIAIRTAVIKNGELHVQAGGGIVADSVPALEWEETLNK 476
                                                   ***************************************************************** PP

                                     TIGR00564 447 akallrai 454
                                                    +a+ ra+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_07230 477 RRAMFRAV 484
                                                   ****9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (491 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 9.57
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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Protein sequences (fasta format)
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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