Alignments for a candidate for trpE in Pseudomonas fluorescens FW300-N2C3

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Pseudomonas fluorescens FW300-N2C3

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate AO356_14420 AO356_14420 anthranilate synthase

Query= SwissProt::P20579
         (493 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_14420
          Length = 493

 Score =  875 bits (2261), Expect = 0.0
 Identities = 437/491 (89%), Positives = 456/491 (92%)

Query: 1   MNREEFLRLAAVGYNRIPLACETLADFDTPLSIYLKLADQPNSYLLESVQGGEKWGRYSM 60
           M REEFLRLAA GYNRIPLACETLADFDTPLSIYLKLADQPNSYLLESVQGGEKWGRYS+
Sbjct: 1   MIREEFLRLAAAGYNRIPLACETLADFDTPLSIYLKLADQPNSYLLESVQGGEKWGRYSI 60

Query: 61  IGLPSRTVMRVHGYHVSILHDGVEVESHDVEDPLAFVESFKDRYKVADIPGLPRFNGGLV 120
           IGLP RTV+RVH + +S+ HDGVE+ES DVEDPLAFVE+FK RY V  IPGLPRFNGGLV
Sbjct: 61  IGLPCRTVLRVHDHRISVTHDGVEIESLDVEDPLAFVETFKARYNVPTIPGLPRFNGGLV 120

Query: 121 GYFGYDCVRYVEKRLGVSPNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVLVDPAEEQA 180
           GYFGYDCVRYVEKRLG  PNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVL DP+ E A
Sbjct: 121 GYFGYDCVRYVEKRLGTCPNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVLADPSREDA 180

Query: 181 FEQGQARLQGLLETLRQPITPRRGLDLSGPQAAEPEFRSSYTREDYENAVGRIKEYILAG 240
           +EQGQ  LQ LLE LRQPITPR GLD S   AA+P FRSS+T++DYE AV  IKEYILAG
Sbjct: 181 YEQGQKSLQALLEKLRQPITPRPGLDFSKQSAADPVFRSSFTQDDYERAVDTIKEYILAG 240

Query: 241 DCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDNL 300
           DCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDNL
Sbjct: 241 DCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDNL 300

Query: 301 VTVRPIAGTRPRGATEEADRALEDDLLSDDKEIAEHLMLIDLGRNDVGRVSSTGSVRLTE 360
           +TVRPIAGTRPRGATEEADRALE+DLLSDDKEIAEHLMLIDLGRND GRVS  GSV+LTE
Sbjct: 301 ITVRPIAGTRPRGATEEADRALEEDLLSDDKEIAEHLMLIDLGRNDTGRVSEIGSVKLTE 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 FRAVALAEQTS 491
           FRAVALAEQTS
Sbjct: 481 FRAVALAEQTS 491


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: 909
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: 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 AO356_14420 AO356_14420 (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.8289.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   4.3e-176  572.3   0.0   4.9e-176  572.1   0.0    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_14420  AO356_14420 anthranilate synthas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_14420  AO356_14420 anthranilate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  572.1   0.0  4.9e-176  4.9e-176       2     454 ..      26     484 ..      25     485 .. 0.92

  Alignments for each domain:
  == domain 1  score: 572.1 bits;  conditional E-value: 4.9e-176
                                       TIGR00564   2 dtltpisvylklakrkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeak. 63 
                                                     d  tp+s+ylkla +++s+llEsv+ +e++gRyS+igl  +++++++d+++  +++d+ e++ 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_14420  26 DFDTPLSIYLKLADQPNSYLLESVQGGEKWGRYSIIGLPCRTVLRVHDHRI-SVTHDGVEIEs 87 
                                                     6679*******************************************9843.33334433333 PP

                                       TIGR00564  64 .ieedelkelrkllekaeesedeld..eplsggavGylgydtvrlveklke..eaedelelpd 121
                                                       +ed+l  ++++ +++  + + ++  + + gg+vGy+gyd+vr+vek     +++d+l +pd
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_14420  88 lDVEDPLAFVETFKARY--NVPTIPglPRFNGGLVGYFGYDCVRYVEKRLGtcPNPDPLGVPD 148
                                                     47777777777776665..4555555556******************98664466******** PP

                                       TIGR00564 122 lllllvetvivfDhvekkvilienarteaersaeeeaaarleellaelqkeleka..vkalee 182
                                                     +ll++ + v+vfD+ + k++ i  a  + e  a+e+ ++ l++ll++l+++++++      + 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_14420 149 ILLMVSDAVVVFDNLAGKMHAIVLADPSRED-AYEQGQKSLQALLEKLRQPITPRpgL--DFS 208
                                                     ************************9666655.9*******************999553..444 PP

                                       TIGR00564 183 kkes....ftsnvekeeyeekvakakeyikaGdifqvvlSqrleakveakpfelYrkLRtvNP 241
                                                     k+      f s++++++ye +v+++keyi aGd +qvv+Sqr++ +++a p++lYr+LR  NP
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_14420 209 KQSAadpvFRSSFTQDDYERAVDTIKEYILAGDCMQVVPSQRMSIDFKAAPIDLYRALRCFNP 271
                                                     33333467******************************************************* PP

                                       TIGR00564 242 SpylyyldledfelvgsSPEllvkvkgkrvetrPiAGtrkRGatkeeDealeeeLladeKerA 304
                                                      py+y++++ df++vgsSPE+lv+v+++ +++rPiAGtr+RGat+e+D+alee+Ll+d Ke A
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_14420 272 TPYMYFFNFGDFHVVGSSPEVLVRVEDNLITVRPIAGTRPRGATEEADRALEEDLLSDDKEIA 334
                                                     *************************************************************** PP

                                       TIGR00564 305 EHlmLvDLaRNDigkvaklgsvevkellkiekyshvmHivSeVeGelkdeltavDalraalPa 367
                                                     EHlmL+DL+RND g+v+++gsv+ +e + ie+ys vmHivS+V+G+lk +lta+Dalra+lPa
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_14420 335 EHLMLIDLGRNDTGRVSEIGSVKLTEKMVIERYSNVMHIVSNVTGQLKAGLTAMDALRAILPA 397
                                                     *************************************************************** PP

                                       TIGR00564 368 GTlsGAPKvrAmelidelEkekRgiYgGavgylsfdgdvdtaiaiRtmvlkdgvayvqAgaGi 430
                                                     GTlsGAPK+rAme+idelE++kRg+YgGavgy+  +g++dtaiaiRt+v+k+g ++vqAg+Gi
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_14420 398 GTLSGAPKIRAMEIIDELEPVKRGVYGGAVGYFAWNGNMDTAIAIRTAVIKNGELHVQAGGGI 460
                                                     *************************************************************** PP

                                       TIGR00564 431 VaDSdpeaEyeEtlnKakallrai 454
                                                     VaDS+p  E+eEtlnK +a+ ra+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_14420 461 VADSVPALEWEETLNKRRAMFRAV 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.50
//
[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