Alignments for a candidate for trpE in Pseudomonas fluorescens FW300-N1B4

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Pseudomonas fluorescens FW300-N1B4

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate Pf1N1B4_2545 Anthranilate synthase, aminase component (EC 4.1.3.27)

Query= SwissProt::P20579
         (493 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2545
          Length = 493

 Score =  879 bits (2271), Expect = 0.0
 Identities = 439/490 (89%), Positives = 457/490 (93%)

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

Query: 61  IGLPSRTVMRVHGYHVSILHDGVEVESHDVEDPLAFVESFKDRYKVADIPGLPRFNGGLV 120
           IGLP RTV+RVH +HVS+ HDGVE+ESHDVEDPLAFVE+FK RY V  I GLPRFNGGLV
Sbjct: 61  IGLPCRTVLRVHDHHVSVTHDGVEIESHDVEDPLAFVEAFKARYNVPTIAGLPRFNGGLV 120

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

Query: 181 FEQGQARLQGLLETLRQPITPRRGLDLSGPQAAEPEFRSSYTREDYENAVGRIKEYILAG 240
           FEQGQARLQ LLE LRQPITPRRGLD S  Q+A+P FRSS+T+ DYE AV  IKEYILAG
Sbjct: 181 FEQGQARLQALLEQLRQPITPRRGLDFSKQQSADPVFRSSFTQNDYEKAVDTIKEYILAG 240

Query: 241 DCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDNL 300
           DCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDNL
Sbjct: 241 DCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDNL 300

Query: 301 VTVRPIAGTRPRGATEEADRALEDDLLSDDKEIAEHLMLIDLGRNDVGRVSSTGSVRLTE 360
           +TVRPIAGTRPRGA EEAD ALE DLLSDDKEIAEHLMLIDLGRND GRVS  GSV+LTE
Sbjct: 301 ITVRPIAGTRPRGANEEADVALEKDLLSDDKEIAEHLMLIDLGRNDTGRVSEIGSVKLTE 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: 903
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: 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 Pf1N1B4_2545 (Anthranilate synthase, aminase component (EC 4.1.3.27))
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.19789.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   6.5e-176  571.7   0.0   7.5e-176  571.5   0.0    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2545  Anthranilate synthase, aminase c


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2545  Anthranilate synthase, aminase component (EC 4.1.3.27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  571.5   0.0  7.5e-176  7.5e-176       2     454 ..      26     484 ..      25     485 .. 0.92

  Alignments for each domain:
  == domain 1  score: 571.5 bits;  conditional E-value: 7.5e-176
                                      TIGR00564   2 dtltpisvylklakrkesfllEsvekeeelgRySliglnpvleikakdgka.vlleaddeeaki 64 
                                                    d  tp+s+ylkla +++s+llEsv+ +e++gRyS+igl  +++++++d+++ v+++  + e++ 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2545  26 DFDTPLSIYLKLADEPNSYLLESVQGGEKWGRYSIIGLPCRTVLRVHDHHVsVTHDGVEIESHD 89 
                                                    6679******************************************998331333334444446 PP

                                      TIGR00564  65 eedelkelrkllekaeesedeld..eplsggavGylgydtvrlveklke..eaedelelpdlll 124
                                                    +ed+l  ++++ +++  + + +   + + gg+vGy+gyd+vr+vek     +++d+l +pd+ll
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2545  90 VEDPLAFVEAFKARY--NVPTIAglPRFNGGLVGYFGYDCVRYVEKRLGkcPNPDPLGVPDILL 151
                                                    666666666666665..3333334456******************97653466*********** PP

                                      TIGR00564 125 llvetvivfDhvekkvilienarteaersaeeeaaarleellaelqkelekavkaleekkes.. 186
                                                    ++ + v+vfD+ + k++ i  a  ++e +a+e+ +arl++ll++l+++++++    + k++s  
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2545 152 MVSDAVVVFDNLAGKMHAIVLADPSQE-DAFEQGQARLQALLEQLRQPITPRRGLDFSKQQSad 214
                                                    *********************966655.59********************99777777666666 PP

                                      TIGR00564 187 ..ftsnvekeeyeekvakakeyikaGdifqvvlSqrleakveakpfelYrkLRtvNPSpylyyl 248
                                                      f s++++++ye++v+++keyi aGd +qvv+Sqr++ +++a p++lYr+LR  NP py+y++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2545 215 pvFRSSFTQNDYEKAVDTIKEYILAGDCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFF 278
                                                    789************************************************************* PP

                                      TIGR00564 249 dledfelvgsSPEllvkvkgkrvetrPiAGtrkRGatkeeDealeeeLladeKerAEHlmLvDL 312
                                                    ++ df++vgsSPE+lv+v+++ +++rPiAGtr+RGa++e+D ale++Ll+d Ke AEHlmL+DL
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2545 279 NFGDFHVVGSSPEVLVRVEDNLITVRPIAGTRPRGANEEADVALEKDLLSDDKEIAEHLMLIDL 342
                                                    **************************************************************** PP

                                      TIGR00564 313 aRNDigkvaklgsvevkellkiekyshvmHivSeVeGelkdeltavDalraalPaGTlsGAPKv 376
                                                    +RND g+v+++gsv+ +e + ie+ys vmHivS+V+G+lk +lta+Dalra+lPaGTlsGAPK+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2545 343 GRNDTGRVSEIGSVKLTEKMVIERYSNVMHIVSNVTGQLKAGLTAMDALRAILPAGTLSGAPKI 406
                                                    **************************************************************** PP

                                      TIGR00564 377 rAmelidelEkekRgiYgGavgylsfdgdvdtaiaiRtmvlkdgvayvqAgaGiVaDSdpeaEy 440
                                                    rAme+idelE++kRg+YgGavgy+  +g++dtaiaiRt+v+k+g ++vqAg+GiVaDS+p  E+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2545 407 RAMEIIDELEPVKRGVYGGAVGYFAWNGNMDTAIAIRTAVIKNGELHVQAGGGIVADSVPALEW 470
                                                    **************************************************************** PP

                                      TIGR00564 441 eEtlnKakallrai 454
                                                    eEtlnK +a+ ra+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2545 471 EETLNKRRAMFRAV 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: 00:00:00.01
# Mc/sec: 12.51
//
[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