Alignments for a candidate for trpE in Desulfurobacterium atlanticum DSM 15668

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Desulfurobacterium atlanticum DSM 15668

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate WP_245807330.1 CHB58_RS03855 anthranilate synthase component I

Query= SwissProt::P20579
         (493 letters)



>NCBI__GCF_900188395.1:WP_245807330.1
          Length = 510

 Score =  441 bits (1135), Expect = e-128
 Identities = 240/495 (48%), Positives = 332/495 (67%), Gaps = 9/495 (1%)

Query: 1   MNREEFLRLAAVGYNRIPLACETLADFDTPLSIYLKLADQPNSYLLESVQGGEKWGRYSM 60
           M  +E  R+   GYN IP+  E L D +TPLS ++KL     + LLESV+GGEKWGRYS+
Sbjct: 11  MTVKEIKRIVDKGYNLIPIYRELLVDTETPLSSFIKLKKLGANILLESVEGGEKWGRYSV 70

Query: 61  IGLPSRTVMRVHGYHVSILHDGVEVESHDVE-DPLAFVESFKDRYKVADIPGLPRFNGGL 119
           IG+ S   ++     V I  +G  +E  ++E DPL  + +   RY    + GLPR  GG 
Sbjct: 71  IGIGSLVTVKSKERFVEINRNG-RIEVKEIETDPLEVLRNEFKRYIPFKMEGLPRMWGGF 129

Query: 120 VGYFGYDCVRYVEKRLGV--SPNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVLVDPAE 177
            GY GYD V++ E R+G+    N +   + D++  +  A+V+FDN++  +  I  +   +
Sbjct: 130 FGYLGYDTVKFFEPRVGMVEEKNKEDSMLYDMVFSIPRALVIFDNVSKTVKLIGYLIVRD 189

Query: 178 EQAFEQGQARLQGLLETLRQPITPRRGLDLSGPQAAE---PEFRSSYTREDYENAVGRIK 234
             + E+    +   L+ +   +   +   L+ P +       +  +++ ED+  AV + K
Sbjct: 190 YSSLEEIYREVNCFLDDIEDSLLNDK--ILNNPPSVSYSVANWSVNFSDEDFAEAVEKAK 247

Query: 235 EYILAGDCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLV 294
           EYI AGD +QVV S+R    FK+  + LYRALR  NP+PYMY+ ++GDF +VG+SPEVLV
Sbjct: 248 EYIKAGDIIQVVLSRRFEKSFKSDALTLYRALRFINPSPYMYYLDYGDFQIVGASPEVLV 307

Query: 295 RVEDNLVTVRPIAGTRPRGATEEADRALEDDLLSDDKEIAEHLMLIDLGRNDVGRVSSTG 354
           RV D ++  RPIAGTR RG T+E D A+E +L+SD+KE AEH+ML+DL RNDVGRV+  G
Sbjct: 308 RVTDGVIETRPIAGTRKRGKTQEEDIAMEKELISDEKERAEHIMLVDLARNDVGRVAKEG 367

Query: 355 SVRLTEKMVIERYSNVMHIVSNVAGQLREGLTAMDALRAILPAGTLSGAPKIRAMEIIDE 414
           SV++T+ MVIERYS+VMHIVSNV G+L+E   A D L+A  PAGT+SGAPK+RAMEII+E
Sbjct: 368 SVKVTDLMVIERYSHVMHIVSNVVGRLKERFDAFDVLKACFPAGTVSGAPKVRAMEIIEE 427

Query: 415 LEPVKRGVYGGAVGYFAWNGNMDTAIAIRTAVINDGELHVQAGGGIVADSVPALEWEETI 474
           +EP KRGVY GAVGYF+++GNMDTAIAIRTA++   +++VQAG GIVADS P LE +ET 
Sbjct: 428 IEPSKRGVYAGAVGYFSFDGNMDTAIAIRTAIVRRDKVYVQAGAGIVADSDPDLEVKETK 487

Query: 475 NKRRAMFRAVALAEQ 489
           NK RA+FRAV  AE+
Sbjct: 488 NKARAIFRAVEFAEK 502


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: 666
Number of extensions: 36
Number of successful extensions: 3
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: 510
Length adjustment: 34
Effective length of query: 459
Effective length of database: 476
Effective search space:   218484
Effective search space used:   218484
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 WP_245807330.1 CHB58_RS03855 (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.3691941.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.8e-176  572.9   0.1   3.3e-176  572.7   0.1    1.0  1  NCBI__GCF_900188395.1:WP_245807330.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900188395.1:WP_245807330.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  572.7   0.1  3.3e-176  3.3e-176       2     454 ..      36     497 ..      35     498 .. 0.92

  Alignments for each domain:
  == domain 1  score: 572.7 bits;  conditional E-value: 3.3e-176
                             TIGR00564   2 dtltpisvylklakrkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeak..ieedelkel 72 
                                           dt+tp+s + kl+k  +++llEsve +e++gRyS+ig+ +  ++k k+  + +++ +++ +   ie+d+l++l
  NCBI__GCF_900188395.1:WP_245807330.1  36 DTETPLSSFIKLKKLGANILLESVEGGEKWGRYSVIGIGSLVTVKSKERFV-EINRNGRIEVkeIETDPLEVL 107
                                           99***********9999******************************9744.4444444333369******** PP

                             TIGR00564  73 rklleka.eesedeldeplsggavGylgydtvrlveklke....eaedelelpdlllllvetvivfDhvekkv 140
                                           r+  +++  ++ ++l+  + gg +Gylgydtv+++e+       +++++  l d+++ + + +++fD+v+k+v
  NCBI__GCF_900188395.1:WP_245807330.1 108 RNEFKRYiPFKMEGLPR-MWGGFFGYLGYDTVKFFEPRVGmveeKNKEDSMLYDMVFSIPRALVIFDNVSKTV 179
                                           ******99999999998.******************865444336699999********************** PP

                             TIGR00564 141 ilienarteaersaeeeaaarleellaelqkeleka..vkaleekkes...ftsnvekeeyeekvakakeyik 208
                                            li + + + + s+ ee  ++++  l +++++l ++   + ++  ++s    + n++ e+++e+v+kakeyik
  NCBI__GCF_900188395.1:WP_245807330.1 180 KLIGYLIVR-DYSSLEEIYREVNCFLDDIEDSLLNDkiLNNPPSVSYSvanWSVNFSDEDFAEAVEKAKEYIK 251
                                           *****9666.555899999999999999999998875423333323334447789999*************** PP

                             TIGR00564 209 aGdifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvkgkrvetrPiAGtrk 281
                                           aGdi+qvvlS+r+e++++ +++ lYr+LR +NPSpy+yyld  df++vg+SPE+lv+v++  +etrPiAGtrk
  NCBI__GCF_900188395.1:WP_245807330.1 252 AGDIIQVVLSRRFEKSFKSDALTLYRALRFINPSPYMYYLDYGDFQIVGASPEVLVRVTDGVIETRPIAGTRK 324
                                           ************************************************************************* PP

                             TIGR00564 282 RGatkeeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellkiekyshvmHivSeVeGelkde 354
                                           RG+t+eeD a+e+eL++deKerAEH+mLvDLaRND+g+vak gsv+v++l+ ie+yshvmHivS+V+G+lk+ 
  NCBI__GCF_900188395.1:WP_245807330.1 325 RGKTQEEDIAMEKELISDEKERAEHIMLVDLARNDVGRVAKEGSVKVTDLMVIERYSHVMHIVSNVVGRLKER 397
                                           ************************************************************************* PP

                             TIGR00564 355 ltavDalraalPaGTlsGAPKvrAmelidelEkekRgiYgGavgylsfdgdvdtaiaiRtmvlkdgvayvqAg 427
                                           ++a+D+l+a++PaGT+sGAPKvrAme+i+e+E++kRg+Y+Gavgy+sfdg++dtaiaiRt++++ +++yvqAg
  NCBI__GCF_900188395.1:WP_245807330.1 398 FDAFDVLKACFPAGTVSGAPKVRAMEIIEEIEPSKRGVYAGAVGYFSFDGNMDTAIAIRTAIVRRDKVYVQAG 470
                                           ************************************************************************* PP

                             TIGR00564 428 aGiVaDSdpeaEyeEtlnKakallrai 454
                                           aGiVaDSdp+ E +Et nKa+a  ra+
  NCBI__GCF_900188395.1:WP_245807330.1 471 AGIVADSDPDLEVKETKNKARAIFRAV 497
                                           ***********************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (510 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 20.98
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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