Alignments for a candidate for trpE in Thiohalospira halophila DSM 15071 HL 3

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Thiohalospira halophila DSM 15071 HL 3

Align anthranilate synthase (subunit 1/2) (EC 4.1.3.27) (characterized)
to candidate WP_093428195.1 BM272_RS07725 anthranilate synthase component I

Query= BRENDA::P20580
         (492 letters)



>NCBI__GCF_900112605.1:WP_093428195.1
          Length = 498

 Score =  612 bits (1579), Expect = e-180
 Identities = 314/492 (63%), Positives = 376/492 (76%), Gaps = 9/492 (1%)

Query: 1   MNREEFLRLAADGYNRIPLSFETLADFDTPLSIYLKLADAPNSYLLESVQGGEKWGRYSI 60
           MN + F RLA +GYNRIPL  E LAD +TP+S YLKLA  P +YL ESVQGGEKWGRYSI
Sbjct: 1   MNPQAFDRLAREGYNRIPLVREVLADLETPVSTYLKLAAGPWTYLFESVQGGEKWGRYSI 60

Query: 61  IGLPCRTVLRVYDHQVRISIDGVETERFDCADPLAFVEEFKARYQVPTVPGLPRFDGGLV 120
           IGLP + V+RV  H V +   G   ER + ADPLA++E+++ RY+V    GLPRF GGLV
Sbjct: 61  IGLPAQAVIRVTGHTVEVEEAGAVIERAEVADPLAWIEDYRGRYRVAEAEGLPRFFGGLV 120

Query: 121 GYFGYDCVRYVEKRLATCPNPDPLGNPDILLMVSDAVVVFDNLAGKIHAIVLADPSEENA 180
           G FGYD VRY E RL+     DP+GNPDILLM S+ VVVFDNL GK++ +V  DPS   A
Sbjct: 121 GCFGYDTVRYAEPRLSGVEKDDPIGNPDILLMRSEEVVVFDNLRGKLYLVVHVDPSRSGA 180

Query: 181 YERGQARLEELLERLRQPITPRRGLDLEAAQGR----EPAFRASFTREDYENAVGRIKDY 236
           +E G+ARL+EL E+L +P+TP      EA+ GR    E  F + F+RE +E AV R + Y
Sbjct: 181 HEAGEARLDELAEQLTRPLTPP-----EASPGRARVEETDFVSGFSREGFEAAVERARQY 235

Query: 237 ILAGDCMQVVPSQRMSIEFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRV 296
           I+ GD MQVV SQR+SI + A  +DLYRALR  NP+PYMY  + G+  VVGSSPE+L R+
Sbjct: 236 IVDGDIMQVVLSQRLSIPYAAGALDLYRALRTLNPSPYMYLLDLGETQVVGSSPEILARL 295

Query: 297 EDGLVTVRPIAGTRPRGINEEADLALEQDLLSDAKEIAEHLMLIDLGRNDVGRVSDIGAV 356
           ED  VTVRPIAGTR RG +E  D AL  +LL+D KE AEH+ML+DLGRNDVGR+S+ G+V
Sbjct: 296 EDDTVTVRPIAGTRHRGADEAEDAALADELLADPKERAEHIMLMDLGRNDVGRISETGSV 355

Query: 357 KVTEKMVIERYSNVMHIVSNVTGQLREGLSAMDALRAILPAGTLSGAPKIRAMEIIDELE 416
           +VTE M IERYS+VMHIVSNVTG+LR GL  MD L+A  PAGT+SGAPKIRAMEIIDELE
Sbjct: 356 RVTESMAIERYSHVMHIVSNVTGRLRSGLGPMDVLKATFPAGTVSGAPKIRAMEIIDELE 415

Query: 417 PVKRGVYGGAVGYLAWNGNMDTAIAIRTAVIKNGELHVQAGGGIVADSVPALEWEETINK 476
           PVKRG+Y GAVGY+ W GNMDTAIAIRTAVI++G+LHVQAG GIVADSVP  EWEET+NK
Sbjct: 416 PVKRGLYAGAVGYIGWAGNMDTAIAIRTAVIRDGQLHVQAGAGIVADSVPEREWEETMNK 475

Query: 477 RRAMFRAVALAE 488
            RA+FRAVA+AE
Sbjct: 476 GRALFRAVAMAE 487


Lambda     K      H
   0.321    0.139    0.408 

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: 720
Number of extensions: 28
Number of successful extensions: 2
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: 492
Length of database: 498
Length adjustment: 34
Effective length of query: 458
Effective length of database: 464
Effective search space:   212512
Effective search space used:   212512
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_093428195.1 BM272_RS07725 (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.2446853.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.6e-175  568.2   0.0   8.8e-175  568.0   0.0    1.0  1  NCBI__GCF_900112605.1:WP_093428195.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900112605.1:WP_093428195.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  568.0   0.0  8.8e-175  8.8e-175       1     454 [.      25     483 ..      25     484 .. 0.92

  Alignments for each domain:
  == domain 1  score: 568.0 bits;  conditional E-value: 8.8e-175
                             TIGR00564   1 adtltpisvylklakrkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeak.ieedelkel 72 
                                           ad +tp+s ylkla  + ++l+Esv+ +e++gRyS+igl  +++i++++++++  ea    ++ +++d+l  +
  NCBI__GCF_900112605.1:WP_093428195.1  25 ADLETPVSTYLKLAAGPWTYLFESVQGGEKWGRYSIIGLPAQAVIRVTGHTVEVEEAGAVIERaEVADPLAWI 97 
                                           5889**********99********************************9955544443333334678888888 PP

                             TIGR00564  73 rklleka.eesedeldeplsggavGylgydtvrlveklke..eaedelelpdlllllvetvivfDhvekkvil 142
                                           ++   ++   + ++l + + gg+vG +gydtvr+ e+  +  e+ d++  pd+ll+  e+v+vfD+ + k++l
  NCBI__GCF_900112605.1:WP_093428195.1  98 EDYRGRYrVAEAEGL-PRFFGGLVGCFGYDTVRYAEPRLSgvEKDDPIGNPDILLMRSEEVVVFDNLRGKLYL 169
                                           888888733444555.56******************98776466999************************** PP

                             TIGR00564 143 ienarteaersaeeeaaarleellaelqkeleka...vkaleekkesftsnvekeeyeekvakakeyikaGdi 212
                                           + ++  + +  a+e+ +arl+el+++l+++l++      +   ++++f s +++e +e++v++a++yi +Gdi
  NCBI__GCF_900112605.1:WP_093428195.1 170 VVHVDPSRSG-AHEAGEARLDELAEQLTRPLTPPeasPGRARVEETDFVSGFSREGFEAAVERARQYIVDGDI 241
                                           **99665555.999****************99874323344555666************************** PP

                             TIGR00564 213 fqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvkgkrvetrPiAGtrkRGat 285
                                           +qvvlSqrl+ +  a +++lYr+LRt NPSpy+y ldl ++++vgsSPE+l ++++++v++rPiAGtr+RGa+
  NCBI__GCF_900112605.1:WP_093428195.1 242 MQVVLSQRLSIPYAAGALDLYRALRTLNPSPYMYLLDLGETQVVGSSPEILARLEDDTVTVRPIAGTRHRGAD 314
                                           ************************************************************************* PP

                             TIGR00564 286 keeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellkiekyshvmHivSeVeGelkdeltav 358
                                           ++eD+al++eLlad+KerAEH+mL+DL+RND+g+++++gsv+v+e++ ie+yshvmHivS+V+G+l+++l ++
  NCBI__GCF_900112605.1:WP_093428195.1 315 EAEDAALADELLADPKERAEHIMLMDLGRNDVGRISETGSVRVTESMAIERYSHVMHIVSNVTGRLRSGLGPM 387
                                           ************************************************************************* PP

                             TIGR00564 359 DalraalPaGTlsGAPKvrAmelidelEkekRgiYgGavgylsfdgdvdtaiaiRtmvlkdgvayvqAgaGiV 431
                                           D+l+a++PaGT+sGAPK+rAme+idelE++kRg+Y+Gavgy++ +g++dtaiaiRt+v++dg+++vqAgaGiV
  NCBI__GCF_900112605.1:WP_093428195.1 388 DVLKATFPAGTVSGAPKIRAMEIIDELEPVKRGLYAGAVGYIGWAGNMDTAIAIRTAVIRDGQLHVQAGAGIV 460
                                           ************************************************************************* PP

                             TIGR00564 432 aDSdpeaEyeEtlnKakallrai 454
                                           aDS+pe+E+eEt+nK +al ra+
  NCBI__GCF_900112605.1:WP_093428195.1 461 ADSVPEREWEETMNKGRALFRAV 483
                                           *******************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (498 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: 21.69
//
[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