Alignments for a candidate for trpE in Methylohalobius crimeensis 10Ki

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Methylohalobius crimeensis 10Ki

Align anthranilate synthase (subunit 1/2) (EC 4.1.3.27) (characterized)
to candidate WP_022948385.1 H035_RS0107570 anthranilate synthase component I

Query= BRENDA::P20580
         (492 letters)



>NCBI__GCF_000421465.1:WP_022948385.1
          Length = 527

 Score =  568 bits (1464), Expect = e-166
 Identities = 301/529 (56%), Positives = 371/529 (70%), Gaps = 42/529 (7%)

Query: 1   MNREEFLRLAADGYNRIPLSFETLADFDTPLSIYLKLADAPNSYLLESVQGGEKWGRYSI 60
           M  + F  LAA GYNRIP++ E LAD DTPLS YLKLA  P +YL ESV GGE+WGRYSI
Sbjct: 1   MTPQRFQELAAQGYNRIPVTREVLADLDTPLSAYLKLASRPYTYLFESVLGGEQWGRYSI 60

Query: 61  IGLPCRTVLRVYDHQVRI--SIDGVET--------------------------------- 85
           IGLP R V+R+   Q+++    D   T                                 
Sbjct: 61  IGLPARKVIRIEGDQIQVWRYPDAAATSPLPTLPPLGGGPSATSPLPPTGGGLGRGEELI 120

Query: 86  ERFDCADPLAFVEEFKARYQVPTVPGLPRFDGGLVGYFGYDCVRYVEKRL-ATCPNPDPL 144
           E      PL +++ F ARY+ P +P +PRF GGLVGYFGY+ + Y+E +L A    PDPL
Sbjct: 121 EEVSSPAPLEWIKAFTARYRTPALPDMPRFSGGLVGYFGYETIAYIEPKLEAAQAKPDPL 180

Query: 145 GNPDILLMVSDAVVVFDNLAGKIHAIVLADPSEENAYERGQARLEELLERLRQ--PITPR 202
            NPDILLMVS+ +VVFDNL+G +  I  ADP E +A ++ Q RLE+ ++RLR   P    
Sbjct: 181 QNPDILLMVSEDLVVFDNLSGTLQLITHADPEEPDALDQAQRRLEQWVDRLRGSCPYPSE 240

Query: 203 RGLDLEAAQGREPAFRASFTREDYENAVGRIKDYILAGDCMQVVPSQRMSIEFKAAPIDL 262
            G      +  E  F + FTRE +E AV  IKDYI+AGD MQVV SQR+SI ++   + +
Sbjct: 241 AG----GRRISEADFISGFTREGFEQAVRGIKDYIVAGDVMQVVLSQRLSIPYRGDSLSV 296

Query: 263 YRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDGLVTVRPIAGTRPRGINEEADLAL 322
           YRALR  NP+PYMY  N GDF +VGSSPE+LVR+ED  VTVRPIAGTRPRG   E D AL
Sbjct: 297 YRALRSLNPSPYMYHLNLGDFQIVGSSPEILVRLEDETVTVRPIAGTRPRGRTSEEDQAL 356

Query: 323 EQDLLSDAKEIAEHLMLIDLGRNDVGRVSDIGAVKVTEKMVIERYSNVMHIVSNVTGQLR 382
           E++LL+D KE+AEHLMLIDLGRND+GRV+++G+V+VT++M+IERYS+VMHIVSNV G+L+
Sbjct: 357 EKELLADPKELAEHLMLIDLGRNDIGRVAEVGSVEVTDQMLIERYSHVMHIVSNVIGKLK 416

Query: 383 EGLSAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKRGVYGGAVGYLAWNGNMDTAIAI 442
            GL A D L A  PAGT+SGAPKIRAMEII ELEPVKRGVY GAVGY+ W+GN+DTAIAI
Sbjct: 417 PGLDAFDVLAATFPAGTVSGAPKIRAMEIIAELEPVKRGVYSGAVGYIGWSGNLDTAIAI 476

Query: 443 RTAVIKNGELHVQAGGGIVADSVPALEWEETINKRRAMFRAVALAEQSV 491
           RTAVIK+ +LHVQAG GIV DS+PA EWEET+NK RA+FRAVA A + +
Sbjct: 477 RTAVIKDEQLHVQAGAGIVHDSIPAKEWEETMNKGRALFRAVARAAEGL 525


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: 758
Number of extensions: 35
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 492
Length of database: 527
Length adjustment: 34
Effective length of query: 458
Effective length of database: 493
Effective search space:   225794
Effective search space used:   225794
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_022948385.1 H035_RS0107570 (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.8760.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.2e-171  556.3   0.0   3.7e-160  519.8   0.0    2.0  2  lcl|NCBI__GCF_000421465.1:WP_022948385.1  H035_RS0107570 anthranilate synt


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000421465.1:WP_022948385.1  H035_RS0107570 anthranilate synthase component I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   5.7e-13   5.7e-13       2      56 ..      26      80 ..      25      91 .. 0.89
   2 !  519.8   0.0  3.7e-160  3.7e-160      68     454 ..     128     518 ..     115     519 .. 0.93

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 5.7e-13
                                 TIGR00564  2 dtltpisvylklakrkesfllEsvekeeelgRySliglnpvleikakdgkavlle 56
                                              d  tp+s+ylkla+r++++l+Esv  +e++gRyS+igl  +++i+ ++++++  +
  lcl|NCBI__GCF_000421465.1:WP_022948385.1 26 DLDTPLSAYLKLASRPYTYLFESVLGGEQWGRYSIIGLPARKVIRIEGDQIQVWR 80
                                              778********************************************99876655 PP

  == domain 2  score: 519.8 bits;  conditional E-value: 3.7e-160
                                 TIGR00564  68 elkelrkllekaeesedeld..eplsggavGylgydtvrlveklke...eaedelelpdlllllvetvi 131
                                               +l+ ++++ ++   +++ l+  + +sgg+vGy+gy+t++++e++ e   +++d+l+ pd+ll++ e+++
  lcl|NCBI__GCF_000421465.1:WP_022948385.1 128 PLEWIKAFTAR--YRTPALPdmPRFSGGLVGYFGYETIAYIEPKLEaaqAKPDPLQNPDILLMVSEDLV 194
                                               45555555555..56778877778******************9877553459***************** PP

                                 TIGR00564 132 vfDhvekkvilienarteaersaeeeaaarleellaelqkeleka..vkaleekkesftsnvekeeyee 198
                                               vfD+ + +++li++a  e e +a ++a++rle+ + +l+ +      +     ++ +f s +++e +e+
  lcl|NCBI__GCF_000421465.1:WP_022948385.1 195 VFDNLSGTLQLITHADPE-EPDALDQAQRRLEQWVDRLRGSCPYPseAGGRRISEADFISGFTREGFEQ 262
                                               ***************666.5559**************99877655336677889999************ PP

                                 TIGR00564 199 kvakakeyikaGdifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvk 267
                                               +v+ +k+yi aGd++qvvlSqrl+ + + +++++Yr+LR+ NPSpy+y+l+l df++vgsSPE+lv+++
  lcl|NCBI__GCF_000421465.1:WP_022948385.1 263 AVRGIKDYIVAGDVMQVVLSQRLSIPYRGDSLSVYRALRSLNPSPYMYHLNLGDFQIVGSSPEILVRLE 331
                                               ********************************************************************* PP

                                 TIGR00564 268 gkrvetrPiAGtrkRGatkeeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellkiek 336
                                               +++v++rPiAGtr+RG+t+eeD+ale+eLlad+Ke AEHlmL+DL+RNDig+va++gsvev++ + ie+
  lcl|NCBI__GCF_000421465.1:WP_022948385.1 332 DETVTVRPIAGTRPRGRTSEEDQALEKELLADPKELAEHLMLIDLGRNDIGRVAEVGSVEVTDQMLIER 400
                                               ********************************************************************* PP

                                 TIGR00564 337 yshvmHivSeVeGelkdeltavDalraalPaGTlsGAPKvrAmelidelEkekRgiYgGavgylsfdgd 405
                                               yshvmHivS+V G+lk++l+a+D+l a++PaGT+sGAPK+rAme+i+elE++kRg+Y+Gavgy++  g+
  lcl|NCBI__GCF_000421465.1:WP_022948385.1 401 YSHVMHIVSNVIGKLKPGLDAFDVLAATFPAGTVSGAPKIRAMEIIAELEPVKRGVYSGAVGYIGWSGN 469
                                               ********************************************************************* PP

                                 TIGR00564 406 vdtaiaiRtmvlkdgvayvqAgaGiVaDSdpeaEyeEtlnKakallrai 454
                                               +dtaiaiRt+v+kd++++vqAgaGiV DS p +E+eEt+nK +al ra+
  lcl|NCBI__GCF_000421465.1:WP_022948385.1 470 LDTAIAIRTAVIKDEQLHVQAGAGIVHDSIPAKEWEETMNKGRALFRAV 518
                                               *********************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (527 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: 00:00:00.01
# Mc/sec: 12.94
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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