Alignments for a candidate for trpE in Ammonifex degensii KC4

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Ammonifex degensii KC4

Align anthranilate synthase (subunit 1/2) (EC 4.1.3.27) (characterized)
to candidate WP_015739156.1 ADEG_RS05865 anthranilate synthase component I

Query= BRENDA::P20580
         (492 letters)



>NCBI__GCF_000024605.1:WP_015739156.1
          Length = 485

 Score =  395 bits (1014), Expect = e-114
 Identities = 224/478 (46%), Positives = 305/478 (63%), Gaps = 11/478 (2%)

Query: 14  YNRIPLSFETLADFDTPLSIYLKLADAPNSYLLESVQGGEKWGRYSIIGLPCRTVLRVYD 73
           Y  +P+    +AD +TP+  Y KL+ +P +YLLESV GGE  GRYS +G       R   
Sbjct: 16  YRVVPVFRRMVADLETPIGAYKKLSPSP-AYLLESVTGGEVLGRYSFLGFRPFLTFRAKG 74

Query: 74  HQVRISIDGVETERFDCADPLAFVEEFKARYQVPTVPGLPRFDGGLVGYFGYDCVRYVEK 133
            +V I + G ET R +  +P   +       + P++P LPRF GG VGYFGYD VR++E+
Sbjct: 75  REVEI-VQGEET-RVE-GNPFTILSRLMEELRGPSLPDLPRFYGGAVGYFGYDLVRHLER 131

Query: 134 RLATCPNPDPLGNPDILLMVSDAVVVFDNLAGKIHAIVLADPSEE--NAYERGQARLEEL 191
                   D L  PDI L+ +  V++FD++  ++  +V   P+ +    Y R    +EE 
Sbjct: 132 LPEKAV--DDLALPDIYLLFTRRVLIFDHVRRELTIVVNTLPANDPKKEYRRAAEEIEET 189

Query: 192 LERLRQPITPRRGLDLEAAQGREPAFRASFTREDYENAVGRIKDYILAGDCMQVVPSQRM 251
           LE L++P+    G+    A    P+  ++F+R+ +  AV  +K+ I AGD +QVV SQR 
Sbjct: 190 LELLQRPLPCEYGVPESPAL---PSPVSNFSRDAFCAAVRYLKERIAAGDALQVVLSQRF 246

Query: 252 SIEFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDGLVTVRPIAGTRP 311
            +   A P   YR LR  NP+PY+++ +FG+  V GSSPE+LVRVE   VT RPIAGTRP
Sbjct: 247 ELPAPADPFAAYRRLRAINPSPYLFYLDFGEPVVAGSSPEMLVRVEGRTVTTRPIAGTRP 306

Query: 312 RGINEEADLALEQDLLSDAKEIAEHLMLIDLGRNDVGRVSDIGAVKVTEKMVIERYSNVM 371
           RG + E D  LE++LL D KE AEHLML+DLGRNDVGR++  G VKVTE M IE+YS+VM
Sbjct: 307 RGRSPEEDAQLEKELLEDPKERAEHLMLVDLGRNDVGRIARPGTVKVTEFMRIEKYSHVM 366

Query: 372 HIVSNVTGQLREGLSAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKRGVYGGAVGYLA 431
           H+VS V G L   LSA++AL A  PAGT++GAPK++AME+I+ELEP +RG+Y GAVGYL+
Sbjct: 367 HLVSEVQGLLPPSLSALEALTASFPAGTVTGAPKVKAMELIEELEPTRRGIYAGAVGYLS 426

Query: 432 WNGNMDTAIAIRTAVIKNGELHVQAGGGIVADSVPALEWEETINKRRAMFRAVALAEQ 489
           + GN+DT I IRT V   G++ VQAG GIVADS P  E+ ET  K RA+   +   E+
Sbjct: 427 FTGNLDTCITIRTMVFCRGKVFVQAGAGIVADSEPEREFMETCAKARALLATLGKEER 484


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: 626
Number of extensions: 29
Number of successful extensions: 6
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: 485
Length adjustment: 34
Effective length of query: 458
Effective length of database: 451
Effective search space:   206558
Effective search space used:   206558
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_015739156.1 ADEG_RS05865 (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.7120.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.5e-174  565.6   0.0   5.2e-174  565.4   0.0    1.0  1  lcl|NCBI__GCF_000024605.1:WP_015739156.1  ADEG_RS05865 anthranilate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000024605.1:WP_015739156.1  ADEG_RS05865 anthranilate synthase component I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  565.4   0.0  5.2e-174  5.2e-174       1     453 [.      27     478 ..      27     480 .. 0.95

  Alignments for each domain:
  == domain 1  score: 565.4 bits;  conditional E-value: 5.2e-174
                                 TIGR00564   1 adtltpisvylklakrkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeakieedel 69 
                                               ad +tpi +y+kl+  +  +llEsv+ +e lgRyS++g +p+l+++ak+ ++++++ +++  ++e+++ 
  lcl|NCBI__GCF_000024605.1:WP_015739156.1  27 ADLETPIGAYKKLSP-SPAYLLESVTGGEVLGRYSFLGFRPFLTFRAKGREVEIVQGEET--RVEGNPF 92 
                                               5889**********7.99******************************987776664444..447**** PP

                                 TIGR00564  70 kelrklleka.eesedeldeplsggavGylgydtvrlveklkeeaedelelpdlllllvetvivfDhve 137
                                               ++l +l+e++   s ++l+  ++ggavGy+gyd+vr++e+l+e+a d+l lpd++ll+++ v++fDhv+
  lcl|NCBI__GCF_000024605.1:WP_015739156.1  93 TILSRLMEELrGPSLPDLPR-FYGGAVGYFGYDLVRHLERLPEKAVDDLALPDIYLLFTRRVLIFDHVR 160
                                               *********75445566655.************************************************ PP

                                 TIGR00564 138 kkvilienarteaers.aeeeaaarleellaelqkelekavkaleekkes.ftsnvekeeyeekvakak 204
                                               ++++++ n+  +++ +  ++ aa+++ee+l+ lq++l  +  ++e  + +   sn++++++ ++v+ +k
  lcl|NCBI__GCF_000024605.1:WP_015739156.1 161 RELTIVVNTLPANDPKkEYRRAAEEIEETLELLQRPLPCEYGVPESPALPsPVSNFSRDAFCAAVRYLK 229
                                               *****999988877665889999**************9997777665554488**************** PP

                                 TIGR00564 205 eyikaGdifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvkgkrvet 273
                                               e i+aGd +qvvlSqr+e +  a+pf++Yr+LR +NPSpyl+yld+ +  + gsSPE+lv+v+g++v+t
  lcl|NCBI__GCF_000024605.1:WP_015739156.1 230 ERIAAGDALQVVLSQRFELPAPADPFAAYRRLRAINPSPYLFYLDFGEPVVAGSSPEMLVRVEGRTVTT 298
                                               ********************************************************************* PP

                                 TIGR00564 274 rPiAGtrkRGatkeeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellkiekyshvmH 342
                                               rPiAGtr+RG+++eeD++le+eLl d+KerAEHlmLvDL+RND+g++a++g+v+v+e+++iekyshvmH
  lcl|NCBI__GCF_000024605.1:WP_015739156.1 299 RPIAGTRPRGRSPEEDAQLEKELLEDPKERAEHLMLVDLGRNDVGRIARPGTVKVTEFMRIEKYSHVMH 367
                                               ********************************************************************* PP

                                 TIGR00564 343 ivSeVeGelkdeltavDalraalPaGTlsGAPKvrAmelidelEkekRgiYgGavgylsfdgdvdtaia 411
                                               +vSeV+G l + l+a++al+a++PaGT++GAPKv+Ameli+elE+++RgiY+Gavgylsf g++dt+i+
  lcl|NCBI__GCF_000024605.1:WP_015739156.1 368 LVSEVQGLLPPSLSALEALTASFPAGTVTGAPKVKAMELIEELEPTRRGIYAGAVGYLSFTGNLDTCIT 436
                                               ********************************************************************* PP

                                 TIGR00564 412 iRtmvlkdgvayvqAgaGiVaDSdpeaEyeEtlnKakallra 453
                                               iRtmv+  g+++vqAgaGiVaDS+pe+E+ Et+ Ka+all +
  lcl|NCBI__GCF_000024605.1:WP_015739156.1 437 IRTMVFCRGKVFVQAGAGIVADSEPEREFMETCAKARALLAT 478
                                               **************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (485 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: 9.80
//
[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