Alignments for a candidate for trpE in Thauera aminoaromatica S2

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Thauera aminoaromatica S2

Align anthranilate synthase (subunit 1/2) (EC 4.1.3.27) (characterized)
to candidate WP_004322780.1 C665_RS16205 anthranilate synthase component I

Query= BRENDA::P20580
         (492 letters)



>NCBI__GCF_000310185.1:WP_004322780.1
          Length = 490

 Score =  565 bits (1456), Expect = e-165
 Identities = 294/492 (59%), Positives = 360/492 (73%), Gaps = 5/492 (1%)

Query: 1   MNREEFLRLAADGYNRIPLSFETLADFDTPLSIYLKLADAPNSYLLESVQGGEKWGRYSI 60
           M   EF  LAA+GYNRIPL+ ET AD DTPLSIYLKLA+ P +YLLESVQGGE++GRYS 
Sbjct: 1   MLEHEFNALAAEGYNRIPLTLETFADLDTPLSIYLKLANEPYTYLLESVQGGERFGRYSF 60

Query: 61  IGLPCRTVLRVYDHQVRISIDGVETERFDCADPLAFVEEFKARYQVPTVPGLPRFDGGLV 120
           IGL   T + VY     +       ER D  DPL FV EF  R +VP    LPRF GGLV
Sbjct: 61  IGLSSPTRIEVYGRSALLLTGNRLVERRDYGDPLNFVAEFMNRIKVPPRQHLPRFAGGLV 120

Query: 121 GYFGYDCVRYVEKRLATCPNPDPLGNPDILLMVSDAVVVFDNLAGKIHAIVLADPSEENA 180
           G FGYD VRY+E RLA     D +G PDILL++S+ V + DNL+GK+  +V A+P    A
Sbjct: 121 GCFGYDTVRYIEPRLAKTEKADTVGTPDILLLLSEEVAIVDNLSGKLTLVVYAEPEVPGA 180

Query: 181 YERGQARLEELLERLRQPITPRRGLDLEAAQGREPAFRASFTREDYENAVGRIKDYILAG 240
           Y+R Q RL ELL RLR+ +        E+A   EP   +SF  E +++AV R K YI+ G
Sbjct: 181 YKRAQRRLRELLARLREAVAIPEEFRGESA---EPV--SSFGEEAFKDAVRRAKQYIVDG 235

Query: 241 DCMQVVPSQRMSIEFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDGL 300
           D MQVV SQRMS  + A+P+ LYRA+R  NP+PY+++FN  DFHVVG+SPE+L R+ED +
Sbjct: 236 DLMQVVLSQRMSKPYAASPMALYRAIRSLNPSPYLFYFNLEDFHVVGASPEILTRLEDDV 295

Query: 301 VTVRPIAGTRPRGINEEADLALEQDLLSDAKEIAEHLMLIDLGRNDVGRVSDIGAVKVTE 360
           VTVRPIAGTR RG     DLALEQ+LL+D KEIAEH+ L+DLGRND GRVS++G V+VTE
Sbjct: 296 VTVRPIAGTRKRGATPAEDLALEQELLADQKEIAEHVQLLDLGRNDAGRVSEVGTVRVTE 355

Query: 361 KMVIERYSNVMHIVSNVTGQLREGLSAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKR 420
           +  +ERYS+VMHIVSNV G+LREGL A+  LRA  PAGT+SGAPK+RAMEIIDELEPVKR
Sbjct: 356 RFTVERYSHVMHIVSNVEGKLREGLDALAVLRATFPAGTVSGAPKVRAMEIIDELEPVKR 415

Query: 421 GVYGGAVGYLAWNGNMDTAIAIRTAVIKNGELHVQAGGGIVADSVPALEWEETINKRRAM 480
           G+Y GAVGYL ++G+MD AIAIRTAV+K+G++HVQAG GIVADS P  EW ET +K RAM
Sbjct: 416 GIYAGAVGYLGFHGDMDLAIAIRTAVVKDGQIHVQAGAGIVADSDPDAEWNETQSKARAM 475

Query: 481 FRAVALAEQSVE 492
            RA  +AE  ++
Sbjct: 476 LRAAEMAEGGLD 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: 693
Number of extensions: 35
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: 490
Length adjustment: 34
Effective length of query: 458
Effective length of database: 456
Effective search space:   208848
Effective search space used:   208848
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_004322780.1 C665_RS16205 (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.10585.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.8e-170  553.8   0.0     2e-170  553.6   0.0    1.0  1  lcl|NCBI__GCF_000310185.1:WP_004322780.1  C665_RS16205 anthranilate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000310185.1:WP_004322780.1  C665_RS16205 anthranilate synthase component I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  553.6   0.0    2e-170    2e-170       2     454 ..      26     479 ..      25     480 .. 0.94

  Alignments for each domain:
  == domain 1  score: 553.6 bits;  conditional E-value: 2e-170
                                 TIGR00564   2 dtltpisvylklakrkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeak.ieedel 69 
                                               d  tp+s+ylkla++++++llEsv+ +e+ gRyS+igl++ ++i++ + +a ll+ +   ++   +d+l
  lcl|NCBI__GCF_000310185.1:WP_004322780.1  26 DLDTPLSIYLKLANEPYTYLLESVQGGERFGRYSFIGLSSPTRIEVYGRSALLLTGNRLVERrDYGDPL 94 
                                               778********************************************9988777766554444889*** PP

                                 TIGR00564  70 kelrkllekaeesedeldeplsggavGylgydtvrlveklke..eaedelelpdlllllvetvivfDhv 136
                                               + + +++++++    +  + ++gg+vG +gydtvr++e+  +  e+ d++ +pd+llll e+v++ D+ 
  lcl|NCBI__GCF_000310185.1:WP_004322780.1  95 NFVAEFMNRIKVPPRQHLPRFAGGLVGCFGYDTVRYIEPRLAktEKADTVGTPDILLLLSEEVAIVDNL 163
                                               *********96555444466******************976633559********************** PP

                                 TIGR00564 137 ekkvilienarteaersaeeeaaarleellaelqkelekavkaleekkes.ftsnvekeeyeekvakak 204
                                               + k++l+ +a+ e    a++ a++rl+ella+l+++++   +++++ +     s++ +e+++++v++ak
  lcl|NCBI__GCF_000310185.1:WP_004322780.1 164 SGKLTLVVYAEPEVPG-AYKRAQRRLRELLARLREAVAI--PEEFRGESAePVSSFGEEAFKDAVRRAK 229
                                               **********888766.9*****************9974..55554443336699************** PP

                                 TIGR00564 205 eyikaGdifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvkgkrvet 273
                                               +yi +Gd++qvvlSqr++++  a+p++lYr++R+ NPSpyl+y++ledf++vg+SPE+l +++++ v++
  lcl|NCBI__GCF_000310185.1:WP_004322780.1 230 QYIVDGDLMQVVLSQRMSKPYAASPMALYRAIRSLNPSPYLFYFNLEDFHVVGASPEILTRLEDDVVTV 298
                                               ***************************************************************999*** PP

                                 TIGR00564 274 rPiAGtrkRGatkeeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellkiekyshvmH 342
                                               rPiAGtrkRGat++eD ale+eLlad+Ke AEH+ L+DL+RND g+v+++g+v+v+e +++e+yshvmH
  lcl|NCBI__GCF_000310185.1:WP_004322780.1 299 RPIAGTRKRGATPAEDLALEQELLADQKEIAEHVQLLDLGRNDAGRVSEVGTVRVTERFTVERYSHVMH 367
                                               ********************************************************************* PP

                                 TIGR00564 343 ivSeVeGelkdeltavDalraalPaGTlsGAPKvrAmelidelEkekRgiYgGavgylsfdgdvdtaia 411
                                               ivS+VeG+l+++l+a+ +lra++PaGT+sGAPKvrAme+idelE++kRgiY+Gavgyl+f+gd+d aia
  lcl|NCBI__GCF_000310185.1:WP_004322780.1 368 IVSNVEGKLREGLDALAVLRATFPAGTVSGAPKVRAMEIIDELEPVKRGIYAGAVGYLGFHGDMDLAIA 436
                                               ********************************************************************* PP

                                 TIGR00564 412 iRtmvlkdgvayvqAgaGiVaDSdpeaEyeEtlnKakallrai 454
                                               iRt+v+kdg+++vqAgaGiVaDSdp+aE++Et  Ka+a+lra+
  lcl|NCBI__GCF_000310185.1:WP_004322780.1 437 IRTAVVKDGQIHVQAGAGIVADSDPDAEWNETQSKARAMLRAA 479
                                               ****************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (490 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: 00:00:00.03
# Mc/sec: 7.37
//
[ok]

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