Alignments for a candidate for trpE in Desulfotomaculum ruminis DSM 2154

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Desulfotomaculum ruminis DSM 2154

Align anthranilate synthase (subunit 1/2) (EC 4.1.3.27) (characterized)
to candidate WP_013841403.1 DESRU_RS06925 anthranilate synthase component I

Query= BRENDA::P20580
         (492 letters)



>NCBI__GCF_000215085.1:WP_013841403.1
          Length = 507

 Score =  419 bits (1078), Expect = e-122
 Identities = 246/498 (49%), Positives = 315/498 (63%), Gaps = 20/498 (4%)

Query: 4   EEFLRLAADGYNRIPLSFETLADFDTPLSIYLKLADAPNSYLLESVQGGEKWGRYSIIGL 63
           EE+ RL+ + YN IP+  E LAD +TP+SIY KL+    S+LLESV+ G    RYS IG 
Sbjct: 7   EEYCRLSQE-YNLIPVYREYLADTETPVSIYGKLSSGDPSFLLESVEEGTTLARYSFIGT 65

Query: 64  PCRTVLRVYDHQVRISIDGVETERFDCADPLAFVEEFKARYQVPTVPGLPRFDGGLVGYF 123
            C    R +  +      G++ +      PL  +    +RY+ P + GLPRF GG  GYF
Sbjct: 66  DCFLNFRFHRGRAEFWGSGMKAKLH--GGPLEALRGLLSRYRTPRLAGLPRFTGGAAGYF 123

Query: 124 GYDCVRYVEKRLATCPN--PDPLGNPDILLMVSDAVVVFDNLAGKIHAIVLADP---SEE 178
           GYD +R++EK     PN  PDPLG P   LM    V+VFD++   +  IV   P   + E
Sbjct: 124 GYDMIRHLEK----LPNDKPDPLGLPLCQLMFPGTVLVFDHIRRTL-LIVANVPFAGNLE 178

Query: 179 NAYERGQARLEELLERLRQPITPRRGLDLEAAQ--GREP-----AFRASFTREDYENAVG 231
            +Y+    +++++  R+  P        L  +Q   RE      A  +S  R ++E AV 
Sbjct: 179 ESYQEAVKKIDQVAGRIFTPSASPAYSTLPYSQPYAREKLNQVLAANSSMNRREFEEAVT 238

Query: 232 RIKDYILAGDCMQVVPSQRMSIEFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPE 291
           R  DYI AGD  QVV SQR S+ F   P DLYR LR  NP+PY+ +FNFGD  +VG+SPE
Sbjct: 239 RALDYIRAGDIFQVVLSQRFSLPFTGDPFDLYRRLRSINPSPYLTYFNFGDLVLVGASPE 298

Query: 292 VLVRVEDGLVTVRPIAGTRPRGINEEADLALEQDLLSDAKEIAEHLMLIDLGRNDVGRVS 351
           +LVRVE+G V  RPIAGTRPRG +E  D  L  ++L+D KE AEHLML+DLGRNDVGRV+
Sbjct: 299 MLVRVEEGKVFTRPIAGTRPRGKDETEDDLLAAEMLADEKERAEHLMLVDLGRNDVGRVA 358

Query: 352 DIGAVKVTEKMVIERYSNVMHIVSNVTGQLREGLSAMDALRAILPAGTLSGAPKIRAMEI 411
             G V+V + M +ERYS+VMH+VS   G L EG   +DAL A  PAGT+SGAPKIRAMEI
Sbjct: 359 VPGTVEVPQYMQVERYSHVMHLVSEAKGILEEGKDHLDALGACFPAGTVSGAPKIRAMEI 418

Query: 412 IDELEPVKRGVYGGAVGYLAWNGNMDTAIAIRTAVIKNGELHVQAGGGIVADSVPALEWE 471
           I+ELEP+ RG Y GAVGY+ + GNMDTAI IRTAV+  G  + Q+G GIVADS PA E+E
Sbjct: 419 IEELEPLHRGPYAGAVGYVDFAGNMDTAITIRTAVVHRGSAYFQSGAGIVADSDPAKEYE 478

Query: 472 ETINKRRAMFRAVALAEQ 489
           ET++K RAM  AV  A Q
Sbjct: 479 ETLHKARAMATAVMAASQ 496


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: 681
Number of extensions: 32
Number of successful extensions: 4
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: 507
Length adjustment: 34
Effective length of query: 458
Effective length of database: 473
Effective search space:   216634
Effective search space used:   216634
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_013841403.1 DESRU_RS06925 (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.29731.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.8e-172  559.0   0.0   5.5e-172  558.8   0.0    1.0  1  lcl|NCBI__GCF_000215085.1:WP_013841403.1  DESRU_RS06925 anthranilate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000215085.1:WP_013841403.1  DESRU_RS06925 anthranilate synthase component I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  558.8   0.0  5.5e-172  5.5e-172       1     454 [.      27     491 ..      27     492 .. 0.94

  Alignments for each domain:
  == domain 1  score: 558.8 bits;  conditional E-value: 5.5e-172
                                 TIGR00564   1 adtltpisvylklakrkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeakieedel 69 
                                               adt+tp+s+y kl++ + sfllEsve++ +l+RyS+ig + +l+++ + g+  ++  ++ +ak ++ +l
  lcl|NCBI__GCF_000215085.1:WP_013841403.1  27 ADTETPVSIYGKLSSGDPSFLLESVEEGTTLARYSFIGTDCFLNFRFHRGR-AEFWGSGMKAKLHGGPL 94 
                                               699************99*******************************995.555668888999***** PP

                                 TIGR00564  70 kelrkllekaeesedeld..eplsggavGylgydtvrlveklkeeaedelelpdlllllvetvivfDhv 136
                                               ++lr ll++++  +++l   + ++gga Gy+gyd++r++ekl++ ++d+l lp + l++  tv+vfDh+
  lcl|NCBI__GCF_000215085.1:WP_013841403.1  95 EALRGLLSRYR--TPRLAglPRFTGGAAGYFGYDMIRHLEKLPNDKPDPLGLPLCQLMFPGTVLVFDHI 161
                                               *********64..555555567*********************************************** PP

                                 TIGR00564 137 ekkvilienarteaers.aeeeaaarleellaelqkeleka..vkaleekkes.........ftsnvek 193
                                               ++++++++n+  + + + +++ea +++++++ ++ +++++    + ++ +++           +s++++
  lcl|NCBI__GCF_000215085.1:WP_013841403.1 162 RRTLLIVANVPFAGNLEeSYQEAVKKIDQVAGRIFTPSASPaySTLPYSQPYAreklnqvlaANSSMNR 230
                                               *********9877776679***************99987664422333333225566788778889999 PP

                                 TIGR00564 194 eeyeekvakakeyikaGdifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEl 262
                                                e+ee+v++a +yi+aGdifqvvlSqr++ +++ +pf+lYr+LR++NPSpyl y+++ d+ lvg+SPE+
  lcl|NCBI__GCF_000215085.1:WP_013841403.1 231 REFEEAVTRALDYIRAGDIFQVVLSQRFSLPFTGDPFDLYRRLRSINPSPYLTYFNFGDLVLVGASPEM 299
                                               ********************************************************************* PP

                                 TIGR00564 263 lvkvkgkrvetrPiAGtrkRGatkeeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkel 331
                                               lv+v++ +v trPiAGtr+RG++++eD+ l++e+ladeKerAEHlmLvDL+RND+g+va +g+vev+++
  lcl|NCBI__GCF_000215085.1:WP_013841403.1 300 LVRVEEGKVFTRPIAGTRPRGKDETEDDLLAAEMLADEKERAEHLMLVDLGRNDVGRVAVPGTVEVPQY 368
                                               ********************************************************************* PP

                                 TIGR00564 332 lkiekyshvmHivSeVeGelkdeltavDalraalPaGTlsGAPKvrAmelidelEkekRgiYgGavgyl 400
                                               +++e+yshvmH+vSe +G l+++++ +Dal a++PaGT+sGAPK+rAme+i+elE+ +Rg+Y+Gavgy+
  lcl|NCBI__GCF_000215085.1:WP_013841403.1 369 MQVERYSHVMHLVSEAKGILEEGKDHLDALGACFPAGTVSGAPKIRAMEIIEELEPLHRGPYAGAVGYV 437
                                               ********************************************************************* PP

                                 TIGR00564 401 sfdgdvdtaiaiRtmvlkdgvayvqAgaGiVaDSdpeaEyeEtlnKakallrai 454
                                               +f+g++dtai+iRt+v++ g ay+q gaGiVaDSdp +EyeEtl+Ka+a+++a+
  lcl|NCBI__GCF_000215085.1:WP_013841403.1 438 DFAGNMDTAITIRTAVVHRGSAYFQSGAGIVADSDPAKEYEETLHKARAMATAV 491
                                               *************************************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (507 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: 7.33
//
[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