GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpE in Marivita geojedonensis DPG-138

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate WP_085639309.1 MGEO_RS14630 anthranilate synthase component I

Query= SwissProt::P20579
         (493 letters)



>NCBI__GCF_002115805.1:WP_085639309.1
          Length = 504

 Score =  422 bits (1086), Expect = e-122
 Identities = 239/494 (48%), Positives = 319/494 (64%), Gaps = 21/494 (4%)

Query: 4   EEFLRLAAVGYNRIPLACETLADFDTPLSIYLKLADQP-NSYLLESVQGGEKWGRYSMIG 62
           + F R    G N++  A    AD DTP+S+ LKL     ++++LESV GGE  GRYS+IG
Sbjct: 9   DSFARAYEAGQNQVVYA-RLAADLDTPVSLMLKLTGAAKDAFVLESVTGGEVRGRYSIIG 67

Query: 63  LPSRTVMRVHGYHVSILHDGVEVESHDVE----DPLAFVESFKDRYKVADIPGLPRFNGG 118
           +    + + HG   S ++     +    E    DPL  + +     K+     LP+   G
Sbjct: 68  MKPDVIWQCHGTR-SRINRAARYDPESFEELEGDPLTTLRALIAESKINLPDDLPQAAAG 126

Query: 119 LVGYFGYDCVRYVEKRLGVSPNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVLVDPA-- 176
           L GY GYD +R VE    +  NPDPLG+PD ++M    V V D + G+   + +V PA  
Sbjct: 127 LFGYLGYDMIRLVEHLPNI--NPDPLGLPDAVMMRPSVVAVLDGVKGE---VTVVSPAWV 181

Query: 177 -----EEQAFEQGQARLQGLLETLRQPITPRRGLDLSGPQAAEPEFRSSYTREDYENAVG 231
                   A+ Q   R+   +  L + + P++  ++ G  A  P   S++T E Y+ AV 
Sbjct: 182 NDGLTARAAYAQAAERVMDAVRDLERAL-PQQAREM-GDAADIPAPVSNFTHEGYKQAVE 239

Query: 232 RIKEYILAGDCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPE 291
           + KEYI AGD  QVVP+QR + DF   P  LYR+LR  NP+P+M++FNFG F V+G+SPE
Sbjct: 240 KAKEYIRAGDIFQVVPAQRWTQDFPLPPFALYRSLRRTNPSPFMFYFNFGGFQVIGASPE 299

Query: 292 VLVRVEDNLVTVRPIAGTRPRGATEEADRALEDDLLSDDKEIAEHLMLIDLGRNDVGRVS 351
           +LVRV  + VT+RPIAGTRPRGAT   D ALE DLL+D KE AEHLML+DLGRNDVGRV+
Sbjct: 300 ILVRVFGSEVTIRPIAGTRPRGATPAEDDALEADLLADAKECAEHLMLLDLGRNDVGRVA 359

Query: 352 STGSVRLTEKMVIERYSNVMHIVSNVAGQLREGLTAMDALRAILPAGTLSGAPKIRAMEI 411
             G+VR TEK +IERYS+VMHIVSNV G+L +   A+ AL A LPAGT+SGAPK+RAMEI
Sbjct: 360 KIGTVRPTEKFIIERYSHVMHIVSNVVGELSDDHDALSALLAGLPAGTVSGAPKVRAMEI 419

Query: 412 IDELEPVKRGVYGGAVGYFAWNGNMDTAIAIRTAVINDGELHVQAGGGIVADSVPALEWE 471
           IDELEP KRG+YGG VGYF+  G+MD  IA+RTA++ D +L++QAGGG+V DS P  E++
Sbjct: 420 IDELEPEKRGIYGGGVGYFSAGGDMDMCIALRTALVKDKKLYIQAGGGVVYDSDPEAEYQ 479

Query: 472 ETINKRRAMFRAVA 485
           ET++K  A+ RA A
Sbjct: 480 ETVHKSNAIRRAAA 493


Lambda     K      H
   0.320    0.138    0.403 

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: 712
Number of extensions: 34
Number of successful extensions: 5
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: 493
Length of database: 504
Length adjustment: 34
Effective length of query: 459
Effective length of database: 470
Effective search space:   215730
Effective search space used:   215730
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_085639309.1 MGEO_RS14630 (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.2791676.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.8e-172  559.7   0.0   3.3e-172  559.5   0.0    1.0  1  NCBI__GCF_002115805.1:WP_085639309.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002115805.1:WP_085639309.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  559.5   0.0  3.3e-172  3.3e-172       2     454 ..      30     492 ..      29     493 .. 0.92

  Alignments for each domain:
  == domain 1  score: 559.5 bits;  conditional E-value: 3.3e-172
                             TIGR00564   2 dtltpisvylklak.rkesfllEsvekeeelgRySliglnpvleikakdg..kavlleaddeeak...ieede 68 
                                           d  tp+s++lkl+   k  f+lEsv+ +e +gRyS+ig++p+  +++++   ++ ++   d+e +    e+d+
  NCBI__GCF_002115805.1:WP_085639309.1  30 DLDTPVSLMLKLTGaAKDAFVLESVTGGEVRGRYSIIGMKPDVIWQCHGTrsRINRAARYDPE-SfeeLEGDP 101
                                           778***********889******************************9984322222222322.234689*** PP

                             TIGR00564  69 lkelrkllekaeesedeldeplsggavGylgydtvrlveklkeeaedelelpdlllllvetvivfDhvekkvi 141
                                           l++lr+l+++ +++ ++  ++ ++g++Gylgyd++rlve+l++ ++d+l lpd++++  + v+v D v+ +v+
  NCBI__GCF_002115805.1:WP_085639309.1 102 LTTLRALIAESKINLPDDLPQAAAGLFGYLGYDMIRLVEHLPNINPDPLGLPDAVMMRPSVVAVLDGVKGEVT 174
                                           **********9777665556689************************************************** PP

                             TIGR00564 142 lienarteaers...aeeeaaarleellaelqkelekavkaleekkes..ftsnvekeeyeekvakakeyika 209
                                           +++ a  +++     a+++aa+r+ + +++l+++l ++++++ ++++     sn+++e y+++v+kakeyi+a
  NCBI__GCF_002115805.1:WP_085639309.1 175 VVSPAWVNDGLTaraAYAQAAERVMDAVRDLERALPQQAREMGDAADIpaPVSNFTHEGYKQAVEKAKEYIRA 247
                                           **9998888776566778888899999999999998876655555544567899******************* PP

                             TIGR00564 210 GdifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvkgkrvetrPiAGtrkR 282
                                           Gdifqvv++qr ++++ ++pf+lYr+LR++NPSp+++y+++ +f+++g+SPE+lv+v g +v++rPiAGtr+R
  NCBI__GCF_002115805.1:WP_085639309.1 248 GDIFQVVPAQRWTQDFPLPPFALYRSLRRTNPSPFMFYFNFGGFQVIGASPEILVRVFGSEVTIRPIAGTRPR 320
                                           ************************************************************************* PP

                             TIGR00564 283 GatkeeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellkiekyshvmHivSeVeGelkdel 355
                                           Gat++eD+ale++Llad Ke+AEHlmL+DL+RND+g+vak+g+v+ +e + ie+yshvmHivS+V+Gel d+ 
  NCBI__GCF_002115805.1:WP_085639309.1 321 GATPAEDDALEADLLADAKECAEHLMLLDLGRNDVGRVAKIGTVRPTEKFIIERYSHVMHIVSNVVGELSDDH 393
                                           ************************************************************************* PP

                             TIGR00564 356 tavDalraalPaGTlsGAPKvrAmelidelEkekRgiYgGavgylsfdgdvdtaiaiRtmvlkdgvayvqAga 428
                                           +a+ al a lPaGT+sGAPKvrAme+idelE+ekRgiYgG+vgy+s+ gd+d++ia+Rt+++kd+++y+qAg+
  NCBI__GCF_002115805.1:WP_085639309.1 394 DALSALLAGLPAGTVSGAPKVRAMEIIDELEPEKRGIYGGGVGYFSAGGDMDMCIALRTALVKDKKLYIQAGG 466
                                           ************************************************************************* PP

                             TIGR00564 429 GiVaDSdpeaEyeEtlnKakallrai 454
                                           G+V+DSdpeaEy+Et++K++a  ra+
  NCBI__GCF_002115805.1:WP_085639309.1 467 GVVYDSDPEAEYQETVHKSNAIRRAA 492
                                           *********************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (504 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 33.20
//
[ok]

This GapMind analysis is from Jul 26 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:

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:

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:

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:

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