GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpE in Trichormus variabilis ATCC 29413

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate WP_011321383.1 AVA_RS23960 anthranilate synthase component I

Query= SwissProt::P20579
         (493 letters)



>NCBI__GCF_000204075.1:WP_011321383.1
          Length = 504

 Score =  402 bits (1033), Expect = e-116
 Identities = 227/500 (45%), Positives = 321/500 (64%), Gaps = 21/500 (4%)

Query: 2   NREEFLRLAAVGYNRIPLACETLADFDTPLSIYLKL-ADQPNSYLLESVQGGEKWGRYSM 60
           N  EF +LA  G N +P+  E +AD DTP+S + K+ A +P S+LLESV+GGEK GRYS+
Sbjct: 5   NFSEFSQLALQG-NFVPVYQEWVADLDTPVSAWYKVCAGEPYSFLLESVEGGEKIGRYSL 63

Query: 61  IGLPSRTVMRVHGYHVSILH-DGVEVESHDVEDPLAFVESFKDRYKVADIPGLPRFNGGL 119
           +G     ++   G   +  + D  +V      DP   +      YK   +P LP   GGL
Sbjct: 64  LGCDPLWILEARGETTTQTNRDASQVVF--TGDPFTALADCLAPYKPVKLPQLPPGIGGL 121

Query: 120 VGYFGYDCVRYVEKRLGVSPNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVLVDPAE-- 177
            G++GY+ +R++E R+ V  + D   +PD L M  D +++FD +  K+ AI   D  +  
Sbjct: 122 FGFWGYELIRWIEPRVPVH-SQDERNIPDGLWMQVDHLLIFDQVKRKIWAIAYADLRDPN 180

Query: 178 ---EQAFEQGQARLQGLLETLRQPITPRRGLDLSGPQAAE-----PEFRSSYTREDYENA 229
              + A++Q   R+  ++  L  P++P++ +    P  ++      E+ S++TR ++  +
Sbjct: 181 VDLKAAYQQACDRVTQMVSKLSLPVSPQKTILEWTPPGSQNVGETQEYTSNFTRPEFCAS 240

Query: 230 VGRIKEYILAGDCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSS 289
           V + KEYI AGD  QVV SQR+S  +   P  LYR+LR  NP+PYM +FNF D+ ++GSS
Sbjct: 241 VQKAKEYIKAGDIFQVVISQRLSTQYTGDPFSLYRSLRQINPSPYMAYFNFQDWQIIGSS 300

Query: 290 PEVLVRVE-----DNLVTVRPIAGTRPRGATEEADRALEDDLLSDDKEIAEHLMLIDLGR 344
           PEV+V+ E     + + TVRPIAGTRPRG T + D  L  DLL D KEIAEH+ML+DLGR
Sbjct: 301 PEVMVKAELDGDGEAVATVRPIAGTRPRGKTTKEDAELAADLLQDPKEIAEHVMLVDLGR 360

Query: 345 NDVGRVSSTGSVRLTEKMVIERYSNVMHIVSNVAGQLREGLTAMDALRAILPAGTLSGAP 404
           ND+GRV ++G+V++ E MV+ERYS+VMHIVSNV G+L     A D L+A  PAGT+SGAP
Sbjct: 361 NDLGRVCASGTVKVDELMVVERYSHVMHIVSNVVGKLAANKNAWDLLKACFPAGTVSGAP 420

Query: 405 KIRAMEIIDELEPVKRGVYGGAVGYFAWNGNMDTAIAIRTAVINDGELHVQAGGGIVADS 464
           KIRAMEII+ELEP +RGVY G  GY+ + G +++AIAIRT V+ D  + VQAG G+VADS
Sbjct: 421 KIRAMEIINELEPSRRGVYSGVYGYYDFEGQLNSAIAIRTMVVRDHTVTVQAGAGLVADS 480

Query: 465 VPALEWEETINKRRAMFRAV 484
            P  E+EET+NK R +  A+
Sbjct: 481 DPEKEYEETLNKARGLLLAI 500


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: 622
Number of extensions: 33
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: 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_011321383.1 AVA_RS23960 (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.847820.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.9e-168  544.7   0.0   1.1e-167  544.6   0.0    1.0  1  NCBI__GCF_000204075.1:WP_011321383.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000204075.1:WP_011321383.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  544.6   0.0  1.1e-167  1.1e-167       2     453 ..      28     499 ..      27     501 .. 0.93

  Alignments for each domain:
  == domain 1  score: 544.6 bits;  conditional E-value: 1.1e-167
                             TIGR00564   2 dtltpisvylklak.rkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeakieedelkelr 73 
                                           d  tp+s+  k+   +++sfllEsve +e++gRySl+g++p   ++a+++++++ + d ++   ++d+ ++l 
  NCBI__GCF_000204075.1:WP_011321383.1  28 DLDTPVSAWYKVCAgEPYSFLLESVEGGEKIGRYSLLGCDPLWILEARGETTTQTNRDASQVVFTGDPFTALA 100
                                           778*****99999889*********************************99999999999999********** PP

                             TIGR00564  74 klleka.eesedeldeplsggavGylgydtvrlveklkeea.edelelpdlllllvetvivfDhvekkvilie 144
                                           ++l+ +   + ++l++   gg++G+ gy+++r +e+  + + +de+++pd l + v+++++fD+v++k+  i+
  NCBI__GCF_000204075.1:WP_011321383.1 101 DCLAPYkPVKLPQLPP-GIGGLFGFWGYELIRWIEPRVPVHsQDERNIPDGLWMQVDHLLIFDQVKRKIWAIA 172
                                           ****986667777765.78******************99887******************************9 PP

                             TIGR00564 145 narteaers....aeeeaaarleellaelqkeleka...vkaleekkes......ftsnvekeeyeekvakak 204
                                           +a  ++ +     a+++a +r+++++++l+ +++++    + +++ +++      +tsn+++ e+ ++v+kak
  NCBI__GCF_000204075.1:WP_011321383.1 173 YADLRDPNVdlkaAYQQACDRVTQMVSKLSLPVSPQktiLEWTPPGSQNvgetqeYTSNFTRPEFCASVQKAK 245
                                           9866554335888999****************999855533333333336666679999999*********** PP

                             TIGR00564 205 eyikaGdifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvk....gkr.ve 272
                                           eyikaGdifqvv+Sqrl+++ + +pf+lYr+LR++NPSpy++y++++d +++gsSPE++vk +    g+   +
  NCBI__GCF_000204075.1:WP_011321383.1 246 EYIKAGDIFQVVISQRLSTQYTGDPFSLYRSLRQINPSPYMAYFNFQDWQIIGSSPEVMVKAEldgdGEAvAT 318
                                           *************************************************************999886666678 PP

                             TIGR00564 273 trPiAGtrkRGatkeeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellkiekyshvmHivS 345
                                           +rPiAGtr+RG+t++eD+ l+++Ll+d+Ke AEH+mLvDL+RND+g+v+  g+v+v+el+ +e+yshvmHivS
  NCBI__GCF_000204075.1:WP_011321383.1 319 VRPIAGTRPRGKTTKEDAELAADLLQDPKEIAEHVMLVDLGRNDLGRVCASGTVKVDELMVVERYSHVMHIVS 391
                                           9************************************************************************ PP

                             TIGR00564 346 eVeGelkdeltavDalraalPaGTlsGAPKvrAmelidelEkekRgiYgGavgylsfdgdvdtaiaiRtmvlk 418
                                           +V+G+l+ +++a+D l+a++PaGT+sGAPK+rAme+i+elE+++Rg+Y+G+ gy++f+g++++aiaiRtmv++
  NCBI__GCF_000204075.1:WP_011321383.1 392 NVVGKLAANKNAWDLLKACFPAGTVSGAPKIRAMEIINELEPSRRGVYSGVYGYYDFEGQLNSAIAIRTMVVR 464
                                           ************************************************************************* PP

                             TIGR00564 419 dgvayvqAgaGiVaDSdpeaEyeEtlnKakallra 453
                                           d+++ vqAgaG+VaDSdpe+EyeEtlnKa++ll a
  NCBI__GCF_000204075.1:WP_011321383.1 465 DHTVTVQAGAGLVADSDPEKEYEETLNKARGLLLA 499
                                           ******************************99866 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: 31.55
//
[ok]

This GapMind analysis is from Jul 25 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