Alignments for a candidate for trpE in Algiphilus aromaticivorans DG1253

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Algiphilus aromaticivorans DG1253

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate WP_043768786.1 U743_RS12770 anthranilate synthase component I

Query= SwissProt::P20579
         (493 letters)



>NCBI__GCF_000733765.1:WP_043768786.1
          Length = 474

 Score =  504 bits (1298), Expect = e-147
 Identities = 264/463 (57%), Positives = 329/463 (71%), Gaps = 3/463 (0%)

Query: 25  ADFDTPLSIYLKLADQPNSYLLESVQGGEKWGRYSMIGLPSRTVMRVHGYHVSILHDGVE 84
           AD DTP+ +Y +LA+   SYL ES+QGGE+WGRYS IGLP+R ++R+    ++   DG  
Sbjct: 14  ADLDTPVGVYRRLANTAFSYLFESMQGGERWGRYSFIGLPAREILRLREGRITRHIDGEL 73

Query: 85  VESHDVEDPLAFVESFKDRYKVADIPGLPRFNGGLVGYFGYDCVRYVEKRLGVSPNPDPL 144
           VE    E P+A++        V   P LPRF+GG VGY GYD VRY+E R+  + N DPL
Sbjct: 74  VEELHPEAPMAWLRDAVADDSVTPDPRLPRFDGGWVGYIGYDAVRYIEPRVACA-NEDPL 132

Query: 145 GVPDILLMVSDAVVVFDNLAGKMHAIVLVDPAEEQAFEQGQARLQGLLETLRQPITPRRG 204
            +P+ LLM S+ +V+FDNL G M+ +      +  A  + + RL G    L +P      
Sbjct: 133 ELPEALLMKSEDLVIFDNLRGLMYLVTHCPAGDAAARAEAETRLDGWQTELAKPAAA--D 190

Query: 205 LDLSGPQAAEPEFRSSYTREDYENAVGRIKEYILAGDCMQVVPSQRMSIDFKAAPIDLYR 264
             +  P+A EP+F S  +RE + + V RI+EYI AGD MQVVPSQR+S  F A P+ LYR
Sbjct: 191 YQMPDPEAPEPDFVSGMSREAFCDVVERIREYIRAGDVMQVVPSQRLSAPFTAEPLALYR 250

Query: 265 ALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDNLVTVRPIAGTRPRGATEEADRALED 324
           A+R  NP+PY+Y  N  D HVVGSSPE+LVRVED+ + VRP+AGTRPRGATEE D  L +
Sbjct: 251 AIRRLNPSPYLYCLNLDDHHVVGSSPEILVRVEDSEMHVRPLAGTRPRGATEEEDIRLAE 310

Query: 325 DLLSDDKEIAEHLMLIDLGRNDVGRVSSTGSVRLTEKMVIERYSNVMHIVSNVAGQLREG 384
           +LL+D KE+AEHLMLIDLGRNDVGRV  TGSV+LTE+M IERYS+VMHIVSNV G+L  G
Sbjct: 311 ELLADPKEVAEHLMLIDLGRNDVGRVCETGSVKLTERMRIERYSHVMHIVSNVVGRLPPG 370

Query: 385 LTAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKRGVYGGAVGYFAWNGNMDTAIAIRT 444
             A+DAL A  P GTLSGAPK+RAMEII+ELEPV+RGVYGGAVGY   +GN+D AIAIRT
Sbjct: 371 THALDALMAAFPTGTLSGAPKVRAMEIIEELEPVRRGVYGGAVGYIGGSGNLDMAIAIRT 430

Query: 445 AVINDGELHVQAGGGIVADSVPALEWEETINKRRAMFRAVALA 487
           AVI  G++HVQ+G G+VADS P  EW ET+NK RAM RAV  A
Sbjct: 431 AVIAGGQVHVQSGAGVVADSDPNAEWVETMNKARAMLRAVGEA 473


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: 715
Number of extensions: 24
Number of successful extensions: 3
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: 474
Length adjustment: 34
Effective length of query: 459
Effective length of database: 440
Effective search space:   201960
Effective search space used:   201960
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_043768786.1 U743_RS12770 (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.337522.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.8e-172  559.3   0.0   4.3e-172  559.1   0.0    1.0  1  NCBI__GCF_000733765.1:WP_043768786.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000733765.1:WP_043768786.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  559.1   0.0  4.3e-172  4.3e-172       2     454 ..      15     470 ..      14     471 .. 0.95

  Alignments for each domain:
  == domain 1  score: 559.1 bits;  conditional E-value: 4.3e-172
                             TIGR00564   2 dtltpisvylklakrkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeak.ieedelkelr 73 
                                           d  tp+ vy++la+ + s+l+Es++ +e++gRyS+igl  +  ++ ++g+++++   +  ++ + e+++  lr
  NCBI__GCF_000733765.1:WP_043768786.1  15 DLDTPVGVYRRLANTAFSYLFESMQGGERWGRYSFIGLPAREILRLREGRITRHIDGELVEElHPEAPMAWLR 87 
                                           778***********9************************99999999997776664444444689******** PP

                             TIGR00564  74 klleka.eesedeldeplsggavGylgydtvrlveklkeea.edelelpdlllllvetvivfDhvekkvilie 144
                                           + ++    + +++l+  + gg+vGy+gyd vr++e+  + a ed+lelp++ll+  e++++fD+ +  ++l++
  NCBI__GCF_000733765.1:WP_043768786.1  88 DAVADDsVTPDPRLPR-FDGGWVGYIGYDAVRYIEPRVACAnEDPLELPEALLMKSEDLVIFDNLRGLMYLVT 159
                                           ***9974455666665.*******************999555******************************* PP

                             TIGR00564 145 narteaersaeeeaaarleellaelqkeleka..vkaleekkesftsnvekeeyeekvakakeyikaGdifqv 215
                                           +   + +  a++ea++rl+   +el k+++ +  ++ +e  + +f s +++e++ + v++++eyi+aGd++qv
  NCBI__GCF_000733765.1:WP_043768786.1 160 HC-PAGDAAARAEAETRLDGWQTELAKPAAADyqMPDPEAPEPDFVSGMSREAFCDVVERIREYIRAGDVMQV 231
                                           99.6666669*******************998556666777777***************************** PP

                             TIGR00564 216 vlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvkgkrvetrPiAGtrkRGatkee 288
                                           v+Sqrl+a+++a+p++lYr++R+ NPSpyly l+l+d ++vgsSPE+lv+v++ ++++rP+AGtr+RGat+ee
  NCBI__GCF_000733765.1:WP_043768786.1 232 VPSQRLSAPFTAEPLALYRAIRRLNPSPYLYCLNLDDHHVVGSSPEILVRVEDSEMHVRPLAGTRPRGATEEE 304
                                           ************************************************************************* PP

                             TIGR00564 289 DealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellkiekyshvmHivSeVeGelkdeltavDal 361
                                           D +l+eeLlad+Ke+AEHlmL+DL+RND+g+v+++gsv+ +e ++ie+yshvmHivS+V+G+l ++++a+Dal
  NCBI__GCF_000733765.1:WP_043768786.1 305 DIRLAEELLADPKEVAEHLMLIDLGRNDVGRVCETGSVKLTERMRIERYSHVMHIVSNVVGRLPPGTHALDAL 377
                                           ************************************************************************* PP

                             TIGR00564 362 raalPaGTlsGAPKvrAmelidelEkekRgiYgGavgylsfdgdvdtaiaiRtmvlkdgvayvqAgaGiVaDS 434
                                           +aa+P GTlsGAPKvrAme+i+elE+++Rg+YgGavgy++  g++d+aiaiRt+v+  g+++vq gaG+VaDS
  NCBI__GCF_000733765.1:WP_043768786.1 378 MAAFPTGTLSGAPKVRAMEIIEELEPVRRGVYGGAVGYIGGSGNLDMAIAIRTAVIAGGQVHVQSGAGVVADS 450
                                           ************************************************************************* PP

                             TIGR00564 435 dpeaEyeEtlnKakallrai 454
                                           dp+aE+ Et+nKa+a+lra+
  NCBI__GCF_000733765.1:WP_043768786.1 451 DPNAEWVETMNKARAMLRAV 470
                                           *****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (474 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 30.21
//
[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:

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