Alignments for a candidate for trpE in Marinobacter adhaerens HP15

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Marinobacter adhaerens HP15

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate GFF3346 HP15_3288 anthranilate synthase component I

Query= SwissProt::P20579
         (493 letters)



>FitnessBrowser__Marino:GFF3346
          Length = 513

 Score =  629 bits (1621), Expect = 0.0
 Identities = 319/488 (65%), Positives = 379/488 (77%), Gaps = 2/488 (0%)

Query: 1   MNREEFLRLAAVGYNRIPLACETLADFDTPLSIYLKLADQPNSYLLESVQGGEKWGRYSM 60
           M  E+F+ LA  G+NRIP+  E LAD DTPLS YLKLA  P SYL ESVQGGEKWGRYS+
Sbjct: 19  MTPEQFIELADAGFNRIPVYREVLADLDTPLSTYLKLASGPYSYLFESVQGGEKWGRYSI 78

Query: 61  IGLPSRTVMRVHGYHVSILHDGVEVESHDVEDPLAFVESFKDRYKVADIPGLPRFNGGLV 120
           IGLPS  V++V  + V I   G  VE+ +V+DPLAFVE+++ R+   D+  LPRFNGGLV
Sbjct: 79  IGLPSHEVLKVFDHRVEISRGGEVVETEEVDDPLAFVEAYQKRFHAPDLDELPRFNGGLV 138

Query: 121 GYFGYDCVRYVEKRLGVSPNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVLVDPAEEQA 180
           GYFGYD VRY+EKRL  S  PD +G PDILLMVS+ +VVFDNL GK+H IV  DPA E A
Sbjct: 139 GYFGYDTVRYIEKRLRKSCPPDKIGTPDILLMVSNEIVVFDNLRGKLHLIVHADPAIEGA 198

Query: 181 FEQGQARLQGLLETLRQPIT--PRRGLDLSGPQAAEPEFRSSYTREDYENAVGRIKEYIL 238
           FE  Q R+  L   L +     PR    L G    E +F S +T++ +E AV +IK Y+L
Sbjct: 199 FETAQNRIDELENHLHRQTADAPRTPEHLRGKAVDESDFISGFTQDKFEAAVDKIKGYVL 258

Query: 239 AGDCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVED 298
            GD MQ V SQRMSI F+A P++LYR+LR  NP+PYMYF + GDFH+VGSSPE+L RVED
Sbjct: 259 DGDVMQTVISQRMSIPFEAPPLNLYRSLRVLNPSPYMYFLDLGDFHIVGSSPEILARVED 318

Query: 299 NLVTVRPIAGTRPRGATEEADRALEDDLLSDDKEIAEHLMLIDLGRNDVGRVSSTGSVRL 358
             VTVRPIAGTR RGAT+  D+ALE +LL+D KEIAEHLMLIDLGRND GRVS TG+VRL
Sbjct: 319 EEVTVRPIAGTRKRGATDAEDKALEAELLADPKEIAEHLMLIDLGRNDAGRVSETGTVRL 378

Query: 359 TEKMVIERYSNVMHIVSNVAGQLREGLTAMDALRAILPAGTLSGAPKIRAMEIIDELEPV 418
           T+KM++ERYS+VMHIVSNV G+L++  + +D LRA LPAGTLSGAPKIRAMEIIDELEPV
Sbjct: 379 TDKMIVERYSHVMHIVSNVTGRLKDNTSCLDVLRATLPAGTLSGAPKIRAMEIIDELEPV 438

Query: 419 KRGVYGGAVGYFAWNGNMDTAIAIRTAVINDGELHVQAGGGIVADSVPALEWEETINKRR 478
           KRGVYGGAVGY ++NGNMDTAIAIRTAVI D  LH+QAG G+VADSVP LEW+ET+NK R
Sbjct: 439 KRGVYGGAVGYLSFNGNMDTAIAIRTAVIKDNTLHIQAGAGVVADSVPRLEWKETMNKGR 498

Query: 479 AMFRAVAL 486
           A+FRAVA+
Sbjct: 499 AIFRAVAM 506


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: 762
Number of extensions: 24
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: 493
Length of database: 513
Length adjustment: 34
Effective length of query: 459
Effective length of database: 479
Effective search space:   219861
Effective search space used:   219861
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 GFF3346 HP15_3288 (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.9937.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-178  580.2   0.0   2.1e-178  579.9   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF3346  HP15_3288 anthranilate synthase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF3346  HP15_3288 anthranilate synthase component I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  579.9   0.0  2.1e-178  2.1e-178       2     454 ..      44     504 ..      43     505 .. 0.92

  Alignments for each domain:
  == domain 1  score: 579.9 bits;  conditional E-value: 2.1e-178
                           TIGR00564   2 dtltpisvylklakrkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeak.ieedelkelrkl 75 
                                         d  tp+s ylkla+ ++s+l+Esv+ +e++gRyS+igl ++ ++k+ d+++++ +  +  ++ +++d+l  +++ 
  lcl|FitnessBrowser__Marino:GFF3346  44 DLDTPLSTYLKLASGPYSYLFESVQGGEKWGRYSIIGLPSHEVLKVFDHRVEISRGGEVVETeEVDDPLAFVEAY 118
                                         778*********************************************966655544433323678888888888 PP

                           TIGR00564  76 lekaeesedeld..eplsggavGylgydtvrlveklkeea..edelelpdlllllvetvivfDhvekkviliena 146
                                          +++  + ++ld  + + gg+vGy+gydtvr++ek  +++  +d++ +pd+ll++ ++++vfD+ + k++li +a
  lcl|FitnessBrowser__Marino:GFF3346 119 QKRF--HAPDLDelPRFNGGLVGYFGYDTVRYIEKRLRKScpPDKIGTPDILLMVSNEIVVFDNLRGKLHLIVHA 191
                                         8776..3455554456*******************9885446********************************* PP

                           TIGR00564 147 rteaersaeeeaaarleellaelqkeleka..vkaleekkes......ftsnvekeeyeekvakakeyikaGdif 213
                                           + e  a+e a++r++el ++l++++++a  ++++ +   +      f s ++++++e++v+k+k y+ +Gd++
  lcl|FitnessBrowser__Marino:GFF3346 192 DPAIEG-AFETAQNRIDELENHLHRQTADAprTPEHLRG--KavdesdFISGFTQDKFEAAVDKIKGYVLDGDVM 263
                                         888777.9*****************99876442222222..1234555*************************** PP

                           TIGR00564 214 qvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvkgkrvetrPiAGtrkRGatkee 288
                                         q v+Sqr++ ++ea+p++lYr+LR+ NPSpy+y+ldl df++vgsSPE+l +v++++v++rPiAGtrkRGat++e
  lcl|FitnessBrowser__Marino:GFF3346 264 QTVISQRMSIPFEAPPLNLYRSLRVLNPSPYMYFLDLGDFHIVGSSPEILARVEDEEVTVRPIAGTRKRGATDAE 338
                                         *************************************************************************** PP

                           TIGR00564 289 DealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellkiekyshvmHivSeVeGelkdeltavDalra 363
                                         D+ale+eLlad+Ke AEHlmL+DL+RND g+v+++g+v+ ++ + +e+yshvmHivS+V+G+lkd+++ +D+lra
  lcl|FitnessBrowser__Marino:GFF3346 339 DKALEAELLADPKEIAEHLMLIDLGRNDAGRVSETGTVRLTDKMIVERYSHVMHIVSNVTGRLKDNTSCLDVLRA 413
                                         *************************************************************************** PP

                           TIGR00564 364 alPaGTlsGAPKvrAmelidelEkekRgiYgGavgylsfdgdvdtaiaiRtmvlkdgvayvqAgaGiVaDSdpea 438
                                         +lPaGTlsGAPK+rAme+idelE++kRg+YgGavgylsf+g++dtaiaiRt+v+kd+++++qAgaG+VaDS+p  
  lcl|FitnessBrowser__Marino:GFF3346 414 TLPAGTLSGAPKIRAMEIIDELEPVKRGVYGGAVGYLSFNGNMDTAIAIRTAVIKDNTLHIQAGAGVVADSVPRL 488
                                         *************************************************************************** PP

                           TIGR00564 439 EyeEtlnKakallrai 454
                                         E++Et+nK +a  ra+
  lcl|FitnessBrowser__Marino:GFF3346 489 EWKETMNKGRAIFRAV 504
                                         ***********99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (513 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 12.20
//
[ok]

This GapMind analysis is from Apr 09 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