Alignments for a candidate for trpE in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Dyella japonica UNC79MFTsu3.2

Align anthranilate synthase (subunit 1/2) (EC 4.1.3.27) (characterized)
to candidate N515DRAFT_2134 N515DRAFT_2134 anthranilate synthase component 1

Query= BRENDA::P20580
         (492 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2134
          Length = 529

 Score =  561 bits (1446), Expect = e-164
 Identities = 281/491 (57%), Positives = 359/491 (73%), Gaps = 1/491 (0%)

Query: 1   MNREEFLRLAADGYNRIPLSFETLADFDTPLSIYLKLADAPNSYLLESVQGGEKWGRYSI 60
           ++RE+F  LAA G+ RIPL  E  +D DTPLS+YLKLAD P ++L ESV+GG  WGRYSI
Sbjct: 40  ISREQFDALAAQGHTRIPLVREVFSDLDTPLSVYLKLADGPYTFLFESVEGGATWGRYSI 99

Query: 61  IGLPCRTVLRVYDHQVRISIDGVETERFDCADPLAFVEEFKARYQVPTVPGLPRFDGGLV 120
           IGLP R V R+  H++ +   G  TER    DPL  +E+ + +Y VP +P LP F GGLV
Sbjct: 100 IGLPARRVYRLRGHELEVEDSGEVTERRHLDDPLGEIEKLRRQYDVPRLPQLPAFSGGLV 159

Query: 121 GYFGYDCVRYVEKRLATCPNPDPLGNPDILLMVSDAVVVFDNLAGKIHAIVLADPSEENA 180
           GYFG++ + Y+E RLA     D LG PD+LLM+++ V VFDNL G+++ IV ADP+  +A
Sbjct: 160 GYFGFETIGYIEPRLARWDRADELGTPDVLLMLAEEVAVFDNLKGRLYLIVHADPARPHA 219

Query: 181 YERGQARLEELLERLRQPITPRRGLDLEAAQGREPAFRASFTREDYENAVGRIKDYILAG 240
           Y   Q RL+ L+ RLRQ       L    A   E  F++SFT+E++E  V R K+YI AG
Sbjct: 220 YAEAQRRLDALVHRLRQGGASYPQLTQSVALD-EGDFKSSFTKEEFEAMVERAKEYIRAG 278

Query: 241 DCMQVVPSQRMSIEFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDGL 300
           D  QVVPSQR+S+ F A P+D+YRALR  NP+PYMYF + GD  +VGSSPE+L R++DG 
Sbjct: 279 DIFQVVPSQRLSVGFNARPVDVYRALRALNPSPYMYFVDLGDTQIVGSSPEILARLKDGK 338

Query: 301 VTVRPIAGTRPRGINEEADLALEQDLLSDAKEIAEHLMLIDLGRNDVGRVSDIGAVKVTE 360
           V VRP+AGTR RG  E  DLALE++LL+D KE AEH+MLIDLGRND+GR+S+ G+V+V+E
Sbjct: 339 VVVRPLAGTRRRGATEAEDLALEEELLADPKERAEHVMLIDLGRNDIGRISETGSVEVSE 398

Query: 361 KMVIERYSNVMHIVSNVTGQLREGLSAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKR 420
             V+ERYS+VMHIVS V G++R  +  MD L+A  PAGTLSGAPKIRA+EII ELEP KR
Sbjct: 399 SFVVERYSHVMHIVSQVQGKVRPEVGYMDVLKATFPAGTLSGAPKIRALEIIQELEPYKR 458

Query: 421 GVYGGAVGYLAWNGNMDTAIAIRTAVIKNGELHVQAGGGIVADSVPALEWEETINKRRAM 480
            +Y GA+G++ W G+ DTAIAIRTAVI++G LHVQAG GIV DS P  EWEET+NK RA+
Sbjct: 459 NIYAGAIGWIGWWGDADTAIAIRTAVIQDGRLHVQAGAGIVYDSDPTAEWEETMNKGRAL 518

Query: 481 FRAVALAEQSV 491
           FRAVA A + +
Sbjct: 519 FRAVAQAAKGL 529


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: 764
Number of extensions: 31
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: 492
Length of database: 529
Length adjustment: 34
Effective length of query: 458
Effective length of database: 495
Effective search space:   226710
Effective search space used:   226710
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 N515DRAFT_2134 N515DRAFT_2134 (anthranilate synthase component 1)
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.28270.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   1.4e-173  564.0   0.0   1.6e-173  563.8   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_2134  N515DRAFT_2134 anthranilate synt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_2134  N515DRAFT_2134 anthranilate synthase component 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  563.8   0.0  1.6e-173  1.6e-173       2     454 ..      65     522 ..      64     523 .. 0.92

  Alignments for each domain:
  == domain 1  score: 563.8 bits;  conditional E-value: 1.6e-173
                                    TIGR00564   2 dtltpisvylklakrkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeak.... 63 
                                                  d  tp+svylkla  +++fl+Esve ++++gRyS+igl  + + + +++   +le++d+ +     
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2134  65 DLDTPLSVYLKLADGPYTFLFESVEGGATWGRYSIIGLPARRVYRLRGH---ELEVEDSGEVterr 127
                                                  778**********99***********************99999999987...33334444440013 PP

                                    TIGR00564  64 ieedelkelrkllekaeesedeld..eplsggavGylgydtvrlveklke..eaedelelpdllll 125
                                                  + +d+l e++kl ++   + ++l+  +++sgg+vGy+g++t+ ++e+  +     del +pd+ll+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2134 128 HLDDPLGEIEKLRRQ--YDVPRLPqlPAFSGGLVGYFGFETIGYIEPRLArwDRADELGTPDVLLM 191
                                                  556666666666555..55777777678******************987744459*********** PP

                                    TIGR00564 126 lvetvivfDhvekkvilienarteaersaeeeaaarleellaelqkeleka...vkaleekkesft 188
                                                  l e+v+vfD+ + +++li +a  +  + a++ea++rl++l+++l++  ++    ++ +  ++ +f+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2134 192 LAEEVAVFDNLKGRLYLIVHADPARPH-AYAEAQRRLDALVHRLRQGGASYpqlTQSVALDEGDFK 256
                                                  *********************777777.9***************99766543345556666777** PP

                                    TIGR00564 189 snvekeeyeekvakakeyikaGdifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfe 254
                                                  s+++kee+e+ v++akeyi+aGdifqvv+Sqrl++ ++a+p+++Yr+LR  NPSpy+y++dl d++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2134 257 SSFTKEEFEAMVERAKEYIRAGDIFQVVPSQRLSVGFNARPVDVYRALRALNPSPYMYFVDLGDTQ 322
                                                  ****************************************************************** PP

                                    TIGR00564 255 lvgsSPEllvkvkgkrvetrPiAGtrkRGatkeeDealeeeLladeKerAEHlmLvDLaRNDigkv 320
                                                  +vgsSPE+l ++k+ +v +rP+AGtr+RGat++eD aleeeLlad+KerAEH+mL+DL+RNDig++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2134 323 IVGSSPEILARLKDGKVVVRPLAGTRRRGATEAEDLALEEELLADPKERAEHVMLIDLGRNDIGRI 388
                                                  ****************************************************************** PP

                                    TIGR00564 321 aklgsvevkellkiekyshvmHivSeVeGelkdeltavDalraalPaGTlsGAPKvrAmelidelE 386
                                                  +++gsvev+e++ +e+yshvmHivS+V+G++++e+  +D+l+a++PaGTlsGAPK+rA+e+i+elE
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2134 389 SETGSVEVSESFVVERYSHVMHIVSQVQGKVRPEVGYMDVLKATFPAGTLSGAPKIRALEIIQELE 454
                                                  ****************************************************************** PP

                                    TIGR00564 387 kekRgiYgGavgylsfdgdvdtaiaiRtmvlkdgvayvqAgaGiVaDSdpeaEyeEtlnKakallr 452
                                                  + kR+iY+Ga+g+++  gd dtaiaiRt+v++dg+++vqAgaGiV+DSdp+aE+eEt+nK +al r
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2134 455 PYKRNIYAGAIGWIGWWGDADTAIAIRTAVIQDGRLHVQAGAGIVYDSDPTAEWEETMNKGRALFR 520
                                                  ****************************************************************99 PP

                                    TIGR00564 453 ai 454
                                                  a+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2134 521 AV 522
                                                  86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (529 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: 00:00:00.02
# Mc/sec: 9.49
//
[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