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.12265.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 8.18
//
[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:

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