Alignments for a candidate for trpE in Saccharomonospora cyanea NA-134

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Saccharomonospora cyanea NA-134

Align anthranilate synthase (subunit 1/2) (EC 4.1.3.27) (characterized)
to candidate WP_005458381.1 SACCYDRAFT_RS18035 anthranilate synthase component I

Query= BRENDA::P20580
         (492 letters)



>NCBI__GCF_000244975.1:WP_005458381.1
          Length = 517

 Score =  389 bits (1000), Expect = e-112
 Identities = 226/497 (45%), Positives = 305/497 (61%), Gaps = 21/497 (4%)

Query: 2   NREEFLRLAADGYNRIPLSFETLADFDTPLSIYLKLA-DAPNSYLLESVQGGEKWGRYSI 60
           +R++F  LA D    IP+    LAD DTP+++Y KLA D P ++LLES + G+ W R+S 
Sbjct: 20  SRDDFRALARDR-RVIPVVRRLLADADTPVALYRKLAGDRPGTFLLESAENGQSWSRWSF 78

Query: 61  IGLPCRTVLRVYDHQVRIS---IDGVETERFDCADPLAFVEEFKARYQVPTVPGLPRFDG 117
           +G+  R  L V D +   +   + G+ TE     DPL  + E   +     +PG+P   G
Sbjct: 79  VGVDSRAALTVRDGKAVWTGKPVAGLPTE----GDPLTILRETLQKLHTEPLPGMPPLTG 134

Query: 118 GLVGYFGYDCVRYVEKRLATCPNPDPLGNPDILLMVSDAVVVFDNLAGKIHAIVLA---D 174
           GLVGY GYD VR++E RL      D L  P++ ++++  +  FD+  G +  I  A   D
Sbjct: 135 GLVGYIGYDAVRWLE-RLPELAERD-LDIPEVTMLLATDLAAFDHHEGTVTLIANAVNWD 192

Query: 175 PSEEN---AYERGQARLEELLERLRQPITPRRGLDLEAAQGREPAFRASFTREDYENAVG 231
            S E    AY+    RL+ + ERL  P      +    A    P F    T+ED+  AV 
Sbjct: 193 DSPERVDAAYDDALRRLDVMTERLASPAPATNAVFERPA----PEFTRKRTKEDFHAAVH 248

Query: 232 RIKDYILAGDCMQVVPSQRMSIEFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPE 291
           +  + I AG+  Q+VPSQR  +   A  +D+YR LR  NP+PYMY      F +VGSSPE
Sbjct: 249 KAVEAIHAGEAFQIVPSQRFEMRTDADALDVYRVLRTSNPSPYMYLLRLEGFDIVGSSPE 308

Query: 292 VLVRVEDGLVTVRPIAGTRPRGINEEADLALEQDLLSDAKEIAEHLMLIDLGRNDVGRVS 351
            LV V DG  +  PIAGTR RG + E D  L +DLL+D KE AEHLML+DLGRND+G+V 
Sbjct: 309 SLVTVRDGRASTHPIAGTRWRGADPEEDAQLAKDLLADEKERAEHLMLVDLGRNDLGKVC 368

Query: 352 DIGAVKVTEKMVIERYSNVMHIVSNVTGQLREGLSAMDALRAILPAGTLSGAPKIRAMEI 411
             G V+V +   IERYS+VMHIVS VTG+L +  +A DA+ A  PAGTLSGAPK+RAME+
Sbjct: 369 RPGTVRVVDSFTIERYSHVMHIVSTVTGELADDATAFDAVLACFPAGTLSGAPKVRAMEL 428

Query: 412 IDELEPVKRGVYGGAVGYLAWNGNMDTAIAIRTAVIKNGELHVQAGGGIVADSVPALEWE 471
           I+ELEP +R +YGG VGYL + G+ DTAIAIRTA++++G  +VQAGGG+VADS    E  
Sbjct: 429 IEELEPTRRALYGGIVGYLDFAGDADTAIAIRTALMRDGVAYVQAGGGVVADSDADYEDN 488

Query: 472 ETINKRRAMFRAVALAE 488
           E++NK R +  AVA A+
Sbjct: 489 ESLNKARTVLSAVAAAD 505


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: 656
Number of extensions: 33
Number of successful extensions: 4
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: 517
Length adjustment: 34
Effective length of query: 458
Effective length of database: 483
Effective search space:   221214
Effective search space used:   221214
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_005458381.1 SACCYDRAFT_RS18035 (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.2406135.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-174  567.3   0.0   1.6e-174  567.1   0.0    1.0  1  NCBI__GCF_000244975.1:WP_005458381.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000244975.1:WP_005458381.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  567.1   0.0  1.6e-174  1.6e-174       2     454 ..      43     501 ..      42     502 .. 0.97

  Alignments for each domain:
  == domain 1  score: 567.1 bits;  conditional E-value: 1.6e-174
                             TIGR00564   2 dtltpisvylklak.rkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeakieedelkelr 73 
                                           d+ tp+ +y+kla  r+ +fllEs+e++++++R+S++g+++++ ++++dgkav+  +      +e+d+l++lr
  NCBI__GCF_000244975.1:WP_005458381.1  43 DADTPVALYRKLAGdRPGTFLLESAENGQSWSRWSFVGVDSRAALTVRDGKAVWTGKPVAGLPTEGDPLTILR 115
                                           889***********89***************************************988888889********* PP

                             TIGR00564  74 kllekaeesedeld..eplsggavGylgydtvrlveklkeeaedelelpdlllllvetvivfDhvekkvilie 144
                                           ++l+k++  ++ l+  +pl+gg+vGy+gyd vr +e+l+e ae +l++p++++ll +++++fDh e +v+li+
  NCBI__GCF_000244975.1:WP_005458381.1 116 ETLQKLH--TEPLPgmPPLTGGLVGYIGYDAVRWLERLPELAERDLDIPEVTMLLATDLAAFDHHEGTVTLIA 186
                                           *****64..666777789******************************************************* PP

                             TIGR00564 145 narteaers.....aeeeaaarleellaelqkelekavkaleekkesftsnvekeeyeekvakakeyikaGdi 212
                                           na + +++      a+++a +rl+ ++++l +++  ++ + e+ + +ft + +ke+++++v+ka e+i+aG+ 
  NCBI__GCF_000244975.1:WP_005458381.1 187 NAVNWDDSPervdaAYDDALRRLDVMTERLASPAPATNAVFERPAPEFTRKRTKEDFHAAVHKAVEAIHAGEA 259
                                           *987766657889999******************9888888888999************************** PP

                             TIGR00564 213 fqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvkgkrvetrPiAGtrkRGat 285
                                           fq+v+Sqr+e++++a+++++Yr+LRt+NPSpy+y l le+f +vgsSPE+lv+v++ r +t+PiAGtr RGa+
  NCBI__GCF_000244975.1:WP_005458381.1 260 FQIVPSQRFEMRTDADALDVYRVLRTSNPSPYMYLLRLEGFDIVGSSPESLVTVRDGRASTHPIAGTRWRGAD 332
                                           ************************************************************************* PP

                             TIGR00564 286 keeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellkiekyshvmHivSeVeGelkdeltav 358
                                           +eeD++l+++LladeKerAEHlmLvDL+RND+gkv+++g+v+v ++++ie+yshvmHivS+V+Gel+d++ta+
  NCBI__GCF_000244975.1:WP_005458381.1 333 PEEDAQLAKDLLADEKERAEHLMLVDLGRNDLGKVCRPGTVRVVDSFTIERYSHVMHIVSTVTGELADDATAF 405
                                           ************************************************************************* PP

                             TIGR00564 359 DalraalPaGTlsGAPKvrAmelidelEkekRgiYgGavgylsfdgdvdtaiaiRtmvlkdgvayvqAgaGiV 431
                                           Da+ a++PaGTlsGAPKvrAmeli+elE+++R +YgG vgyl+f+gd dtaiaiRt++++dgvayvqAg+G+V
  NCBI__GCF_000244975.1:WP_005458381.1 406 DAVLACFPAGTLSGAPKVRAMELIEELEPTRRALYGGIVGYLDFAGDADTAIAIRTALMRDGVAYVQAGGGVV 478
                                           ************************************************************************* PP

                             TIGR00564 432 aDSdpeaEyeEtlnKakallrai 454
                                           aDSd + E +E+lnKa+++l+a+
  NCBI__GCF_000244975.1:WP_005458381.1 479 ADSDADYEDNESLNKARTVLSAV 501
                                           *****************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (517 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: 15.63
//
[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