Alignments for a candidate for trpE in Stenotrophomonas chelatiphaga DSM 21508

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Stenotrophomonas chelatiphaga DSM 21508

Align anthranilate synthase (subunit 1/2) (EC 4.1.3.27) (characterized)
to candidate WP_057509108.1 ABB28_RS13445 anthranilate synthase component I

Query= BRENDA::P20580
         (492 letters)



>NCBI__GCF_001431535.1:WP_057509108.1
          Length = 496

 Score =  548 bits (1412), Expect = e-160
 Identities = 288/492 (58%), Positives = 356/492 (72%), Gaps = 6/492 (1%)

Query: 5   EFLRLAADGYNRIPLSFETLADFDTPLSIYLKLADAPNSYLLESVQGGEKWGRYSIIGLP 64
           +F + AA+G+ RIP+  E L+D DTPLS+YLKLAD P++YL ESV+GGE++GRYSIIGLP
Sbjct: 6   QFQQQAAEGHTRIPVVREVLSDLDTPLSVYLKLADGPHTYLFESVEGGERFGRYSIIGLP 65

Query: 65  CRTVLRVYDHQVRISIDGVETERFDCADPLAFVEEFKARYQVPTVPGLPRFDGGLVGYFG 124
            R V     H + I+  G   E  D ADP A VE  ++ + VP + GLP F GGLVG+FG
Sbjct: 66  ARRVYTFRGHTLTIAEHGQVVETRDVADPFAEVEALRSAHSVPKLDGLPGFTGGLVGWFG 125

Query: 125 YDCVRYVEKRLATCPNPDPLGNPDILLMVSDAVVVFDNLAGKIHAIVLADPSEENAYERG 184
           ++C+ Y+E RLA     D LG PDILLM S+ + VFDNL G+++ IV ADP +  A++  
Sbjct: 126 FECIGYIEPRLAPPAGRDELGTPDILLMHSEELAVFDNLKGRLYLIVHADPRQPGAWDEA 185

Query: 185 QARLEELLERLRQPITPRRGLDLEAAQGREPAFRASFTREDYENAVGRIKDYILAGDCMQ 244
           QARL+ L  +LR P        L +    E  F + FTRE + +AV R KDYI +GD  Q
Sbjct: 186 QARLDALAGKLRAPGAGYPA-PLHSDVLDEGDFISGFTREGFIDAVERSKDYIRSGDIFQ 244

Query: 245 VVPSQRMSIEFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVED-----G 299
           VV SQR+S+ FKA P+D+YRALR  NP+PYMYF + GD  VVGSSPE+LVR++      G
Sbjct: 245 VVLSQRLSVPFKARPVDVYRALRALNPSPYMYFLDVGDMQVVGSSPEILVRLQHDAEGVG 304

Query: 300 LVTVRPIAGTRPRGINEEADLALEQDLLSDAKEIAEHLMLIDLGRNDVGRVSDIGAVKVT 359
            VTVRPIAGTRPRG   E D ALE +LL+D KE AEHLMLIDLGRND GRVS  G V+V 
Sbjct: 305 HVTVRPIAGTRPRGATVEEDNALEAELLADPKERAEHLMLIDLGRNDAGRVSRAGTVEVG 364

Query: 360 EKMVIERYSNVMHIVSNVTGQLREGLSAMDALRAILPAGTLSGAPKIRAMEIIDELEPVK 419
           E+ VIERYS+VMHIVS VTGQL+ GLS  D LRA  PAGT+SGAPKIRA+E+I ELEP+K
Sbjct: 365 EQFVIERYSHVMHIVSEVTGQLQPGLSYADVLRATFPAGTVSGAPKIRALEVIRELEPIK 424

Query: 420 RGVYGGAVGYLAWNGNMDTAIAIRTAVIKNGELHVQAGGGIVADSVPALEWEETINKRRA 479
           R VY G++GY+ W+G+ DTAIAIRTAVIK+G LHVQAG GIV DS P  EW+ET+NK RA
Sbjct: 425 RNVYAGSIGYIGWHGDADTAIAIRTAVIKDGRLHVQAGAGIVYDSDPQKEWDETMNKGRA 484

Query: 480 MFRAVALAEQSV 491
           +FRAVA A + +
Sbjct: 485 LFRAVAQAAKGL 496


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: 706
Number of extensions: 36
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: 492
Length of database: 496
Length adjustment: 34
Effective length of query: 458
Effective length of database: 462
Effective search space:   211596
Effective search space used:   211596
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_057509108.1 ABB28_RS13445 (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.32033.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.6e-168  546.2   0.0   4.2e-168  546.0   0.0    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057509108.1  ABB28_RS13445 anthranilate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057509108.1  ABB28_RS13445 anthranilate synthase component I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  546.0   0.0  4.2e-168  4.2e-168       2     454 ..      27     489 ..      26     490 .. 0.92

  Alignments for each domain:
  == domain 1  score: 546.0 bits;  conditional E-value: 4.2e-168
                                 TIGR00564   2 dtltpisvylklakrkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeak.ieedel 69 
                                               d  tp+svylkla  ++++l+Esve +e+ gRyS+igl  + + + ++++ +++e+ +  ++  ++d+ 
  lcl|NCBI__GCF_001431535.1:WP_057509108.1  27 DLDTPLSVYLKLADGPHTYLFESVEGGERFGRYSIIGLPARRVYTFRGHTLTIAEHGQVVETrDVADPF 95 
                                               778**********99***********************9999999999855555533332223567777 PP

                                 TIGR00564  70 kelrkllekaeesedeld..eplsggavGylgydtvrlveklkeea..edelelpdlllllvetvivfD 134
                                                e+++l ++  +s ++ld  + ++gg+vG++g++++ ++e+  +++  +del +pd+ll+  e+++vfD
  lcl|NCBI__GCF_001431535.1:WP_057509108.1  96 AEVEALRSA--HSVPKLDglPGFTGGLVGWFGFECIGYIEPRLAPPagRDELGTPDILLMHSEELAVFD 162
                                               777766555..78899998888******************98774447********************* PP

                                 TIGR00564 135 hvekkvilienarteaersaeeeaaarleellaelqkeleka...vkaleekkesftsnvekeeyeekv 200
                                               + + +++li +a  ++   a++ea+arl++l+ +l+ + +      +    ++ +f s +++e + ++v
  lcl|NCBI__GCF_001431535.1:WP_057509108.1 163 NLKGRLYLIVHADPRQPG-AWDEAQARLDALAGKLRAPGAGYpapLHSDVLDEGDFISGFTREGFIDAV 230
                                               ***********9777666.9*****************998654334445555666************** PP

                                 TIGR00564 201 akakeyikaGdifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvk.. 267
                                               ++ k+yi++GdifqvvlSqrl+++++a+p+++Yr+LR  NPSpy+y+ld+ d+++vgsSPE+lv+++  
  lcl|NCBI__GCF_001431535.1:WP_057509108.1 231 ERSKDYIRSGDIFQVVLSQRLSVPFKARPVDVYRALRALNPSPYMYFLDVGDMQVVGSSPEILVRLQhd 299
                                               ******************************************************************987 PP

                                 TIGR00564 268 ...gkrvetrPiAGtrkRGatkeeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellk 333
                                                    +v++rPiAGtr+RGat eeD+ale+eLlad+KerAEHlmL+DL+RND g+v+++g+vev e + 
  lcl|NCBI__GCF_001431535.1:WP_057509108.1 300 aegVGHVTVRPIAGTRPRGATVEEDNALEAELLADPKERAEHLMLIDLGRNDAGRVSRAGTVEVGEQFV 368
                                               763345*************************************************************** PP

                                 TIGR00564 334 iekyshvmHivSeVeGelkdeltavDalraalPaGTlsGAPKvrAmelidelEkekRgiYgGavgylsf 402
                                               ie+yshvmHivSeV+G+l+++l+  D+lra++PaGT+sGAPK+rA+e+i elE+ kR++Y+G++gy++ 
  lcl|NCBI__GCF_001431535.1:WP_057509108.1 369 IERYSHVMHIVSEVTGQLQPGLSYADVLRATFPAGTVSGAPKIRALEVIRELEPIKRNVYAGSIGYIGW 437
                                               ********************************************************************* PP

                                 TIGR00564 403 dgdvdtaiaiRtmvlkdgvayvqAgaGiVaDSdpeaEyeEtlnKakallrai 454
                                               +gd dtaiaiRt+v+kdg+++vqAgaGiV+DSdp++E++Et+nK +al ra+
  lcl|NCBI__GCF_001431535.1:WP_057509108.1 438 HGDADTAIAIRTAVIKDGRLHVQAGAGIVYDSDPQKEWDETMNKGRALFRAV 489
                                               ************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (496 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: 00:00:00.01
# Mc/sec: 12.83
//
[ok]

This GapMind analysis is from Apr 10 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