Alignments for a candidate for trpE in Beijerinckia indica ATCC 9039

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Beijerinckia indica ATCC 9039

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate WP_012384444.1 BIND_RS07350 anthranilate synthase component I

Query= SwissProt::P20579
         (493 letters)



>NCBI__GCF_000019845.1:WP_012384444.1
          Length = 506

 Score =  402 bits (1032), Expect = e-116
 Identities = 228/474 (48%), Positives = 301/474 (63%), Gaps = 12/474 (2%)

Query: 19  LACETLADFDTPLSIYLKLADQPNS--YLLESVQGGEKWGRYSMIGLPSRTVMRVHGYHV 76
           ++ + + D +TP+S +LKLA   +   +LLESV+GG   GRYSMIGL    + R      
Sbjct: 21  VSTKLVGDLETPVSAFLKLARDRDGGIFLLESVEGGATRGRYSMIGLDPDIIWRAFAEQA 80

Query: 77  SILHDGVEVESHDV---EDPLAFVESFKDRYKVADIPGLPRFNGGLVGYFGYDCVRYVEK 133
            I  D     +  +   E PL  + +      +  +  LP    G+ GY GYD VR +E+
Sbjct: 81  EINRDAQRDPAAFLPCKEPPLQALRALIKESAIPYVAELPPMAAGIFGYLGYDMVRQMEE 140

Query: 134 RLGVSPNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVLVDP----AEEQAFEQGQARLQ 189
            LG +   DP+GVPD +L+    +VVFD++  ++  +  + P    +   A+EQ   R++
Sbjct: 141 -LGPAKT-DPIGVPDAILIRPTVMVVFDSVRDEISIVTPLRPRPGLSASAAYEQAMDRIE 198

Query: 190 GLLETLRQPITPRRGLDLSGPQAAEPEFRSSYTREDYENAVGRIKEYILAGDCMQVVPSQ 249
            ++ TL  P+    GL+     +A P  RS+    ++   V R K+YI AGD  QVV SQ
Sbjct: 199 AVVATLESPLAHPAGLEADPLLSAVPP-RSNTEPAEFAAMVERAKDYIRAGDIFQVVLSQ 257

Query: 250 RMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDNLVTVRPIAGT 309
           R S  F      LYRALR  NP P++ + +FG F VV SSPE+LVR+ D  VT+RPIAGT
Sbjct: 258 RFSAPFALPAFSLYRALRRVNPAPFLCYLDFGAFQVVCSSPEILVRLRDGKVTIRPIAGT 317

Query: 310 RPRGATEEADRALEDDLLSDDKEIAEHLMLIDLGRNDVGRVSSTGSVRLTEKMVIERYSN 369
           RPRGATEEAD AL  +LL+D+KE AEHLML+DLGRNDVGRV+  GSV +T++  IERYS+
Sbjct: 318 RPRGATEEADAALAAELLADEKECAEHLMLLDLGRNDVGRVAEIGSVTVTDQYAIERYSH 377

Query: 370 VMHIVSNVAGQLREGLTAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKRGVYGGAVGY 429
           VMHIVSNV G+   G  A+DAL A  PAGT+SGAPK+RAMEIIDELE  KRG+YGG +GY
Sbjct: 378 VMHIVSNVEGRFAAGQDAIDALCAGFPAGTVSGAPKVRAMEIIDELEIDKRGIYGGCIGY 437

Query: 430 FAWNGNMDTAIAIRTAVINDGELHVQAGGGIVADSVPALEWEETINKRRAMFRA 483
           F  +G MDT I +RT+V+ DG +HVQAG GIV DS PA E  E INK  A+F+A
Sbjct: 438 FGASGEMDTCIVLRTSVVKDGVMHVQAGAGIVYDSDPASEQRECINKAAALFKA 491


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: 679
Number of extensions: 36
Number of successful extensions: 6
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: 506
Length adjustment: 34
Effective length of query: 459
Effective length of database: 472
Effective search space:   216648
Effective search space used:   216648
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_012384444.1 BIND_RS07350 (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.25550.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     2e-174  566.8   0.0   2.3e-174  566.6   0.0    1.0  1  lcl|NCBI__GCF_000019845.1:WP_012384444.1  BIND_RS07350 anthranilate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000019845.1:WP_012384444.1  BIND_RS07350 anthranilate synthase component I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  566.6   0.0  2.3e-174  2.3e-174       2     454 ..      28     492 ..      27     493 .. 0.94

  Alignments for each domain:
  == domain 1  score: 566.6 bits;  conditional E-value: 2.3e-174
                                 TIGR00564   2 dtltpisvylklak.r.kesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeak....i 64 
                                               d +tp+s++lkla+ r    fllEsve ++++gRyS+igl+p++ ++a  ++a++ + ++++       
  lcl|NCBI__GCF_000019845.1:WP_012384444.1  28 DLETPVSAFLKLARdRdGGIFLLESVEGGATRGRYSMIGLDPDIIWRAFAEQAEINRDAQRDPAaflpC 96 
                                               789**********9634789***************************9999766655444444357899 PP

                                 TIGR00564  65 eedelkelrkllekaee.sedeldeplsggavGylgydtvrlveklkeeaedelelpdlllllvetviv 132
                                               +e +l++lr+l+++ ++    el +p+++g++Gylgyd+vr +e+l ++++d++ +pd++l+  + ++v
  lcl|NCBI__GCF_000019845.1:WP_012384444.1  97 KEPPLQALRALIKESAIpYVAEL-PPMAAGIFGYLGYDMVRQMEELGPAKTDPIGVPDAILIRPTVMVV 164
                                               99************854034444.67******************************************* PP

                                 TIGR00564 133 fDhvekkvilienarteaers...aeeeaaarleellaelqkeleka...vkaleekkesftsnvekee 195
                                               fD v++++ +++  r + + s   a+e+a++r+e+++a+l+++l++       +  ++++  sn+e +e
  lcl|NCBI__GCF_000019845.1:WP_012384444.1 165 FDSVRDEISIVTPLRPRPGLSasaAYEQAMDRIEAVVATLESPLAHPaglEADPLLSAVPPRSNTEPAE 233
                                               **************9998888778999*****************99844333345566669999***** PP

                                 TIGR00564 196 yeekvakakeyikaGdifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllv 264
                                               +++ v++ak+yi+aGdifqvvlSqr++a++ +++f+lYr+LR+vNP+p+l yld+  f++v sSPE+lv
  lcl|NCBI__GCF_000019845.1:WP_012384444.1 234 FAAMVERAKDYIRAGDIFQVVLSQRFSAPFALPAFSLYRALRRVNPAPFLCYLDFGAFQVVCSSPEILV 302
                                               ********************************************************************* PP

                                 TIGR00564 265 kvkgkrvetrPiAGtrkRGatkeeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellk 333
                                               ++++ +v++rPiAGtr+RGat+e+D+al++eLladeKe+AEHlmL+DL+RND+g+va++gsv v++ + 
  lcl|NCBI__GCF_000019845.1:WP_012384444.1 303 RLRDGKVTIRPIAGTRPRGATEEADAALAAELLADEKECAEHLMLLDLGRNDVGRVAEIGSVTVTDQYA 371
                                               ********************************************************************* PP

                                 TIGR00564 334 iekyshvmHivSeVeGelkdeltavDalraalPaGTlsGAPKvrAmelidelEkekRgiYgGavgylsf 402
                                               ie+yshvmHivS+VeG+ + + +a+Dal a +PaGT+sGAPKvrAme+idelE  kRgiYgG++gy+++
  lcl|NCBI__GCF_000019845.1:WP_012384444.1 372 IERYSHVMHIVSNVEGRFAAGQDAIDALCAGFPAGTVSGAPKVRAMEIIDELEIDKRGIYGGCIGYFGA 440
                                               ********************************************************************* PP

                                 TIGR00564 403 dgdvdtaiaiRtmvlkdgvayvqAgaGiVaDSdpeaEyeEtlnKakallrai 454
                                                g++dt+i++Rt v+kdgv++vqAgaGiV+DSdp +E +E++nKa+al +a+
  lcl|NCBI__GCF_000019845.1:WP_012384444.1 441 SGEMDTCIVLRTSVVKDGVMHVQAGAGIVYDSDPASEQRECINKAAALFKAA 492
                                               ************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (506 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 9.85
//
[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