Alignments for a candidate for trpE in Nitriliruptor alkaliphilus DSM 45188

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Nitriliruptor alkaliphilus DSM 45188

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate WP_052667665.1 NITAL_RS18710 anthranilate synthase component I

Query= SwissProt::P20579
         (493 letters)



>NCBI__GCF_000969705.1:WP_052667665.1
          Length = 515

 Score =  380 bits (975), Expect = e-110
 Identities = 229/508 (45%), Positives = 299/508 (58%), Gaps = 30/508 (5%)

Query: 3   REEFLRLAAVGYNRIPLACETLADFDTPLSIYLKL-----------ADQPNSYLLESVQG 51
           REEF+   A  +  +P+  E LAD +TPLS++ KL           A  P S+LLES + 
Sbjct: 7   REEFVA-HATDHGVVPVWREVLADLETPLSVFAKLGGAAAGGAADGAIPPRSFLLESAEH 65

Query: 52  GEKWGRYSMIGL-PSRTVMRVHGYHVSILHDGVEVES-HDVEDPLAFVESFKDRYKVADI 109
           GE+WGRYS IG  P  T++   G    +  +G       +   PL  +    D Y+   +
Sbjct: 66  GERWGRYSFIGFDPFLTLLGRDG---EVSWEGTPPAGCAEATGPLDALARATDAYRAPQL 122

Query: 110 PGLPRFNGGLVGYFGYDCVRYVEKRLGVSPNPDPLGVPDILLMVSDAVVVFDNLAGKMHA 169
             LP  +GG VG+ GYD VR +E  +  +   D LG+PD++++    VV  D+    M  
Sbjct: 123 LDLP-LHGGAVGFIGYDAVREIE--VIPATGRDDLGMPDVVMLFPRHVVALDHARQVMTV 179

Query: 170 IVLV---DPAEEQAFEQGQ------ARLQGLLETLRQPITPRRGLDLSGPQAAEPEFRSS 220
           +  V   D     A E G       A   G+++ L     P   +     + A P   S+
Sbjct: 180 VTNVTVDDLTSADADELGARYDAAVAATDGVVDRLAAAAPPLPPV-APPERVAPPRVPSN 238

Query: 221 YTREDYENAVGRIKEYILAGDCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNF 280
               +YE  V  +KE+I AGD  Q V SQR S+D      DLYR LR  NP+PY+Y  + 
Sbjct: 239 LAEGEYEQLVEVVKEHIRAGDTFQTVVSQRFSVDTTVTAFDLYRVLRVINPSPYLYLLDL 298

Query: 281 GDFHVVGSSPEVLVRVEDNLVTVRPIAGTRPRGATEEADRALEDDLLSDDKEIAEHLMLI 340
           GD  +VGSSPE LV+V+ + V   PIAGTRPRGAT   DR  E  L++D KE AEH+ML+
Sbjct: 299 GDAQIVGSSPEALVQVQGDHVETWPIAGTRPRGATPAEDREHERSLMADAKERAEHVMLV 358

Query: 341 DLGRNDVGRVSSTGSVRLTEKMVIERYSNVMHIVSNVAGQLREGLTAMDALRAILPAGTL 400
           DL RND+GRV  TGSV + + M +ERYS+VMH+VS+V+G LREGLT +D LRA+ PAGT+
Sbjct: 359 DLARNDIGRVCETGSVTVDDLMHVERYSHVMHLVSSVSGTLREGLTPVDVLRAVFPAGTV 418

Query: 401 SGAPKIRAMEIIDELEPVKRGVYGGAVGYFAWNGNMDTAIAIRTAVINDGELHVQAGGGI 460
           SGAPK+RAM+IIDELEP +RG Y GAVGY  + GN+DT I IRT V+ DG  HVQAG GI
Sbjct: 419 SGAPKVRAMQIIDELEPTRRGPYAGAVGYVDFAGNLDTCITIRTVVLKDGVAHVQAGAGI 478

Query: 461 VADSVPALEWEETINKRRAMFRAVALAE 488
           VADS P  E EET +K  A+  AV  AE
Sbjct: 479 VADSRPTSEEEETRSKAGAVLAAVQAAE 506


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: 712
Number of extensions: 32
Number of successful extensions: 5
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: 515
Length adjustment: 34
Effective length of query: 459
Effective length of database: 481
Effective search space:   220779
Effective search space used:   220779
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_052667665.1 NITAL_RS18710 (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.13588.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-169  550.8   0.0   1.7e-169  550.6   0.0    1.0  1  lcl|NCBI__GCF_000969705.1:WP_052667665.1  NITAL_RS18710 anthranilate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000969705.1:WP_052667665.1  NITAL_RS18710 anthranilate synthase component I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  550.6   0.0  1.7e-169  1.7e-169       2     454 ..      29     502 ..      28     503 .. 0.93

  Alignments for each domain:
  == domain 1  score: 550.6 bits;  conditional E-value: 1.7e-169
                                 TIGR00564   2 dtltpisvylklakr...........kesfllEsvekeeelgRySliglnpvleikakdgkavlleadd 59 
                                               d +tp+sv+ kl              + sfllEs+e++e++gRyS+ig +p+l++  +dg++ +  +  
  lcl|NCBI__GCF_000969705.1:WP_052667665.1  29 DLETPLSVFAKLGGAaaggaadgaipPRSFLLESAEHGERWGRYSFIGFDPFLTLLGRDGEVSWEGTPP 97 
                                               7899999999999844799999999999********************************888888777 PP

                                 TIGR00564  60 eeakieedelkelrkllekaeesedeldeplsggavGylgydtvrlveklkeeaedelelpdlllllve 128
                                                   + + +l++l +  ++++   + ld pl ggavG++gyd vr +e ++++ +d+l +pd+++l+ +
  lcl|NCBI__GCF_000969705.1:WP_052667665.1  98 AGCAEATGPLDALARATDAYR-APQLLDLPLHGGAVGFIGYDAVREIEVIPATGRDDLGMPDVVMLFPR 165
                                               77779999***9999999965.566799***************************************** PP

                                 TIGR00564 129 tvivfDhvekkvilienarteaers........aeeeaaarleellaelqkelekavkaleekkes... 186
                                               +v++ Dh ++ +++++n++ ++ +s         +++a a+ + ++ +l  ++ +  ++ +++++    
  lcl|NCBI__GCF_000969705.1:WP_052667665.1 166 HVVALDHARQVMTVVTNVTVDDLTSadadelgaRYDAAVAATDGVVDRLAAAAPPLPPVAPPERVAppr 234
                                               *****************9988877777778887667777778888888888777665555544444555 PP

                                 TIGR00564 187 ftsnvekeeyeekvakakeyikaGdifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfel 255
                                               + sn+ + eye+ v+ +ke+i+aGd fq v+Sqr+++++++++f+lYr+LR++NPSpyly ldl d ++
  lcl|NCBI__GCF_000969705.1:WP_052667665.1 235 VPSNLAEGEYEQLVEVVKEHIRAGDTFQTVVSQRFSVDTTVTAFDLYRVLRVINPSPYLYLLDLGDAQI 303
                                               99******************************************************************* PP

                                 TIGR00564 256 vgsSPEllvkvkgkrvetrPiAGtrkRGatkeeDealeeeLladeKerAEHlmLvDLaRNDigkvaklg 324
                                               vgsSPE+lv+v+g++vet PiAGtr+RGat++eD+  e+ L+ad KerAEH+mLvDLaRNDig+v+++g
  lcl|NCBI__GCF_000969705.1:WP_052667665.1 304 VGSSPEALVQVQGDHVETWPIAGTRPRGATPAEDREHERSLMADAKERAEHVMLVDLARNDIGRVCETG 372
                                               ********************************************************************* PP

                                 TIGR00564 325 svevkellkiekyshvmHivSeVeGelkdeltavDalraalPaGTlsGAPKvrAmelidelEkekRgiY 393
                                               sv v++l+++e+yshvmH+vS+V+G+l+++lt+vD+lra++PaGT+sGAPKvrAm++idelE+++Rg+Y
  lcl|NCBI__GCF_000969705.1:WP_052667665.1 373 SVTVDDLMHVERYSHVMHLVSSVSGTLREGLTPVDVLRAVFPAGTVSGAPKVRAMQIIDELEPTRRGPY 441
                                               ********************************************************************* PP

                                 TIGR00564 394 gGavgylsfdgdvdtaiaiRtmvlkdgvayvqAgaGiVaDSdpeaEyeEtlnKakallrai 454
                                               +Gavgy++f+g++dt+i+iRt+vlkdgva+vqAgaGiVaDS p++E eEt  Ka a+l a+
  lcl|NCBI__GCF_000969705.1:WP_052667665.1 442 AGAVGYVDFAGNLDTCITIRTVVLKDGVAHVQAGAGIVADSRPTSEEEETRSKAGAVLAAV 502
                                               ********************************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (515 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: 00:00:00.03
# Mc/sec: 7.48
//
[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