Alignments for a candidate for trpE in Thermocrinis albus DSM 14484

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Thermocrinis albus DSM 14484

Align anthranilate synthase (subunit 1/2) (EC 4.1.3.27) (characterized)
to candidate WP_012992587.1 THAL_RS07900 anthranilate synthase component I

Query= BRENDA::P20580
         (492 letters)



>NCBI__GCF_000025605.1:WP_012992587.1
          Length = 487

 Score =  402 bits (1032), Expect = e-116
 Identities = 226/480 (47%), Positives = 311/480 (64%), Gaps = 18/480 (3%)

Query: 14  YNRIPLSFETLADFDTPLSIYLKLA-DAPNSYLLESVQGGEKWGRYSIIGLPCRTVLRVY 72
           Y  + L  E LAD +TPLS++LKL  +   + LLES +GG +WGRYS I        ++ 
Sbjct: 17  YRPVALYTEVLADTETPLSLFLKLRKEGAFNILLESAEGGSQWGRYSFIIRSESFYWKLL 76

Query: 73  DHQVRISIDG----VETERFDCADPLAFVEEFKARYQVPTVPGLPRFDGGLVGYFGYDCV 128
             +  +   G    V TE     DP   + +  + +Q    P LPRF GGLVGY  YD V
Sbjct: 77  RKRGEVFQRGRFREVVTE-----DPFGELNKVMSTFQPYRDPSLPRFWGGLVGYVSYDVV 131

Query: 129 RYVEKRLATCPNPDPLGNPDILLMVSDAVVVFDNLAGKIHAIVLADPSEENAYERGQARL 188
           ++ E    +    DPL  PDI+++++D VV+ DNL GK+  +V    S    Y RG+  +
Sbjct: 132 KHYEPVRDSLD--DPLMLPDIMMVLTDLVVIHDNLTGKVKVVVPLFESSVEEYRRGERTI 189

Query: 189 EELLERLRQPITPRRGLDLEAAQGREPA-FRASFTREDYENAVGRIKDYILAGDCMQVVP 247
           E+ L  +       R +   + + +EP+ + ++ +++++ + V R K+YI AGD +QVV 
Sbjct: 190 EDTLHHIFH-----RSVLPSSFKEKEPSGWTSNTSQQEFIDMVTRAKEYIAAGDVIQVVL 244

Query: 248 SQRMSIEFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDGLVTVRPIA 307
           SQR    +K  P ++YR LR  NP+PYMY+ + G F V+GSSPEVLVRVED     RPIA
Sbjct: 245 SQRFYKSWKGDPQNIYRVLRYINPSPYMYYLDMGSFQVIGSSPEVLVRVEDKTAHTRPIA 304

Query: 308 GTRPRGINEEADLALEQDLLSDAKEIAEHLMLIDLGRNDVGRVSDIGAVKVTEKMVIERY 367
           GTR RG  EE D+ LE++L+ D KE AEHLML+DL RND+ RV   G+VKV E M +ERY
Sbjct: 305 GTRRRGRTEEEDVRLEEELVKDEKERAEHLMLVDLARNDLARVCVPGSVKVKEFMKVERY 364

Query: 368 SNVMHIVSNVTGQLREGLSAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKRGVYGGAV 427
           S+VMH+VS+V G L EG+S  D L+A+ PAGT+SGAPK+RAM+II+ELE  +RG+Y G+V
Sbjct: 365 SHVMHMVSHVDGILAEGVSPFDVLKAVFPAGTVSGAPKVRAMQIIEELEKERRGIYAGSV 424

Query: 428 GYLAWNGNMDTAIAIRTAVIKNGELHVQAGGGIVADSVPALEWEETINKRRAMFRAVALA 487
           GY+++ GNMD AIAIRTAV + GE+ VQAG GIVADS P  EW ET+NK +A+ +AV +A
Sbjct: 425 GYVSFEGNMDMAIAIRTAVYRGGEIFVQAGAGIVADSDPYREWLETVNKAKAVMKAVDMA 484


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: 574
Number of extensions: 29
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: 492
Length of database: 487
Length adjustment: 34
Effective length of query: 458
Effective length of database: 453
Effective search space:   207474
Effective search space used:   207474
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_012992587.1 THAL_RS07900 (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.1099.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.9e-175  568.8   0.0   5.6e-175  568.6   0.0    1.0  1  lcl|NCBI__GCF_000025605.1:WP_012992587.1  THAL_RS07900 anthranilate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025605.1:WP_012992587.1  THAL_RS07900 anthranilate synthase component I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  568.6   0.0  5.6e-175  5.6e-175       1     454 [.      28     481 ..      28     482 .. 0.96

  Alignments for each domain:
  == domain 1  score: 568.6 bits;  conditional E-value: 5.6e-175
                                 TIGR00564   1 adtltpisvylklak.rkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeakieede 68 
                                               adt+tp+s++lkl+k  + ++llEs+e ++++gRyS+i  ++ + +k   ++ + ++    ++ ++ed+
  lcl|NCBI__GCF_000025605.1:WP_012992587.1  28 ADTETPLSLFLKLRKeGAFNILLESAEGGSQWGRYSFIIRSESFYWKLLRKRGEVFQRGRFREVVTEDP 96 
                                               699***********966999***************************999988999988888889**** PP

                                 TIGR00564  69 lkelrklleka.eesedeldeplsggavGylgydtvrlveklkeeaedelelpdlllllvetvivfDhv 136
                                                 el+k+++++   ++++l+  + gg+vGy++yd+v+++e+++++  d+l lpd++++l++ v+++D+ 
  lcl|NCBI__GCF_000025605.1:WP_012992587.1  97 FGELNKVMSTFqPYRDPSLPR-FWGGLVGYVSYDVVKHYEPVRDSLDDPLMLPDIMMVLTDLVVIHDNL 164
                                               ***********7777788876.*********************************************** PP

                                 TIGR00564 137 ekkvilienarteaersaeeeaaarleellaelqkelekavkaleekkesftsnvekeeyeekvakake 205
                                               + kv ++    ++ +++ ++  ++++e++l+++ + +    +++e+++   tsn++++e+ + v++ake
  lcl|NCBI__GCF_000025605.1:WP_012992587.1 165 TGKVKVVVPLFES-SVEEYRRGERTIEDTLHHIFHRSVLPSSFKEKEPSGWTSNTSQQEFIDMVTRAKE 232
                                               *******999555.55589999******9999988888778888888888******************* PP

                                 TIGR00564 206 yikaGdifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvkgkrvetr 274
                                               yi+aGd++qvvlSqr+ ++ + +p ++Yr+LR +NPSpy+yyld+  f+++gsSPE+lv+v++k+ +tr
  lcl|NCBI__GCF_000025605.1:WP_012992587.1 233 YIAAGDVIQVVLSQRFYKSWKGDPQNIYRVLRYINPSPYMYYLDMGSFQVIGSSPEVLVRVEDKTAHTR 301
                                               ********************************************************************* PP

                                 TIGR00564 275 PiAGtrkRGatkeeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellkiekyshvmHi 343
                                               PiAGtr+RG+t+eeD +leeeL++deKerAEHlmLvDLaRND+++v+ +gsv+vke++k+e+yshvmH+
  lcl|NCBI__GCF_000025605.1:WP_012992587.1 302 PIAGTRRRGRTEEEDVRLEEELVKDEKERAEHLMLVDLARNDLARVCVPGSVKVKEFMKVERYSHVMHM 370
                                               ********************************************************************* PP

                                 TIGR00564 344 vSeVeGelkdeltavDalraalPaGTlsGAPKvrAmelidelEkekRgiYgGavgylsfdgdvdtaiai 412
                                               vS+V G l+++++++D+l+a++PaGT+sGAPKvrAm++i+elEke+RgiY+G+vgy+sf+g++d+aiai
  lcl|NCBI__GCF_000025605.1:WP_012992587.1 371 VSHVDGILAEGVSPFDVLKAVFPAGTVSGAPKVRAMQIIEELEKERRGIYAGSVGYVSFEGNMDMAIAI 439
                                               ********************************************************************* PP

                                 TIGR00564 413 RtmvlkdgvayvqAgaGiVaDSdpeaEyeEtlnKakallrai 454
                                               Rt+v++ g ++vqAgaGiVaDSdp++E+ Et+nKaka+++a+
  lcl|NCBI__GCF_000025605.1:WP_012992587.1 440 RTAVYRGGEIFVQAGAGIVADSDPYREWLETVNKAKAVMKAV 481
                                               ***************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (487 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: 7.86
//
[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