Alignments for a candidate for aroG in Thiomicrospira cyclica ALM1

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Thiomicrospira cyclica ALM1

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_013835577.1 THICY_RS05275 3-deoxy-7-phosphoheptulonate synthase

Query= BRENDA::C3TIE2
         (350 letters)



>NCBI__GCF_000214825.1:WP_013835577.1
          Length = 355

 Score =  423 bits (1088), Expect = e-123
 Identities = 212/348 (60%), Positives = 262/348 (75%), Gaps = 1/348 (0%)

Query: 3   YQNDDLRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGPCS 62
           +Q DDLRI  I E+ PP+AL EKFP T+ AA TV   R+AI  IL G+DDRLLVVIGPCS
Sbjct: 4   FQTDDLRINHITEVQPPIALHEKFPITDTAATTVFKTRQAIKAILNGDDDRLLVVIGPCS 63

Query: 63  IHDPVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQINDG 122
           IHD  A   YA +L    ++  ++L IVMRVYFEKPRTTVGWKGLINDP ++ +F+IN G
Sbjct: 64  IHDTQAGLAYAEKLATQIDKYANDLLIVMRVYFEKPRTTVGWKGLINDPDLNETFKINKG 123

Query: 123 LRIARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLSCP 182
           L  AR  LL++N  G+PAA EFLD+I+PQY++DL+SWGAIGARTTESQ HRELASGLSCP
Sbjct: 124 LEKARGFLLNVNSLGVPAATEFLDLISPQYISDLVSWGAIGARTTESQGHRELASGLSCP 183

Query: 183 VGFKNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKE-PNY 241
           VGFKNGTDG  KVA+DAI AA  PH F+S+TK GHSAI +T+GN DCH+ILRGG + PNY
Sbjct: 184 VGFKNGTDGGFKVAVDAIRAANRPHIFMSLTKQGHSAIFSTTGNEDCHVILRGGNDGPNY 243

Query: 242 SAKHVAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVMV 301
           +   V +  + L KAG+  ++MID SHANSSK   KQM+V   + +Q+A G   I+G MV
Sbjct: 244 AHPFVEQAVQELQKAGVQPKLMIDCSHANSSKDHLKQMEVARSINEQLANGSPYIMGAMV 303

Query: 302 ESHLVEGNQSLESGEPLAYGKSITDACIGWEDTDALLRQLANAVKARR 349
           ESHLV G Q + SG+ L +G+SITDACI W  ++ LL  LA+ V++RR
Sbjct: 304 ESHLVAGRQDVISGQSLTFGQSITDACIDWPMSETLLEMLADGVRSRR 351


Lambda     K      H
   0.317    0.134    0.397 

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: 422
Number of extensions: 11
Number of successful extensions: 2
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: 350
Length of database: 355
Length adjustment: 29
Effective length of query: 321
Effective length of database: 326
Effective search space:   104646
Effective search space used:   104646
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate WP_013835577.1 THICY_RS05275 (3-deoxy-7-phosphoheptulonate synthase)
to HMM TIGR00034 (3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54))

# 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/TIGR00034.hmm
# target sequence database:        /tmp/gapView.2705287.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00034  [M=342]
Accession:   TIGR00034
Description: aroFGH: 3-deoxy-7-phosphoheptulonate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.5e-162  524.3   0.0   6.3e-162  524.1   0.0    1.0  1  NCBI__GCF_000214825.1:WP_013835577.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000214825.1:WP_013835577.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  524.1   0.0  6.3e-162  6.3e-162       1     342 []       7     351 ..       7     351 .. 0.99

  Alignments for each domain:
  == domain 1  score: 524.1 bits;  conditional E-value: 6.3e-162
                             TIGR00034   1 ddlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakrlkk 73 
                                           ddlri +i e+ +P +l++kfp+t +aa++v k+r++i+ il+G+ddrllvviGPcsihd +a l ya++l++
  NCBI__GCF_000214825.1:WP_013835577.1   7 DDLRINHITEVQPPIALHEKFPITDTAATTVFKTRQAIKAILNGDDDRLLVVIGPCSIHDTQAGLAYAEKLAT 79 
                                           799********************************************************************** PP

                             TIGR00034  74 laeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatelldtispq 146
                                             +k+ +dl ivmrvyfekPrttvGWkGlindPdlne+f++nkGl+ ar +ll+++ lg+p+ate+ld ispq
  NCBI__GCF_000214825.1:WP_013835577.1  80 QIDKYANDLLIVMRVYFEKPRTTVGWKGLINDPDLNETFKINKGLEKARGFLLNVNSLGVPAATEFLDLISPQ 152
                                           ************************************************************************* PP

                             TIGR00034 147 yladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvtkaGqvaivetk 219
                                           y++dl+swgaiGarttesq hrelasgls+pvgfkngtdG+ kva+dairaa+++h+f+s tk+G++ai +t+
  NCBI__GCF_000214825.1:WP_013835577.1 153 YISDLVSWGAIGARTTESQGHRELASGLSCPVGFKNGTDGGFKVAVDAIRAANRPHIFMSLTKQGHSAIFSTT 225
                                           ************************************************************************* PP

                             TIGR00034 220 GnedghiilrGGkk.pnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlevaesvveqiaeGekai 291
                                           Gned+h+ilrGG++ pny    v+++ +el+kag +++lmid+sh+ns+kd+ +q+eva+s+ eq+a+G+  i
  NCBI__GCF_000214825.1:WP_013835577.1 226 GNEDCHVILRGGNDgPNYAHPFVEQAVQELQKAGVQPKLMIDCSHANSSKDHLKQMEVARSINEQLANGSPYI 298
                                           ************************************************************************* PP

                             TIGR00034 292 iGvmiesnleeGnqsl..keelkyGksvtdacigwedteallrklaeavkerr 342
                                           +G m+es+l+ G+q++  +++l++G+s+tdaci+w ++e+ll+ la+ v++rr
  NCBI__GCF_000214825.1:WP_013835577.1 299 MGAMVESHLVAGRQDVisGQSLTFGQSITDACIDWPMSETLLEMLADGVRSRR 351
                                           ***************988899*****************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (355 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: 00:00:00.00
# Mc/sec: 22.34
//
[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