Alignments for a candidate for aroG in Pseudarthrobacter sulfonivorans Ar51

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Pseudarthrobacter sulfonivorans Ar51

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_058931376.1 AU252_RS14800 3-deoxy-7-phosphoheptulonate synthase

Query= BRENDA::P35170
         (366 letters)



>NCBI__GCF_001484605.1:WP_058931376.1
          Length = 368

 Score =  395 bits (1016), Expect = e-115
 Identities = 208/359 (57%), Positives = 254/359 (70%), Gaps = 7/359 (1%)

Query: 12  STSNKRVVAFHELPSPTDLIAANPLTPKQASKVEQDRQDIADIFAGDDDRLVVVVGPCSV 71
           STSN RV  F  LPSP +LIA  PL  +    VE+ R ++  I  G DDRL+V+VGPCS+
Sbjct: 11  STSNLRVSEFTPLPSPQELIAELPLDARVTDVVERGRDEVRAIMDGVDDRLLVIVGPCSI 70

Query: 72  HDPEAAIDYANRLAPLAKRLDQDLKIVMRVYFEKPRTIVGWKGLINDPHLNETYDIPEGL 131
           HDP+A ++YA RL   A++   DL IVMR YFEKPRT VGWKGLINDP L+ ++D+  GL
Sbjct: 71  HDPKAGLEYARRLVSQAEKHRDDLLIVMRTYFEKPRTTVGWKGLINDPRLDGSHDMVTGL 130

Query: 132 RIARKVLIDVVNLDLPVGCEFLEPNSPQYYADTVAWGAIGARTTESQVHRQLASGMSMPI 191
           R AR+ L  V  L LP   EFLEP SPQY AD ++WGAIGARTTESQ+HRQLASG+SMPI
Sbjct: 131 RTAREFLQQVTALGLPTATEFLEPISPQYMADLISWGAIGARTTESQIHRQLASGLSMPI 190

Query: 192 GFKNGTDGNIQVAVDAVQAAQNPHFFFGTSDDGALSVVETAGNSNSHIILRGGTSGPNHD 251
           GFKNGTDG++QVA+DA  AA     F G   DG  ++V TAGN ++H+ILRGG  GPN+ 
Sbjct: 191 GFKNGTDGDLQVALDACGAAAAAQAFLGIDGDGRAALVATAGNPDTHVILRGGRKGPNYS 250

Query: 252 AASVEAVVEKL---GENARLMIDASHANSGKDHIRQVEVVREIAEQISGGSE---AVAGI 305
           AA VE+   KL   G N RL++DASHANSGK H RQ EV  EI  Q+  G E   A+AG+
Sbjct: 251 AADVESASAKLAGKGLNPRLIVDASHANSGKSHHRQAEVALEIGAQLEDGGEAAQAIAGV 310

Query: 306 MIESFLVGGAQNLDPAKLRINGGEGLVYGQSVTDKCIDIDTTIDLLAELAAAVRERRAA 364
           M+ESFLVGGAQNLD  +    G   LVYGQSVTD C+D D ++ +L +LAA+ R+RR A
Sbjct: 311 MLESFLVGGAQNLDVTE-HAAGRAELVYGQSVTDACMDWDVSVSVLDQLAASARKRRTA 368


Lambda     K      H
   0.315    0.133    0.378 

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: 343
Number of extensions: 9
Number of successful extensions: 4
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: 366
Length of database: 368
Length adjustment: 30
Effective length of query: 336
Effective length of database: 338
Effective search space:   113568
Effective search space used:   113568
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 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate WP_058931376.1 AU252_RS14800 (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.2565.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.3e-147  475.3   0.0     5e-147  475.1   0.0    1.0  1  lcl|NCBI__GCF_001484605.1:WP_058931376.1  AU252_RS14800 3-deoxy-7-phosphoh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001484605.1:WP_058931376.1  AU252_RS14800 3-deoxy-7-phosphoheptulonate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  475.1   0.0    5e-147    5e-147       2     342 .]      14     366 ..      13     366 .. 0.96

  Alignments for each domain:
  == domain 1  score: 475.1 bits;  conditional E-value: 5e-147
                                 TIGR00034   2 dlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakr 70 
                                               +lr+ ++ +l +P+el+a+ pl +++++ v++ r+e+  i++G ddrllv++GPcsihdp+a leya+r
  lcl|NCBI__GCF_001484605.1:WP_058931376.1  14 NLRVSEFTPLPSPQELIAELPLDARVTDVVERGRDEVRAIMDGVDDRLLVIVGPCSIHDPKAGLEYARR 82 
                                               7899***************************************************************** PP

                                 TIGR00034  71 lkklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatel 139
                                               l + aek +ddl ivmr+yfekPrttvGWkGlindP l++s+d+ +Glr ar++l +++ lglp+ate+
  lcl|NCBI__GCF_001484605.1:WP_058931376.1  83 LVSQAEKHRDDLLIVMRTYFEKPRTTVGWKGLINDPRLDGSHDMVTGLRTAREFLQQVTALGLPTATEF 151
                                               ********************************************************************* PP

                                 TIGR00034 140 ldtispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvt 208
                                               l++ispqy+adl+swgaiGarttesq+hr+lasgls+p+gfkngtdG+l+va+da+ aaaa   fl+++
  lcl|NCBI__GCF_001484605.1:WP_058931376.1 152 LEPISPQYMADLISWGAIGARTTESQIHRQLASGLSMPIGFKNGTDGDLQVALDACGAAAAAQAFLGID 220
                                               ********************************************************************* PP

                                 TIGR00034 209 kaGqvaivetkGnedghiilrGGkk.pnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlev 276
                                                +G++a+v t+Gn+d+h+ilrGG+k pny+a+dv+++ ++l   gl+++l++d+sh+ns k ++rq ev
  lcl|NCBI__GCF_001484605.1:WP_058931376.1 221 GDGRAALVATAGNPDTHVILRGGRKgPNYSAADVESASAKLAGKGLNPRLIVDASHANSGKSHHRQAEV 289
                                               ********************************************************************* PP

                                 TIGR00034 277 aesvveqiaeG...ekaiiGvmiesnleeGnqsl..k......eelkyGksvtdacigwedteallrkl 334
                                               a ++ +q+++G    +ai+Gvm+es+l++G+q+l  +      +el+yG+svtdac++w+ + ++l +l
  lcl|NCBI__GCF_001484605.1:WP_058931376.1 290 ALEIGAQLEDGgeaAQAIAGVMLESFLVGGAQNLdvTehaagrAELVYGQSVTDACMDWDVSVSVLDQL 358
                                               *********99333368***************87432222222589*********************** PP

                                 TIGR00034 335 aeavkerr 342
                                               a++ ++rr
  lcl|NCBI__GCF_001484605.1:WP_058931376.1 359 AASARKRR 366
                                               *9999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (368 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: 00:00:00.01
# Mc/sec: 8.84
//
[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