GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroG in Epibacterium ulvae U95

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_090221190.1 CV091_RS19330 3-deoxy-7-phosphoheptulonate synthase

Query= BRENDA::C3TIE2
         (350 letters)



>NCBI__GCF_002796795.1:WP_090221190.1
          Length = 356

 Score =  410 bits (1053), Expect = e-119
 Identities = 207/349 (59%), Positives = 255/349 (73%), Gaps = 1/349 (0%)

Query: 1   MNYQNDDLRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGP 60
           M ++  +LRI  ++EL  P  L+ + PA+  A  TV H+R AI  IL+G DDRL+VV+GP
Sbjct: 1   MPHKTANLRITAMQELASPETLIAELPASSVALETVVHSRTAIQNILQGQDDRLIVVVGP 60

Query: 61  CSIHDPVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQIN 120
           CSIHDP AA +YA RLL L++EL D+LEIVMRVYFEKPRT  GWKGLINDP +D SFQIN
Sbjct: 61  CSIHDPSAALDYARRLLPLKQELGDQLEIVMRVYFEKPRTIGGWKGLINDPGLDESFQIN 120

Query: 121 DGLRIARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLS 180
           DGL++AR L  +IN  GLP   EFLD   PQY++DL++W AIGARTTESQ+HRE+ASGLS
Sbjct: 121 DGLKLARSLCEEINALGLPVGTEFLDASVPQYISDLVAWAAIGARTTESQIHREMASGLS 180

Query: 181 CPVGFKNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPN 240
           CPVGFKNGT G +++AIDA+ +A  PH F++++K G +AI  T+GN DCHIILRGG   N
Sbjct: 181 CPVGFKNGTRGNVQIAIDAVRSAARPHHFMALSKTGRAAIAGTAGNPDCHIILRGGGGTN 240

Query: 241 YSAKHVAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVM 300
           + A  V        K G+  QVMID SHANS K  +KQ +V ADV  Q+A G+  I GVM
Sbjct: 241 FDADSVDAACRIAEKDGIRGQVMIDASHANSGKDPEKQPEVLADVGGQMAAGDTRITGVM 300

Query: 301 VESHLVEGNQSLESGEPLAYGKSITDACIGWEDTDALLRQLANAVKARR 349
           +ESHLV GNQ L   +PL YG+SITD CIGW+DT A L +LA AV  RR
Sbjct: 301 IESHLVAGNQKL-GEDPLTYGQSITDGCIGWQDTVAELHKLAEAVSRRR 348


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: 404
Number of extensions: 7
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: 356
Length adjustment: 29
Effective length of query: 321
Effective length of database: 327
Effective search space:   104967
Effective search space used:   104967
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_090221190.1 CV091_RS19330 (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.2505605.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.9e-155  502.8   0.0   2.2e-155  502.6   0.0    1.0  1  NCBI__GCF_002796795.1:WP_090221190.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002796795.1:WP_090221190.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  502.6   0.0  2.2e-155  2.2e-155       2     342 .]       7     348 ..       6     348 .. 0.99

  Alignments for each domain:
  == domain 1  score: 502.6 bits;  conditional E-value: 2.2e-155
                             TIGR00034   2 dlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakrlkkl 74 
                                           +lri++++el++Pe+l+a+ p+++ a e+v +sr++i++il+G+ddrl+vv+GPcsihdp+aal+ya+rl +l
  NCBI__GCF_002796795.1:WP_090221190.1   7 NLRITAMQELASPETLIAELPASSVALETVVHSRTAIQNILQGQDDRLIVVVGPCSIHDPSAALDYARRLLPL 79 
                                           689********************************************************************** PP

                             TIGR00034  75 aeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatelldtispqy 147
                                           +++l d+leivmrvyfekPrt+ GWkGlindP l+esf++n+Gl++ar l  +++ lglp++te+ld+  pqy
  NCBI__GCF_002796795.1:WP_090221190.1  80 KQELGDQLEIVMRVYFEKPRTIGGWKGLINDPGLDESFQINDGLKLARSLCEEINALGLPVGTEFLDASVPQY 152
                                           ************************************************************************* PP

                             TIGR00034 148 ladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvtkaGqvaivetkG 220
                                           ++dl++w+aiGarttesq+hre+asgls+pvgfkngt G++++aida+r+aa++h+f++ +k+G++ai  t+G
  NCBI__GCF_002796795.1:WP_090221190.1 153 ISDLVAWAAIGARTTESQIHREMASGLSCPVGFKNGTRGNVQIAIDAVRSAARPHHFMALSKTGRAAIAGTAG 225
                                           ************************************************************************* PP

                             TIGR00034 221 nedghiilrGGkkpnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlevaesvveqiaeGekaiiG 293
                                           n+d+hiilrGG  +n+da++v+++++  ek g + ++mid+sh+ns kd ++q+ev ++v  q+a G++ i+G
  NCBI__GCF_002796795.1:WP_090221190.1 226 NPDCHIILRGGGGTNFDADSVDAACRIAEKDGIRGQVMIDASHANSGKDPEKQPEVLADVGGQMAAGDTRITG 298
                                           ************************************************************************* PP

                             TIGR00034 294 vmiesnleeGnqsl.keelkyGksvtdacigwedteallrklaeavkerr 342
                                           vmies+l+ Gnq+l +++l+yG+s+td cigw+dt a l+klaeav++rr
  NCBI__GCF_002796795.1:WP_090221190.1 299 VMIESHLVAGNQKLgEDPLTYGQSITDGCIGWQDTVAELHKLAEAVSRRR 348
                                           **************8889****************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (356 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 14.42
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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:

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:

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:

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:

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