Alignments for a candidate for aroE in Pyrolobus fumarii 1A

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroE in Pyrolobus fumarii 1A

Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25) (characterized)
to candidate WP_083818495.1 PYRFU_RS03905 shikimate dehydrogenase

Query= BRENDA::O27957
         (269 letters)



>NCBI__GCF_000223395.1:WP_083818495.1
          Length = 301

 Score =  174 bits (441), Expect = 2e-48
 Identities = 107/276 (38%), Positives = 155/276 (56%), Gaps = 17/276 (6%)

Query: 5   GVIGYPIKHSVSPAMHNAALQHEGIEGIYLAFEVKPDRLRDAVFGAKALGFRGLNVTIPF 64
           G+IG+P+  S+SP +H +  +  G+E +YL ++V+   +   V G + L   G NVTIP 
Sbjct: 20  GLIGHPVAQSLSPVIHESVYRKVGVEAVYLLWDVEGREVHFVVEGLRNLA-NGFNVTIPH 78

Query: 65  KESVVEFVELEGEAAKIKTVNTIDLVEMVG-----YNTDVYGVKAALSGTELGGKTALVV 119
           KE V      + E++++  +  ++ V++ G     +NTDVYGV+  L G    G T LV+
Sbjct: 79  KERVR--AHCDSESSEVSILGAVNTVKVEGAKLHCFNTDVYGVERCLRGLASDGFTMLVL 136

Query: 120 GAGGAGKAAALALLDMG-STVIVANRTEEKGREAVEMLRRYG---ECIFWPLSRVEELKG 175
           GAGGA KAA LA   +G STVI++NRT  +  +   +    G     + WP  R  E   
Sbjct: 137 GAGGAAKAAVLAAQHLGASTVIISNRTRSRAVQLAGIAEALGLRARVVAWPPPR--EAIE 194

Query: 176 KVDVVVNATPLGMRGFKAEIPVPPSMLDGVELVFDTVYNPMETPLIREAKKRGCKVVYGI 235
           + DV+ NATPLGM G     PV    +    +VFD +Y P+ETPLIR A++R  + V G+
Sbjct: 195 EADVLFNATPLGMEGVGGAPPVDTDAISPKHVVFDAIYKPLETPLIRAARERNARTVDGL 254

Query: 236 EMLVHQGAKAFEIWTGIEPD---VGVMREAALRALR 268
            MLV Q  +A  IW GI+P        R+AAL AL+
Sbjct: 255 CMLVWQALEADRIWLGIDPSEKLYQAARKAALEALQ 290


Lambda     K      H
   0.320    0.139    0.401 

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: 236
Number of extensions: 10
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: 269
Length of database: 301
Length adjustment: 26
Effective length of query: 243
Effective length of database: 275
Effective search space:    66825
Effective search space used:    66825
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: 47 (22.7 bits)

Align candidate WP_083818495.1 PYRFU_RS03905 (shikimate dehydrogenase)
to HMM TIGR00507 (aroE: shikimate dehydrogenase (EC 1.1.1.25))

# 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/TIGR00507.hmm
# target sequence database:        /tmp/gapView.5292.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00507  [M=270]
Accession:   TIGR00507
Description: aroE: shikimate dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    5.7e-67  211.7   0.0      7e-67  211.4   0.0    1.0  1  lcl|NCBI__GCF_000223395.1:WP_083818495.1  PYRFU_RS03905 shikimate dehydrog


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000223395.1:WP_083818495.1  PYRFU_RS03905 shikimate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.4   0.0     7e-67     7e-67       2     264 ..      18     280 ..      17     289 .. 0.93

  Alignments for each domain:
  == domain 1  score: 211.4 bits;  conditional E-value: 7e-67
                                 TIGR00507   2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlel 70 
                                               l+g+iG+p+++S+sp+ih+ + ++ g+e +Yl  +ve  e++ +++g+++l ++G+nvT+P+Ke+v + 
  lcl|NCBI__GCF_000223395.1:WP_083818495.1  18 LYGLIGHPVAQSLSPVIHESVYRKVGVEAVYLLWDVEGREVHFVVEGLRNL-ANGFNVTIPHKERVRAH 85 
                                               79**********************************************999.69*************** PP

                                 TIGR00507  71 lDeieesakligavNTlkledgklvgynTDgiGlvssLeklsklksekrvliiGAGGaakavaleLlka 139
                                               +D  + ++  +gavNT+k+e+ kl   nTD++G+   L+ l    ++ ++l++GAGGaaka++l+ ++ 
  lcl|NCBI__GCF_000223395.1:WP_083818495.1  86 CDSESSEVSILGAVNTVKVEGAKLHCFNTDVYGVERCLRGLA--SDGFTMLVLGAGGAAKAAVLAAQHL 152
                                               ****************************************54..4579****************99999 PP

                                 TIGR00507 140 .dkeviiaNRtvekaeelaerlqe...lgeilalsleevelkkvdliinatsaglsgeideaevkaell 204
                                                 ++vii NRt ++a +la   ++      ++a++  +   ++ d++ nat++g++g    ++v+++ +
  lcl|NCBI__GCF_000223395.1:WP_083818495.1 153 gASTVIISNRTRSRAVQLAGIAEAlglRARVVAWPPPREAIEEADVLFNATPLGMEGVGGAPPVDTDAI 221
                                               6799**************999999444557899**9*********************999********* PP

                                 TIGR00507 205 kegklvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvfea 264
                                               + +++v+D +y+pletpl++ a++++++++dGl Mlv Qa+ + ++w g+ p  +  ++a
  lcl|NCBI__GCF_000223395.1:WP_083818495.1 222 SPKHVVFDAIYKPLETPLIRAARERNARTVDGLCMLVWQALEADRIWLGIDPSEK-LYQA 280
                                               *************************************************998643.3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (301 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: 9.70
//
[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