Alignments for a candidate for aroE in Methylocapsa acidiphila B2

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroE in Methylocapsa acidiphila B2

Align shikimate dehydrogenase (EC 1.1.1.25) (characterized)
to candidate WP_026607795.1 METAC_RS0115810 shikimate dehydrogenase

Query= reanno::Caulo:CCNA_00003
         (285 letters)



>NCBI__GCF_000427445.1:WP_026607795.1
          Length = 283

 Score =  185 bits (470), Expect = 9e-52
 Identities = 118/266 (44%), Positives = 145/266 (54%), Gaps = 6/266 (2%)

Query: 14  VCGQPIKHSMSPVIHNAWIAAAGLDAAYVPFAPAADRFETFVDGLRGGAVRGLNVTIPFK 73
           + G P  HS SP+IH  W+A   +  AY       + F  F+  L      G NVT+P K
Sbjct: 13  IIGWPAGHSRSPMIHGFWLAELRIAGAYERAPVPPEDFARFIRNLAANGFVGANVTLPHK 72

Query: 74  ERALAVADTASDLARMAGAANLLVFNEDGSVHADNTDGPGLLGAIAIQAPGFDVTAAPVV 133
           E A A+ D  ++ A    AAN L + EDG +H DNTD  G L A+   APG+   +   V
Sbjct: 73  EAAFALCDRTTETAAKLRAANTL-WIEDGELHGDNTDVEGFLAALDQDAPGWADRSGKAV 131

Query: 134 ILGAGGAARGAVAALLLAGAPRIAVVNRTVARAQDLADTFGEKVVAKGEDALPALLPEAG 193
           +LGAGGAAR  V ALL  G  RI +VNRT  RAQ LA+  G  VVA  E    + L EA 
Sbjct: 132 VLGAGGAARAIVHALLSRGVERIVLVNRTKDRAQALAEQAGAGVVA-AEWGDASALAEAD 190

Query: 194 LIINATSLGLGGGAGPSADLTLTPKT--AVVMDMVYKPLRTEFLRRAEAAGRRTVDGLEM 251
           L++N TSLG+ G   P  DL L P +  A V D+VY PL TE LRRA   G R V GL M
Sbjct: 191 LLVNTTSLGMSG--QPPLDLDLAPLSAGATVCDIVYVPLETELLRRARTRGLRGVSGLGM 248

Query: 252 LLRQAIPTFETIYGQAPSPKIDVRVL 277
           LL QA P F   +G  P    ++R L
Sbjct: 249 LLHQAAPGFARWFGAKPCVSPELRAL 274


Lambda     K      H
   0.319    0.136    0.390 

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: 186
Number of extensions: 10
Number of successful extensions: 3
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: 285
Length of database: 283
Length adjustment: 26
Effective length of query: 259
Effective length of database: 257
Effective search space:    66563
Effective search space used:    66563
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_026607795.1 METAC_RS0115810 (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.4172892.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.3e-71  226.9   0.0    1.5e-71  226.7   0.0    1.0  1  NCBI__GCF_000427445.1:WP_026607795.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000427445.1:WP_026607795.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  226.7   0.0   1.5e-71   1.5e-71       4     261 ..      12     270 ..       9     277 .. 0.94

  Alignments for each domain:
  == domain 1  score: 226.7 bits;  conditional E-value: 1.5e-71
                             TIGR00507   4 gviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlellDeiee 76 
                                            +iG p  hS sp+ih   l++l +++ Y + +v++e++ +++ ++ a+g+ G+nvT+P+Ke++++l+D+ +e
  NCBI__GCF_000427445.1:WP_026607795.1  12 CIIGWPAGHSRSPMIHGFWLAELRIAGAYERAPVPPEDFARFIRNLAANGFVGANVTLPHKEAAFALCDRTTE 84 
                                           68*********************************************************************** PP

                             TIGR00507  77 sakligavNTlkledgklvgynTDgiGlvssLek..lsklksekrvliiGAGGaakavaleLlka.dkeviia 146
                                           +a+++ a NTl +edg+l g+nTD++G++++L +    +     +++++GAGGaa+a++ +Ll+   ++++++
  NCBI__GCF_000427445.1:WP_026607795.1  85 TAAKLRAANTLWIEDGELHGDNTDVEGFLAALDQdaPGWADRSGKAVVLGAGGAARAIVHALLSRgVERIVLV 157
                                           **********************************76678888899****************99994578999* PP

                             TIGR00507 147 NRtvekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkaellkegklvvDlvynple 219
                                           NRt+++a++lae+  + g + a   +   l + dl++n+ts+g+sg+     ++   l++g+ v+D+vy ple
  NCBI__GCF_000427445.1:WP_026607795.1 158 NRTKDRAQALAEQAGA-GVVAAEWGDASALAEADLLVNTTSLGMSGQP-PLDLDLAPLSAGATVCDIVYVPLE 228
                                           ************9998.88887778999999***************98.678888999*************** PP

                             TIGR00507 220 tpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekv 261
                                           t ll+ a+ +g + + GlgMl +Qaa  F  w+g +p v+  
  NCBI__GCF_000427445.1:WP_026607795.1 229 TELLRRARTRGLRGVSGLGMLLHQAAPGFARWFGAKPCVSPE 270
                                           ***********************************9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (283 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: 13.72
//
[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