Alignments for a candidate for aroE in Rhodobacter sphaeroides ATCC 17029

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroE in Rhodobacter sphaeroides ATCC 17029

Align shikimate dehydrogenase (EC 1.1.1.25) (characterized)
to candidate WP_011841953.1 RSPH17029_RS14595 shikimate dehydrogenase

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



>NCBI__GCF_000015985.1:WP_011841953.1
          Length = 279

 Score =  200 bits (508), Expect = 3e-56
 Identities = 118/270 (43%), Positives = 147/270 (54%), Gaps = 2/270 (0%)

Query: 11  VGGVCGQPIKHSMSPVIHNAWIAAAGLDAAYVPFAPA-ADRFETFVDGLRGGAVRGLNVT 69
           + GV G PI HS SP +H  W+   GL   Y+P   A AD  +      R G V G NVT
Sbjct: 9   LAGVIGSPIAHSRSPALHGYWLKRYGLKGHYIPMDVAQADLRDVLAAMPRMGFV-GCNVT 67

Query: 70  IPFKERALAVADTASDLARMAGAANLLVFNEDGSVHADNTDGPGLLGAIAIQAPGFDVTA 129
           IP KE  + +AD  +D A + GAAN L+F +DG ++ADNTDG G    +   AP +   +
Sbjct: 68  IPHKESVIGLADIVTDRAALIGAANTLIFRKDGKIYADNTDGTGFTANLRQNAPAWQPQS 127

Query: 130 APVVILGAGGAARGAVAALLLAGAPRIAVVNRTVARAQDLADTFGEKVVAKGEDALPALL 189
            P V+ GAGGAAR  +AAL+  G P I + NR+ ARA  L   FG KV          +L
Sbjct: 128 GPAVVWGAGGAARAVIAALIEVGVPEIRLANRSRARADALRSDFGAKVHVHDWVQAGNIL 187

Query: 190 PEAGLIINATSLGLGGGAGPSADLTLTPKTAVVMDMVYKPLRTEFLRRAEAAGRRTVDGL 249
            +A  ++N TSLG+ G       L      AVV D+VY PLRT  L  AEAAG RTVDGL
Sbjct: 188 EDAMTVVNTTSLGMVGKPEFRVPLDALNPKAVVTDLVYAPLRTRLLVEAEAAGCRTVDGL 247

Query: 250 EMLLRQAIPTFETIYGQAPSPKIDVRVLAL 279
            MLL QA P FE  +G  P    + R   L
Sbjct: 248 GMLLHQAAPGFERWFGVRPEVDEETRAAVL 277


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: 211
Number of extensions: 8
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: 279
Length adjustment: 26
Effective length of query: 259
Effective length of database: 253
Effective search space:    65527
Effective search space used:    65527
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_011841953.1 RSPH17029_RS14595 (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.19245.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
      3e-71  225.7   0.0    3.6e-71  225.5   0.0    1.0  1  lcl|NCBI__GCF_000015985.1:WP_011841953.1  RSPH17029_RS14595 shikimate dehy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015985.1:WP_011841953.1  RSPH17029_RS14595 shikimate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.5   0.0   3.6e-71   3.6e-71       2     261 ..       9     271 ..       8     278 .. 0.94

  Alignments for each domain:
  == domain 1  score: 225.5 bits;  conditional E-value: 3.6e-71
                                 TIGR00507   2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlel 70 
                                               l gviG pi+hS sp++h   lk  gl+++Y+ ++v + +l+++l ++   g+ G+nvT+P+Ke+v+ l
  lcl|NCBI__GCF_000015985.1:WP_011841953.1   9 LAGVIGSPIAHSRSPALHGYWLKRYGLKGHYIPMDVAQADLRDVLAAMPRMGFVGCNVTIPHKESVIGL 77 
                                               679****************************************************************** PP

                                 TIGR00507  71 lDeieesakligavNTlk.ledgklvgynTDgiGlvssLek.lsklks.ekrvliiGAGGaakavaleL 136
                                               +D ++++a+liga NTl  ++dgk++++nTDg G++++L++     ++    +++ GAGGaa+av+ +L
  lcl|NCBI__GCF_000015985.1:WP_011841953.1  78 ADIVTDRAALIGAANTLIfRKDGKIYADNTDGTGFTANLRQnAPAWQPqSGPAVVWGAGGAARAVIAAL 146
                                               *****************9999********************64434431456999************** PP

                                 TIGR00507 137 lka.dkeviiaNRtvekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkaell 204
                                                +    e+ +aNR+ ++a +l + + +  ++  + ++   l+    ++n+ts+g+ g+  e  v+ + l
  lcl|NCBI__GCF_000015985.1:WP_011841953.1 147 IEVgVPEIRLANRSRARADALRSDFGAKVHVHDWVQAGNILEDAMTVVNTTSLGMVGKP-EFRVPLDAL 214
                                               ***5579*******************999999999999999999999*********987.********* PP

                                 TIGR00507 205 kegklvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekv 261
                                               + +++v Dlvy+pl t ll ea+  g++++dGlgMl +Qaa  Fe w+gv p+v++ 
  lcl|NCBI__GCF_000015985.1:WP_011841953.1 215 NPKAVVTDLVYAPLRTRLLVEAEAAGCRTVDGLGMLLHQAAPGFERWFGVRPEVDEE 271
                                               ****************************************************99764 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (279 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: 8.93
//
[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