Alignments for a candidate for aroE in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroE in Pseudomonas stutzeri RCH2

Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25) (characterized)
to candidate GFF29 Psest_0029 shikimate 5-dehydrogenase

Query= BRENDA::Q88RQ5
         (274 letters)



>FitnessBrowser__psRCH2:GFF29
          Length = 270

 Score =  383 bits (983), Expect = e-111
 Identities = 197/272 (72%), Positives = 220/272 (80%), Gaps = 2/272 (0%)

Query: 1   MDQYVVFGNPIGHSKSPLIHRLFAEQTGQDLEYATLLAPLDEFSDCARGFFKQGSGGNVT 60
           MD+Y VFGNPIGHSKSP IH LFA QTGQ L Y  LLAPLD+F   AR FF+ G G NVT
Sbjct: 1   MDRYGVFGNPIGHSKSPQIHALFAAQTGQVLRYEALLAPLDDFVGFARAFFQDGLGANVT 60

Query: 61  VPFKEEAFRLCDSLTPRARRAGAVNTLSKLADGTLQGDNTDGAGLVRDLTVNAGVELAGK 120
           VPFKE+A+R+ D LT RARRAGAVNTL KL DG L GDNTDGAGLV DL ++AGV L G+
Sbjct: 61  VPFKEQAYRMTDQLTERARRAGAVNTLKKLEDGHLLGDNTDGAGLVSDL-LHAGVALRGR 119

Query: 121 RILILGAGGAVRGVLEPILAHKPQSLVIANRTVEKAEQLAREFDELGPVVASGFAWLQEP 180
           RIL+LGAGGAVRG LEP+LA +P +L+IANRTV KAEQLA+EF ELGP+ AS F  L EP
Sbjct: 120 RILLLGAGGAVRGALEPLLAQRPAALIIANRTVSKAEQLAQEFAELGPLSASTFTDLAEP 179

Query: 181 VDVIINATSASLAGELPPIADSLVEAGRTVCYDMMYGKEPTPFCQWATKLGAAKVLDGLG 240
           VD+IIN TSASL GELPP+ADSL++ G T CYDMMY  +PT FCQWA  LG A   DGLG
Sbjct: 180 VDLIINGTSASLGGELPPLADSLIQPGHTFCYDMMYAAKPTAFCQWAAALG-ADTRDGLG 238

Query: 241 MLAEQAAEAFFIWRGVRPDTAPVLAELRRQLA 272
           ML EQAAEAF +WRGVRPDTAPVLAELRRQL+
Sbjct: 239 MLVEQAAEAFELWRGVRPDTAPVLAELRRQLS 270


Lambda     K      H
   0.319    0.137    0.405 

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: 282
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: 274
Length of database: 270
Length adjustment: 25
Effective length of query: 249
Effective length of database: 245
Effective search space:    61005
Effective search space used:    61005
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 GFF29 Psest_0029 (shikimate 5-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.24727.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    7.5e-83  263.8   0.0    8.3e-83  263.6   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF29  Psest_0029 shikimate 5-dehydroge


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF29  Psest_0029 shikimate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  263.6   0.0   8.3e-83   8.3e-83       3     269 ..       4     269 ..       2     270 .] 0.95

  Alignments for each domain:
  == domain 1  score: 263.6 bits;  conditional E-value: 8.3e-83
                         TIGR00507   3 lgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlellDeieesak 79 
                                       +gv+Gnpi hSksp ih  +++q+g+ l+Y a+ ++++++  +  ++++ gl G+nvTvPfKe+++++ D+++e+a+
  lcl|FitnessBrowser__psRCH2:GFF29   4 YGVFGNPIGHSKSPQIHALFAAQTGQVLRYEALLAPLDDFVGFARAFFQDGL-GANVTVPFKEQAYRMTDQLTERAR 79 
                                       9***********************************************9996.************************ PP

                         TIGR00507  80 ligavNTlk.ledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaakavaleLlka.dkeviiaNRtveka 153
                                        +gavNTlk ledg+l+g+nTDg Glvs+L +    l+ ++r+l++GAGGa ++++ +Ll + + ++iiaNRtv+ka
  lcl|FitnessBrowser__psRCH2:GFF29  80 RAGAVNTLKkLEDGHLLGDNTDGAGLVSDLLHaGVALR-GRRILLLGAGGAVRGALEPLLAQrPAALIIANRTVSKA 155
                                       *********9*********************9556666.*******************9988799************ PP

                         TIGR00507 154 eelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkaellkegk.lvvDlvynpletpllkeakkk 229
                                       e+la++++elg   a    ++  + vdliin tsa+l ge+  +++  +l++ g+ +++D++y+ + t++ ++a  +
  lcl|FitnessBrowser__psRCH2:GFF29 156 EQLAQEFAELGPLSASTFTDLA-EPVDLIINGTSASLGGEL--PPLADSLIQPGHtFCYDMMYAAKPTAFCQWAAAL 229
                                       ***********99998877664.45****************..9******998752689****************** PP

                         TIGR00507 230 gtkvidGlgMlvaQaalsFelwtgvepdvekvfealkekl 269
                                       g+ + dGlgMlv+Qaa +Felw+gv pd   v   l+++l
  lcl|FitnessBrowser__psRCH2:GFF29 230 GADTRDGLGMLVEQAAEAFELWRGVRPDTAPVLAELRRQL 269
                                       *******************************999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (270 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: 9.18
//
[ok]

This GapMind analysis is from Apr 09 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