Alignments for a candidate for aroG in Shewanella loihica PV-4

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Shewanella loihica PV-4

Align 3-deoxy-7-phosphoheptulonate synthase, Trp-sensitive (EC 2.5.1.54) (characterized)
to candidate 5209069 Shew_1547 phospho-2-dehydro-3-deoxyheptonate aldolase (RefSeq)

Query= ecocyc::AROH-MONOMER
         (348 letters)



>FitnessBrowser__PV4:5209069
          Length = 353

 Score =  462 bits (1190), Expect = e-135
 Identities = 223/345 (64%), Positives = 268/345 (77%)

Query: 3   RTDELRTARIESLVTPAELALRYPVTPGVATHVTDSRRRIEKILNGEDKRLLVIIGPCSI 62
           +TDELRT  +   ++PA+LA  YP+T   A ++   RR +E IL GEDKRLLVIIGPCSI
Sbjct: 4   KTDELRTTLLCKAISPAKLASEYPLTQDAADYLVQQRREVEAILTGEDKRLLVIIGPCSI 63

Query: 63  HDLTAAMEYATRLQSLRNQYQSRLEIVMRTYFEKPRTVVGWKGLISDPDLNGSYRVNHGL 122
           HD  AA++YA RL  L  + +  L I+MR YFEKPRT VGWKGLISDPDL+GS+  N GL
Sbjct: 64  HDTQAAIDYAKRLAVLHKELKDSLCILMRVYFEKPRTTVGWKGLISDPDLDGSFNANKGL 123

Query: 123 ELARKLLLQVNELGVPTATEFLDMVTGQFIADLISWGAIGARTTESQIHREMASALSCPV 182
            LAR LL ++ EL +P ATEFLDMV GQ+IADLI+WGA+GARTTESQIHREMASALSCPV
Sbjct: 124 RLARHLLQEITELNLPIATEFLDMVNGQYIADLITWGAVGARTTESQIHREMASALSCPV 183

Query: 183 GFKNGTDGNTRIAVDAIRAARASHMFLSPDKNGQMTIYQTSGNPYGHIIMRGGKKPNYHA 242
           GFKNGTDGN  IA+DA+RAA+  H+F SPDK+G M +Y+TSGNPYGHII+RGGK+PNYH 
Sbjct: 184 GFKNGTDGNINIAIDAVRAAKEPHIFYSPDKDGAMAVYRTSGNPYGHIILRGGKQPNYHE 243

Query: 243 DDIAAACDTLHEFDLPEHLVVDFSHGNCQKQHRRQLEVCEDICQQIRNGSTAIAGIMAES 302
            DI AA   L +  L   +VVDFSHGN QKQH+RQLEV +DI  Q+ +GSTAIAGIMAES
Sbjct: 244 ADIQAAAQKLKDVGLSHRMVVDFSHGNSQKQHKRQLEVAKDIMTQVASGSTAIAGIMAES 303

Query: 303 FLREGTQKIVGSQPLTYGQSITDPCLGWEDTERLVEKLASAVDTR 347
           F+ EG QK+V  +PL YG+SITD CL W D+E+L+  LA+A   R
Sbjct: 304 FIEEGNQKVVAGEPLIYGKSITDACLDWADSEKLLRDLAAASKAR 348


Lambda     K      H
   0.320    0.135    0.399 

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: 380
Number of extensions: 4
Number of successful extensions: 1
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: 348
Length of database: 353
Length adjustment: 29
Effective length of query: 319
Effective length of database: 324
Effective search space:   103356
Effective search space used:   103356
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: 49 (23.5 bits)

Align candidate 5209069 Shew_1547 (phospho-2-dehydro-3-deoxyheptonate aldolase (RefSeq))
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.8017.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   2.9e-165  535.0   0.0   3.3e-165  534.8   0.0    1.0  1  lcl|FitnessBrowser__PV4:5209069  Shew_1547 phospho-2-dehydro-3-de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5209069  Shew_1547 phospho-2-dehydro-3-deoxyheptonate aldolase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  534.8   0.0  3.3e-165  3.3e-165       1     341 [.       6     348 ..       6     349 .. 0.99

  Alignments for each domain:
  == domain 1  score: 534.8 bits;  conditional E-value: 3.3e-165
                        TIGR00034   1 ddlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakrlkklaekl 78 
                                      d+lr++ + + ++P++l++++plt++aa+ + ++r+e++ il+G+d+rllv+iGPcsihd +aa++yakrl+ l ++l
  lcl|FitnessBrowser__PV4:5209069   6 DELRTTLLCKAISPAKLASEYPLTQDAADYLVQQRREVEAILTGEDKRLLVIIGPCSIHDTQAAIDYAKRLAVLHKEL 83 
                                      678888889999****************************************************************** PP

                        TIGR00034  79 kddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatelldtispqyladllswga 156
                                      kd+l i+mrvyfekPrttvGWkGli+dPdl++sf+ nkGlr+ar+ll +++el+lp+ate+ld++ +qy+adl++wga
  lcl|FitnessBrowser__PV4:5209069  84 KDSLCILMRVYFEKPRTTVGWKGLISDPDLDGSFNANKGLRLARHLLQEITELNLPIATEFLDMVNGQYIADLITWGA 161
                                      ****************************************************************************** PP

                        TIGR00034 157 iGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvtkaGqvaivetkGnedghiilrGGkkp 234
                                      +Garttesq+hre+as+ls+pvgfkngtdG++++aida+raa+++h+f s++k+G++a+++t+Gn++ghiilrGGk+p
  lcl|FitnessBrowser__PV4:5209069 162 VGARTTESQIHREMASALSCPVGFKNGTDGNINIAIDAVRAAKEPHIFYSPDKDGAMAVYRTSGNPYGHIILRGGKQP 239
                                      ****************************************************************************** PP

                        TIGR00034 235 nydaedvaevkeelekaglkeelmidfshgnsnkdykrqlevaesvveqiaeGekaiiGvmiesnleeGnqsl..kee 310
                                      ny+++d++++ ++l+++gl++++++dfshgns+k++krqleva++++ q+a+G++ai+G+m es++eeGnq++  +e+
  lcl|FitnessBrowser__PV4:5209069 240 NYHEADIQAAAQKLKDVGLSHRMVVDFSHGNSQKQHKRQLEVAKDIMTQVASGSTAIAGIMAESFIEEGNQKVvaGEP 317
                                      ************************************************************************98899* PP

                        TIGR00034 311 lkyGksvtdacigwedteallrklaeavker 341
                                      l+yGks+tdac++w d+e+llr+la+a k+r
  lcl|FitnessBrowser__PV4:5209069 318 LIYGKSITDACLDWADSEKLLRDLAAASKAR 348
                                      *************************998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (353 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: 00:00:00.01
# Mc/sec: 8.61
//
[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