Alignments for a candidate for aroG in Shewanella amazonensis SB2B

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Shewanella amazonensis SB2B

Align 3-deoxy-7-phosphoheptulonate synthase, Trp-sensitive (EC 2.5.1.54) (characterized)
to candidate 6937933 Sama_2074 phospho-2-dehydro-3-deoxyheptonate aldolase (RefSeq)

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



>FitnessBrowser__SB2B:6937933
          Length = 353

 Score =  451 bits (1159), Expect = e-131
 Identities = 219/345 (63%), Positives = 267/345 (77%)

Query: 3   RTDELRTARIESLVTPAELALRYPVTPGVATHVTDSRRRIEKILNGEDKRLLVIIGPCSI 62
           +TDELRT+ +  +++P++LA  YP+T   A ++   RR +E IL G+DKRLLVIIGPCSI
Sbjct: 4   KTDELRTSLLCKVISPSQLAAEYPLTQEAADYLVAQRREVEAILTGQDKRLLVIIGPCSI 63

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

Query: 123 ELARKLLLQVNELGVPTATEFLDMVTGQFIADLISWGAIGARTTESQIHREMASALSCPV 182
            LAR LL Q+ EL +P ATEFLDMV GQ+IADLI+WGAIGARTTESQIHREMASALSCPV
Sbjct: 124 RLARHLLQQITELKLPIATEFLDMVNGQYIADLITWGAIGARTTESQIHREMASALSCPV 183

Query: 183 GFKNGTDGNTRIAVDAIRAARASHMFLSPDKNGQMTIYQTSGNPYGHIIMRGGKKPNYHA 242
           GFKNGTDGN  IAVDA+RAA+  H+F SPDK+G M++Y+T GNPYGHII+RGGK PNY  
Sbjct: 184 GFKNGTDGNINIAVDAVRAAKVPHIFYSPDKDGHMSVYRTHGNPYGHIILRGGKNPNYAQ 243

Query: 243 DDIAAACDTLHEFDLPEHLVVDFSHGNCQKQHRRQLEVCEDICQQIRNGSTAIAGIMAES 302
           + +  A + L    +   +V+DFSHGN QKQH++QLEV E++  QIR GSTAIAGIMAES
Sbjct: 244 EHVQKAHEQLKATGIDTGMVIDFSHGNSQKQHKKQLEVAENVMAQIRAGSTAIAGIMAES 303

Query: 303 FLREGTQKIVGSQPLTYGQSITDPCLGWEDTERLVEKLASAVDTR 347
           F+ EG Q +V  QPL YG+SITD CL W DTE L+  LA+A   R
Sbjct: 304 FIEEGNQAVVEGQPLCYGKSITDACLSWGDTEPLLRNLAAAARVR 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: 408
Number of extensions: 8
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 6937933 Sama_2074 (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.13084.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.1e-163  528.9   0.0   2.5e-163  528.7   0.0    1.0  1  lcl|FitnessBrowser__SB2B:6937933  Sama_2074 phospho-2-dehydro-3-de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6937933  Sama_2074 phospho-2-dehydro-3-deoxyheptonate aldolase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  528.7   0.0  2.5e-163  2.5e-163       1     341 [.       6     348 ..       6     349 .. 0.99

  Alignments for each domain:
  == domain 1  score: 528.7 bits;  conditional E-value: 2.5e-163
                         TIGR00034   1 ddlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakrlkklaek 77 
                                       d+lr+  + ++++P++l+a++plt++aa+ +  +r+e++ il+G+d+rllv+iGPcsihd eaaleya rl+kl ++
  lcl|FitnessBrowser__SB2B:6937933   6 DELRTSLLCKVISPSQLAAEYPLTQEAADYLVAQRREVEAILTGQDKRLLVIIGPCSIHDTEAALEYAGRLAKLHHE 82 
                                       688999999******************************************************************** PP

                         TIGR00034  78 lkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatelldtispqyladllsw 154
                                       lkddl i+mrvyfekPrt+vGWkGli+dPdl++sf+ nkGlr+ar+ll +++el lp+ate+ld++ +qy+adl++w
  lcl|FitnessBrowser__SB2B:6937933  83 LKDDLCILMRVYFEKPRTIVGWKGLISDPDLDGSFSANKGLRLARHLLQQITELKLPIATEFLDMVNGQYIADLITW 159
                                       ***************************************************************************** PP

                         TIGR00034 155 gaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvtkaGqvaivetkGnedghiilrGG 231
                                       gaiGarttesq+hre+as+ls+pvgfkngtdG++++a+da+raa+ +h+f s++k+G++++++t+Gn++ghiilrGG
  lcl|FitnessBrowser__SB2B:6937933 160 GAIGARTTESQIHREMASALSCPVGFKNGTDGNINIAVDAVRAAKVPHIFYSPDKDGHMSVYRTHGNPYGHIILRGG 236
                                       ***************************************************************************** PP

                         TIGR00034 232 kkpnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlevaesvveqiaeGekaiiGvmiesnleeGnqsl. 307
                                       k+pny +e+v++++e+l+++g    ++idfshgns+k++k+qlevae+v++qi+ G++ai+G+m es++eeGnq + 
  lcl|FitnessBrowser__SB2B:6937933 237 KNPNYAQEHVQKAHEQLKATGIDTGMVIDFSHGNSQKQHKKQLEVAENVMAQIRAGSTAIAGIMAESFIEEGNQAVv 313
                                       ***************************************************************************98 PP

                         TIGR00034 308 .keelkyGksvtdacigwedteallrklaeavker 341
                                        +++l yGks+tdac++w dte llr+la+a + r
  lcl|FitnessBrowser__SB2B:6937933 314 eGQPLCYGKSITDACLSWGDTEPLLRNLAAAARVR 348
                                       8899*************************998877 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: 8.79
//
[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