Alignments for a candidate for aroG in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Shewanella oneidensis MR-1

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate 200536 SO1361 phospho-2-dehydro-3-deoxyheptonate aldolase, tyr-sensitive (NCBI ptt file)

Query= BRENDA::P00888
         (356 letters)



>FitnessBrowser__MR1:200536
          Length = 363

 Score =  463 bits (1192), Expect = e-135
 Identities = 223/354 (62%), Positives = 281/354 (79%)

Query: 1   MQKDALNNVHITDEQVLMTPEQLKAAFPLSLQQEAQIADSRKSISDIIAGRDPRLLVVCG 60
           MQ+D +NNVHI+ E VL+TP++LKAA PLS      I ++RK+++DI+  RD R+L++ G
Sbjct: 1   MQQDTINNVHISSENVLITPQELKAALPLSEHAYRYILNARKTVADIVHKRDNRVLIITG 60

Query: 61  PCSIHDPETALEYARRFKALAAEVSDSLYLVMRVYFEKPRTTVGWKGLINDPHMDGSFDV 120
           PCSIHD + A EYA + K L  E+SD  Y++MRVYFEKPRTTVGWKG+INDP MDGSFDV
Sbjct: 61  PCSIHDIDAAKEYALKLKKLHDELSDEFYILMRVYFEKPRTTVGWKGMINDPDMDGSFDV 120

Query: 121 EAGLQIARKLLLELVNMGLPLATEALDPNSPQYLGDLFSWSAIGARTTESQTHREMASGL 180
           E GL++AR+L++ L  + LP+ATEALDP SPQY+ +L +WSAIGARTTESQTHREMASGL
Sbjct: 121 EKGLKLARELMIWLAELELPVATEALDPISPQYISELVTWSAIGARTTESQTHREMASGL 180

Query: 181 SMPVGFKNGTDGSLATAINAMRAAAQPHRFVGINQAGQVALLQTQGNPDGHVILRGGKAP 240
           SMPVGFKNGTDG L  AINA+++AA  HRF+GINQ GQVALLQT GNPDGHVILRGG  P
Sbjct: 181 SMPVGFKNGTDGKLDVAINALKSAASSHRFMGINQQGQVALLQTAGNPDGHVILRGGVTP 240

Query: 241 NYSPADVAQCEKEMEQAGLRPSLMVDCSHGNSNKDYRRQPAVAESVVAQIKDGNRSIIGL 300
           NY  A VA+CE ++ +A L   L++DCSHGNS+KDY RQ  V E V AQI +GN+SIIG+
Sbjct: 241 NYDAASVAECEAQLHKAKLNARLIIDCSHGNSSKDYARQVPVCEDVFAQIYNGNKSIIGV 300

Query: 301 MIESNIHEGNQSSEQPRSEMKYGVSVTDACISWEMTDALLREIHQDLNGQLTAR 354
           M+ES+++EGNQS ++P  E+ YGVSVTD+CI+WE T+++LR     L+  L  R
Sbjct: 301 MLESHLNEGNQSCDKPSGELAYGVSVTDSCINWEKTESVLRAGASKLSSVLPTR 354


Lambda     K      H
   0.316    0.131    0.378 

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: 426
Number of extensions: 6
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: 356
Length of database: 363
Length adjustment: 29
Effective length of query: 327
Effective length of database: 334
Effective search space:   109218
Effective search space used:   109218
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate 200536 SO1361 (phospho-2-dehydro-3-deoxyheptonate aldolase, tyr-sensitive (NCBI ptt file))
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.23222.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   6.8e-158  510.8   0.0     8e-158  510.6   0.0    1.0  1  lcl|FitnessBrowser__MR1:200536  SO1361 phospho-2-dehydro-3-deoxy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:200536  SO1361 phospho-2-dehydro-3-deoxyheptonate aldolase, tyr-sensitive (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  510.6   0.0    8e-158    8e-158       4     337 ..      10     346 ..       4     351 .. 0.96

  Alignments for each domain:
  == domain 1  score: 510.6 bits;  conditional E-value: 8e-158
                       TIGR00034   4 rivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakrlkklaeklkddl 82 
                                     +i + + l+tP+elka+ pl+e+a   + ++rk++adi++ +d+r+l++ GPcsihd  aa+eya +lkkl ++l+d++
  lcl|FitnessBrowser__MR1:200536  10 HISSENVLITPQELKAALPLSEHAYRYILNARKTVADIVHKRDNRVLIITGPCSIHDIDAAKEYALKLKKLHDELSDEF 88 
                                     344446688********************************************************************** PP

                       TIGR00034  83 eivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatelldtispqyladllswgaiGart 161
                                     +i+mrvyfekPrttvGWkG+indPd+++sfdv+kGl++ar+l++ l+el+lp+ate+ld+ispqy+++l++w+aiGart
  lcl|FitnessBrowser__MR1:200536  89 YILMRVYFEKPRTTVGWKGMINDPDMDGSFDVEKGLKLARELMIWLAELELPVATEALDPISPQYISELVTWSAIGART 167
                                     ******************************************************************************* PP

                       TIGR00034 162 tesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvtkaGqvaivetkGnedghiilrGGkkpnydaed 240
                                     tesq+hre+asgls+pvgfkngtdG+l vai+a+++aa++h+f++++++Gqva+++t+Gn+dgh+ilrGG +pnyda++
  lcl|FitnessBrowser__MR1:200536 168 TESQTHREMASGLSMPVGFKNGTDGKLDVAINALKSAASSHRFMGINQQGQVALLQTAGNPDGHVILRGGVTPNYDAAS 246
                                     ******************************************************************************* PP

                       TIGR00034 241 vaevkeelekaglkeelmidfshgnsnkdykrqlevaesvveqiaeGekaiiGvmiesnleeGnqsl...keelkyGks 316
                                     vae++++l+ka+l+++l+id+shgns+kdy rq+ v+e+v +qi +G+k+iiGvm+es+l+eGnqs    + el+yG+s
  lcl|FitnessBrowser__MR1:200536 247 VAECEAQLHKAKLNARLIIDCSHGNSSKDYARQVPVCEDVFAQIYNGNKSIIGVMLESHLNEGNQSCdkpSGELAYGVS 325
                                     *****************************************************************994334579***** PP

                       TIGR00034 317 vtdacigwedteallrklaea 337
                                     vtd+ci+we+te++lr  a++
  lcl|FitnessBrowser__MR1:200536 326 VTDSCINWEKTESVLRAGASK 346
                                     ***************986665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (363 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: 10.14
//
[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