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 (EC 2.5.1.54) (characterized)
to candidate 5208556 Shew_1067 phospho-2-dehydro-3-deoxyheptonate aldolase (RefSeq)

Query= BRENDA::P00888
         (356 letters)



>FitnessBrowser__PV4:5208556
          Length = 363

 Score =  466 bits (1200), Expect = e-136
 Identities = 227/356 (63%), Positives = 282/356 (79%)

Query: 1   MQKDALNNVHITDEQVLMTPEQLKAAFPLSLQQEAQIADSRKSISDIIAGRDPRLLVVCG 60
           MQ+D +NNVHI+ E+VL+TPE+LK   PLS      + ++R+++SDI+  RD R+LVV G
Sbjct: 1   MQQDTINNVHISSEKVLVTPEELKQQLPLSTAAYHYVLNARRTVSDIVHKRDNRVLVVSG 60

Query: 61  PCSIHDPETALEYARRFKALAAEVSDSLYLVMRVYFEKPRTTVGWKGLINDPHMDGSFDV 120
           PCSIHD  +A EYA R K L  E+ D  Y++MRVYFEKPRTTVGWKG+INDP MD SFDV
Sbjct: 61  PCSIHDIASAKEYALRLKTLHDELKDEFYILMRVYFEKPRTTVGWKGMINDPDMDESFDV 120

Query: 121 EAGLQIARKLLLELVNMGLPLATEALDPNSPQYLGDLFSWSAIGARTTESQTHREMASGL 180
           E GL+ AR+L++ L  +GLP+ATEALDP SPQY+ +L +WSAIGARTTESQTHREMASGL
Sbjct: 121 EKGLRQARELMIWLAELGLPVATEALDPISPQYISELVTWSAIGARTTESQTHREMASGL 180

Query: 181 SMPVGFKNGTDGSLATAINAMRAAAQPHRFVGINQAGQVALLQTQGNPDGHVILRGGKAP 240
           SMPVGFKNGTDG L  AINA+++AA  HRF+GINQAGQVALLQT GNPDGHVILRGGK P
Sbjct: 181 SMPVGFKNGTDGKLGVAINALQSAASSHRFMGINQAGQVALLQTAGNPDGHVILRGGKTP 240

Query: 241 NYSPADVAQCEKEMEQAGLRPSLMVDCSHGNSNKDYRRQPAVAESVVAQIKDGNRSIIGL 300
           NY  + VA+CE+++  A L   L+VDCSHGNS+KD+ RQP+V + V  QI +GN+SIIG+
Sbjct: 241 NYDASSVAECEQQLHAAKLNARLVVDCSHGNSSKDHTRQPSVCQDVFDQIANGNKSIIGV 300

Query: 301 MIESNIHEGNQSSEQPRSEMKYGVSVTDACISWEMTDALLREIHQDLNGQLTARVA 356
           M+ES+++EGNQSS++P SE+ YGVSVTDACI W+ T+ LLR+    L   L  R A
Sbjct: 301 MLESHLNEGNQSSDKPMSELAYGVSVTDACIDWQTTEDLLRQGAAQLASVLPGRFA 356


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: 423
Number of extensions: 5
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 5208556 Shew_1067 (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.5072.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   3.2e-160  518.4   0.1   3.8e-160  518.2   0.1    1.0  1  lcl|FitnessBrowser__PV4:5208556  Shew_1067 phospho-2-dehydro-3-de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5208556  Shew_1067 phospho-2-dehydro-3-deoxyheptonate aldolase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  518.2   0.1  3.8e-160  3.8e-160       4     338 ..      10     347 ..       4     351 .. 0.96

  Alignments for each domain:
  == domain 1  score: 518.2 bits;  conditional E-value: 3.8e-160
                        TIGR00034   4 rivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakrlkklaeklkdd 81 
                                      +i + + l+tPeelk++ pl+++a + v ++r++++di++ +d+r+lvv GPcsihd  +a+eya rlk+l ++lkd+
  lcl|FitnessBrowser__PV4:5208556  10 HISSEKVLVTPEELKQQLPLSTAAYHYVLNARRTVSDIVHKRDNRVLVVSGPCSIHDIASAKEYALRLKTLHDELKDE 87 
                                      344446688********************************************************************* PP

                        TIGR00034  82 leivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatelldtispqyladllswgaiGa 159
                                      ++i+mrvyfekPrttvGWkG+indPd++esfdv+kGlr ar+l++ l+elglp+ate+ld+ispqy+++l++w+aiGa
  lcl|FitnessBrowser__PV4:5208556  88 FYILMRVYFEKPRTTVGWKGMINDPDMDESFDVEKGLRQARELMIWLAELGLPVATEALDPISPQYISELVTWSAIGA 165
                                      ****************************************************************************** PP

                        TIGR00034 160 rttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvtkaGqvaivetkGnedghiilrGGkkpnyd 237
                                      rttesq+hre+asgls+pvgfkngtdG+l vai+a+++aa++h+f+++++aGqva+++t+Gn+dgh+ilrGGk+pnyd
  lcl|FitnessBrowser__PV4:5208556 166 RTTESQTHREMASGLSMPVGFKNGTDGKLGVAINALQSAASSHRFMGINQAGQVALLQTAGNPDGHVILRGGKTPNYD 243
                                      ****************************************************************************** PP

                        TIGR00034 238 aedvaevkeelekaglkeelmidfshgnsnkdykrqlevaesvveqiaeGekaiiGvmiesnleeGnqsl...keelk 312
                                      a++vae++++l++a+l+++l++d+shgns+kd+ rq++v+++v +qia+G+k+iiGvm+es+l+eGnqs+    +el+
  lcl|FitnessBrowser__PV4:5208556 244 ASSVAECEQQLHAAKLNARLVVDCSHGNSSKDHTRQPSVCQDVFDQIANGNKSIIGVMLESHLNEGNQSSdkpMSELA 321
                                      *********************************************************************943345789 PP

                        TIGR00034 313 yGksvtdacigwedteallrklaeav 338
                                      yG+svtdaci+w++te+llr+ a+++
  lcl|FitnessBrowser__PV4:5208556 322 YGVSVTDACIDWQTTEDLLRQGAAQL 347
                                      ********************977665 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: 11.16
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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