Alignments for a candidate for aroG in Shewanella sp. ANA-3

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Shewanella sp. ANA-3

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate 7025864 Shewana3_3013 phospho-2-dehydro-3-deoxyheptonate aldolase (RefSeq)

Query= BRENDA::P00888
         (356 letters)



>FitnessBrowser__ANA3:7025864
          Length = 363

 Score =  456 bits (1174), Expect = e-133
 Identities = 221/354 (62%), Positives = 279/354 (78%)

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

Query: 61  PCSIHDPETALEYARRFKALAAEVSDSLYLVMRVYFEKPRTTVGWKGLINDPHMDGSFDV 120
           PCSIHD + A EYA + K L  E+SD  Y++MRVYFEKPRTTVGWKG+INDP MD SFDV
Sbjct: 61  PCSIHDIDAAKEYALKLKQLHDELSDEFYILMRVYFEKPRTTVGWKGMINDPDMDESFDV 120

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

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

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

Query: 301 MIESNIHEGNQSSEQPRSEMKYGVSVTDACISWEMTDALLREIHQDLNGQLTAR 354
           M+ES+++EGNQS ++P SE+ YGVSVTD+CI+WE T+++LR     L+  L  R
Sbjct: 301 MLESHLNEGNQSCDKPLSELAYGVSVTDSCINWEKTESVLRAGASKLSSVLATR 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: 414
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 7025864 Shewana3_3013 (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.30968.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.5e-158  512.9   0.0   1.9e-158  512.7   0.0    1.0  1  lcl|FitnessBrowser__ANA3:7025864  Shewana3_3013 phospho-2-dehydro-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7025864  Shewana3_3013 phospho-2-dehydro-3-deoxyheptonate aldolase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  512.7   0.0  1.9e-158  1.9e-158       4     337 ..      10     346 ..       4     351 .. 0.96

  Alignments for each domain:
  == domain 1  score: 512.7 bits;  conditional E-value: 1.9e-158
                         TIGR00034   4 rivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakrlkklaeklkd 80 
                                       +i + + l+tP+elka  pl+e+a   + ++rk++adi++ +d+r+l+v GPcsihd  aa+eya +lk+l ++l+d
  lcl|FitnessBrowser__ANA3:7025864  10 HISSEKVLITPQELKATLPLSEHAYRYILNARKTVADIVHKRDNRVLIVTGPCSIHDIDAAKEYALKLKQLHDELSD 86 
                                       344446688******************************************************************** PP

                         TIGR00034  81 dleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatelldtispqyladllswgai 157
                                       +++i+mrvyfekPrttvGWkG+indPd++esfdv+kGl++ar+l++ l+el+lp+ate+ld+ispqy+++l++w+ai
  lcl|FitnessBrowser__ANA3:7025864  87 EFYILMRVYFEKPRTTVGWKGMINDPDMDESFDVEKGLKMARELMIWLAELELPVATEALDPISPQYISELVTWSAI 163
                                       ***************************************************************************** PP

                         TIGR00034 158 GarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvtkaGqvaivetkGnedghiilrGGkkp 234
                                       Garttesq+hre+asgls+pvgfkngtdG+l vai+a+++aa++h+f++++++Gqva+++t+Gn+dgh+ilrGG +p
  lcl|FitnessBrowser__ANA3:7025864 164 GARTTESQTHREMASGLSMPVGFKNGTDGKLDVAINALKSAASSHRFMGINQQGQVALLQTAGNPDGHVILRGGATP 240
                                       ***************************************************************************** PP

                         TIGR00034 235 nydaedvaevkeelekaglkeelmidfshgnsnkdykrqlevaesvveqiaeGekaiiGvmiesnleeGnqslke.. 309
                                       nyda++vae++++l+ka+l+++l+id+shgns+kdy rq+ v+e+v +qi +G+k+iiGvm+es+l+eGnqs ++  
  lcl|FitnessBrowser__ANA3:7025864 241 NYDAQSVAECEAQLHKAKLNARLIIDCSHGNSSKDYTRQIPVCEDVFNQIYNGNKSIIGVMLESHLNEGNQSCDKpl 317
                                       ************************************************************************96512 PP

                         TIGR00034 310 .elkyGksvtdacigwedteallrklaea 337
                                        el+yG+svtd+ci+we+te++lr  a++
  lcl|FitnessBrowser__ANA3:7025864 318 sELAYGVSVTDSCINWEKTESVLRAGASK 346
                                       2689*******************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: 9.54
//
[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