Alignments for a candidate for aroB in Synechococcus elongatus PCC 7942

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Synechococcus elongatus PCC 7942

Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate Synpcc7942_0525 Synpcc7942_0525 3-dehydroquinate synthase

Query= BRENDA::Q3M4V2
         (363 letters)



>FitnessBrowser__SynE:Synpcc7942_0525
          Length = 368

 Score =  466 bits (1198), Expect = e-136
 Identities = 240/363 (66%), Positives = 287/363 (79%), Gaps = 2/363 (0%)

Query: 1   MTSVINVNLPTQSYEIAIAPASLDQIGQSL--AGLKLGKKVLLVSNPTIFKHFGKVAVDS 58
           M+  I V LP  +YEIAIA   L   G  L  A LK G K+L+V+NP I + +G   V +
Sbjct: 1   MSVQIPVALPQNAYEIAIANGGLAAAGTWLQQADLKAGTKLLIVTNPAIGRRYGDRLVAA 60

Query: 59  LEAAGFQVASYCLPAGERYKTLNSIQKLYDIALENRLERSSTMVALGGGVIGDMTGFAAA 118
           L+ AGF V    LPAGERYKT  ++Q++YD ALE RLER S +VALGGGVIGDMTGFAAA
Sbjct: 61  LQEAGFIVDCLTLPAGERYKTPATVQRIYDKALELRLERRSALVALGGGVIGDMTGFAAA 120

Query: 119 TWLRGINVVQVPTTLLAMVDSAIGGKTGVNHPHGKNLIGAFHQPRFVLIDPQVLKTLPVR 178
           TWLRGI+ VQ+PT+LLAMVD++IGGKTGVNHP GKNLIGAFHQP+ VLIDP+ L+TLPVR
Sbjct: 121 TWLRGISFVQIPTSLLAMVDASIGGKTGVNHPRGKNLIGAFHQPKLVLIDPETLQTLPVR 180

Query: 179 EFRAGMAEVIKYGVIWDAELFNQLEQSKRLDQLRYIKPELMDAILTRSCQAKADVVGKDE 238
           EFRAGMAEVIKYGVIWD +LF +LE S  LD+ R +   L+  IL RSC+AKA+VV KDE
Sbjct: 181 EFRAGMAEVIKYGVIWDRDLFERLEASPFLDRPRSLPANLLTLILERSCRAKAEVVAKDE 240

Query: 239 KEGGLRAILNYGHTVGHAVESLTNYRLLKHGEAVGIGMVAAGQIAVNLGLWQQADADRQN 298
           KE GLRAILNYGHT+GHAVESLT YR++ HGEAV IGMVAAG++AV LGLW Q + DRQ 
Sbjct: 241 KESGLRAILNYGHTIGHAVESLTGYRIVNHGEAVAIGMVAAGRLAVALGLWNQDECDRQE 300

Query: 299 ALIEKAGLPTKLPAGLDIEGIIEALQLDKKVKDGKVRFVLPTQIGVVTVTDEVTSDHIRQ 358
           A+I KAGLPT+LP G+D   I+EALQLDKKV+ GKVRF+LPT +G VT+TD+V S  +++
Sbjct: 301 AVIAKAGLPTRLPEGIDQAAIVEALQLDKKVQAGKVRFILPTTLGHVTITDQVPSQTLQE 360

Query: 359 VLQ 361
           VLQ
Sbjct: 361 VLQ 363


Lambda     K      H
   0.319    0.136    0.388 

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: 478
Number of extensions: 10
Number of successful extensions: 2
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: 363
Length of database: 368
Length adjustment: 30
Effective length of query: 333
Effective length of database: 338
Effective search space:   112554
Effective search space used:   112554
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate Synpcc7942_0525 Synpcc7942_0525 (3-dehydroquinate synthase)
to HMM TIGR01357 (aroB: 3-dehydroquinate synthase (EC 4.2.3.4))

# 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/TIGR01357.hmm
# target sequence database:        /tmp/gapView.25286.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01357  [M=344]
Accession:   TIGR01357
Description: aroB: 3-dehydroquinate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.2e-124  399.6   0.0   7.1e-124  399.4   0.0    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_0525  Synpcc7942_0525 3-dehydroquinate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_0525  Synpcc7942_0525 3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  399.4   0.0  7.1e-124  7.1e-124       1     342 [.      14     361 ..      14     363 .. 0.96

  Alignments for each domain:
  == domain 1  score: 399.4 bits;  conditional E-value: 7.1e-124
                                 TIGR01357   1 ykvkvgegllkklveelae...ka.sklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsl 65 
                                               y++ + +g l+++ ++l++   ka +kl+++t+ ++ + ++++l +al+++g+ v+ l++p+ge++K+ 
  lcl|FitnessBrowser__SynE:Synpcc7942_0525  14 YEIAIANGGLAAAGTWLQQadlKAgTKLLIVTNPAIGRRYGDRLVAALQEAGFIVDCLTLPAGERYKTP 82 
                                               67889999999999999997753369******************************************* PP

                                 TIGR01357  66 etvaklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginl 134
                                               +tv++++d+ le  ler+s+lva+GGGv+gD++GF+Aat+lRGi++vq+PT+llamvD+s+GGKtg+n+
  lcl|FitnessBrowser__SynE:Synpcc7942_0525  83 ATVQRIYDKALELRLERRSALVALGGGVIGDMTGFAAATWLRGISFVQIPTSLLAMVDASIGGKTGVNH 151
                                               ********************************************************************* PP

                                 TIGR01357 135 plgkNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeeleknekl.llklaelea 202
                                               p+gkNliGaf+qPk+Vlid+++l+tlp re+r+GmaEviK+g+i+d++lfe+le    l + ++   + 
  lcl|FitnessBrowser__SynE:Synpcc7942_0525 152 PRGKNLIGAFHQPKLVLIDPETLQTLPVREFRAGMAEVIKYGVIWDRDLFERLEASPFLdRPRSLPANL 220
                                               ******************************************************976544666678899 PP

                                 TIGR01357 203 leelikrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklg 270
                                               l+ +++rs++ KaevV++DekesglRa+LN+GHt+gHa+E+l++y+ ++HGeaVaiGmv + +l+ +lg
  lcl|FitnessBrowser__SynE:Synpcc7942_0525 221 LTLILERSCRAKAEVVAKDEKESGLRAILNYGHTIGHAVESLTGYRiVNHGEAVAIGMVAAGRLAVALG 289
                                               9******************************************************************** PP

                                 TIGR01357 271 llkaellerlvallkklglptklkkklsveellkallkDKKnegskiklvlleeiGkaalasevteeel 339
                                               l ++++ +r +a++ k+glpt+l++ ++  ++++al+ DKK +++k++++l++ +G+++++++v++++l
  lcl|FitnessBrowser__SynE:Synpcc7942_0525 290 LWNQDECDRQEAVIAKAGLPTRLPEGIDQAAIVEALQLDKKVQAGKVRFILPTTLGHVTITDQVPSQTL 358
                                               ****************************************************************99988 PP

                                 TIGR01357 340 lea 342
                                               +e+
  lcl|FitnessBrowser__SynE:Synpcc7942_0525 359 QEV 361
                                               775 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (368 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 12.25
//
[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