Alignments for a candidate for aroB in Nostoc punctiforme ATCC 29133; PCC 73102

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Nostoc punctiforme ATCC 29133; PCC 73102

Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate WP_012411972.1 NPUN_RS29000 3-dehydroquinate synthase

Query= BRENDA::Q3M4V2
         (363 letters)



>NCBI__GCF_000020025.1:WP_012411972.1
          Length = 363

 Score =  618 bits (1593), Expect = 0.0
 Identities = 310/363 (85%), Positives = 338/363 (93%)

Query: 1   MTSVINVNLPTQSYEIAIAPASLDQIGQSLAGLKLGKKVLLVSNPTIFKHFGKVAVDSLE 60
           MTS+INVNLP QSYEIAIAP++LDQ+GQ +A LKLGKKVLLVSNPTIFKH+G+ A+ SL+
Sbjct: 1   MTSLINVNLPEQSYEIAIAPSNLDQLGQQMANLKLGKKVLLVSNPTIFKHYGERAITSLK 60

Query: 61  AAGFQVASYCLPAGERYKTLNSIQKLYDIALENRLERSSTMVALGGGVIGDMTGFAAATW 120
           +AGF+VAS  LP GERYK LNSIQKLYD+ALENRLERS+TMVALGGGVIGDMTGFAAATW
Sbjct: 61  SAGFEVASCTLPPGERYKNLNSIQKLYDVALENRLERSATMVALGGGVIGDMTGFAAATW 120

Query: 121 LRGINVVQVPTTLLAMVDSAIGGKTGVNHPHGKNLIGAFHQPRFVLIDPQVLKTLPVREF 180
           LRGINVVQVPTTLLAMVDSAIGGKTGVNHPHGKNLIGAFHQPR VLIDP VLKTLP+REF
Sbjct: 121 LRGINVVQVPTTLLAMVDSAIGGKTGVNHPHGKNLIGAFHQPRLVLIDPDVLKTLPMREF 180

Query: 181 RAGMAEVIKYGVIWDAELFNQLEQSKRLDQLRYIKPELMDAILTRSCQAKADVVGKDEKE 240
           RAGMAEVIKYGVIWDAELF QLE SKRLDQLRY+KPEL+D+ILTRSCQAKADVVGKDEKE
Sbjct: 181 RAGMAEVIKYGVIWDAELFAQLEASKRLDQLRYVKPELIDSILTRSCQAKADVVGKDEKE 240

Query: 241 GGLRAILNYGHTVGHAVESLTNYRLLKHGEAVGIGMVAAGQIAVNLGLWQQADADRQNAL 300
           GGLRAILNYGHT+GHAVESLT YRL+ HGEAV IGMVAAGQIAV LG+WQ+ D +RQNAL
Sbjct: 241 GGLRAILNYGHTIGHAVESLTGYRLVNHGEAVAIGMVAAGQIAVELGMWQKEDTERQNAL 300

Query: 301 IEKAGLPTKLPAGLDIEGIIEALQLDKKVKDGKVRFVLPTQIGVVTVTDEVTSDHIRQVL 360
           I+K GLPT+LP+G+DIE II+ALQLDKKVK GKVRFVLPT+IGVVTVTDEV SD IRQVL
Sbjct: 301 IQKTGLPTQLPSGVDIEAIIDALQLDKKVKAGKVRFVLPTEIGVVTVTDEVPSDIIRQVL 360

Query: 361 QQM 363
           Q M
Sbjct: 361 QGM 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: 527
Number of extensions: 9
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: 363
Length of database: 363
Length adjustment: 29
Effective length of query: 334
Effective length of database: 334
Effective search space:   111556
Effective search space used:   111556
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 WP_012411972.1 NPUN_RS29000 (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.15349.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-127  411.5   0.1   1.6e-127  411.4   0.1    1.0  1  lcl|NCBI__GCF_000020025.1:WP_012411972.1  NPUN_RS29000 3-dehydroquinate sy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020025.1:WP_012411972.1  NPUN_RS29000 3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  411.4   0.1  1.6e-127  1.6e-127       1     341 [.      14     358 ..      14     361 .. 0.96

  Alignments for each domain:
  == domain 1  score: 411.4 bits;  conditional E-value: 1.6e-127
                                 TIGR01357   1 ykvkvgegllkklveelae..kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKslet 67 
                                               y++ +  + l++l +++a+    +k++++++ ++ k+++e+    lks+g+ev  +++p+ge++K+l++
  lcl|NCBI__GCF_000020025.1:WP_012411972.1  14 YEIAIAPSNLDQLGQQMANlkLGKKVLLVSNPTIFKHYGERAITSLKSAGFEVASCTLPPGERYKNLNS 82 
                                               678999999999*9999995444***************99999999999******************** PP

                                 TIGR01357  68 vaklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlpl 136
                                               ++kl+d  le+ ler+ ++va+GGGv+gD++GF+Aat+lRGi++vqvPTtllamvDs++GGKtg+n+p+
  lcl|NCBI__GCF_000020025.1:WP_012411972.1  83 IQKLYDVALENRLERSATMVALGGGVIGDMTGFAAATWLRGINVVQVPTTLLAMVDSAIGGKTGVNHPH 151
                                               ********************************************************************* PP

                                 TIGR01357 137 gkNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeeleknekl.llklaeleale 204
                                               gkNliGaf+qP++Vlid++vl+tlp re+r+GmaEviK+g+i+daelf++le  ++l  l+ ++ e ++
  lcl|NCBI__GCF_000020025.1:WP_012411972.1 152 GKNLIGAFHQPRLVLIDPDVLKTLPMREFRAGMAEVIKYGVIWDAELFAQLEASKRLdQLRYVKPELID 220
                                               ****************************************************98876444557889*** PP

                                 TIGR01357 205 elikrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgll 272
                                               ++++rs++ Ka+vV +Deke glRa+LN+GHt+gHa+E+l++y+ ++HGeaVaiGmv + +++ +lg+ 
  lcl|NCBI__GCF_000020025.1:WP_012411972.1 221 SILTRSCQAKADVVGKDEKEGGLRAILNYGHTIGHAVESLTGYRlVNHGEAVAIGMVAAGQIAVELGMW 289
                                               ********************************************************************* PP

                                 TIGR01357 273 kaellerlvallkklglptklkkklsveellkallkDKKnegskiklvlleeiGkaalasevteeelle 341
                                               ++e++er  al++k+glpt+l++ +++e++++al+ DKK +++k+++vl++eiG +++++ev+++ + +
  lcl|NCBI__GCF_000020025.1:WP_012411972.1 290 QKEDTERQNALIQKTGLPTQLPSGVDIEAIIDALQLDKKVKAGKVRFVLPTEIGVVTVTDEVPSDIIRQ 358
                                               ***********************************************************9999887666 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 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: 10.23
//
[ok]

This GapMind analysis is from Apr 10 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