Alignments for a candidate for aroB in Methylobacterium nodulans ORS 2060

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Methylobacterium nodulans ORS 2060

Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate WP_015927835.1 MNOD_RS05465 3-dehydroquinate synthase

Query= BRENDA::P07639
         (362 letters)



>NCBI__GCF_000022085.1:WP_015927835.1
          Length = 370

 Score =  271 bits (692), Expect = 3e-77
 Identities = 165/357 (46%), Positives = 205/357 (57%), Gaps = 9/357 (2%)

Query: 9   GERSYPITIASGLFNEPASFLPLKSGEQVMLVTNETLAPLYLDKVRGVLEQAGVNVDSVI 68
           G R+Y I +  GL  E  +         V +VT+ T+A LY + VR  LE AG+    V 
Sbjct: 13  GGRAYDILVGRGLLAEVGARCAALGARAVAVVTDTTVAGLYGEAVRASLEAAGLRAALVA 72

Query: 69  LPDGEQYKSLAVLDTVFTALLQKPHGRDTTLVALGGGVVGDLTGFAAASYQRGVRFIQVP 128
           +P GE  KS A    V  ALL     R   ++ALGGGVVGDL GFAA+  +RGVRF+Q P
Sbjct: 73  VPPGEGSKSYATFTEVCDALLAHRIERRDLVLALGGGVVGDLAGFAASVLRRGVRFVQAP 132

Query: 129 TTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPASVVVDLDCLKTLPPRELASGLAEVIKY 188
           TTLL+QVDSSVGGKT +N P GKN+IGAF+QP+ V+ D   L TL  RE+ +G AEV KY
Sbjct: 133 TTLLAQVDSSVGGKTGINSPHGKNLIGAFHQPSLVLADTAALDTLSAREMRAGYAEVAKY 192

Query: 189 GIILDGAFFNWLEENLDALLRLDGPAMAYCIRRCCELKAEVVAADERETGLRALLNLGHT 248
           G+I D AFF W E N   +    GPA    +  CC  KA VV  DERE G RALLNLGHT
Sbjct: 193 GLIDDPAFFAWCEANFSEIFS-GGPARDRAVASCCRAKAGVVVRDEREDGERALLNLGHT 251

Query: 249 FGHAIEAEMGY--GNWLHGEAVAAGMVMAARTSERLGQFSSAETQRIITLLKRAGLPVNG 306
           F HA+E    Y     +HGEAVA G+ +A R S RLG     +  R+   L  AGLP   
Sbjct: 252 FAHALERLTRYESARLVHGEAVAIGLALAFRFSARLGLCPGQDAGRVANHLALAGLPTT- 310

Query: 307 PREM-----SAQAYLPHMLRDKKVLAGEMRLILPLAIGKSEVRSGVSHELVLNAIAD 358
            R++      A   L  M +DKKV  G +  IL   IG+S +  G+  E V   +A+
Sbjct: 311 LRQVPGGCGDADQLLDAMRQDKKVRDGALTFILARGIGRSFIAPGIEPEAVRAFLAE 367


Lambda     K      H
   0.320    0.136    0.392 

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: 313
Number of extensions: 14
Number of successful extensions: 4
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: 362
Length of database: 370
Length adjustment: 30
Effective length of query: 332
Effective length of database: 340
Effective search space:   112880
Effective search space used:   112880
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 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate WP_015927835.1 MNOD_RS05465 (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.451096.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.2e-110  355.0   0.0   2.6e-110  354.8   0.0    1.0  1  NCBI__GCF_000022085.1:WP_015927835.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000022085.1:WP_015927835.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  354.8   0.0  2.6e-110  2.6e-110       1     334 [.      17     356 ..      17     365 .. 0.96

  Alignments for each domain:
  == domain 1  score: 354.8 bits;  conditional E-value: 2.6e-110
                             TIGR01357   1 ykvkvgegllkklveelae.kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletvakll 72 
                                           y++ vg+gll+++ + +a   a+ + v+td +v+ l++e +++ l+++g ++  + vp+ge sKs +t++++ 
  NCBI__GCF_000022085.1:WP_015927835.1  17 YDILVGRGLLAEVGARCAAlGARAVAVVTDTTVAGLYGEAVRASLEAAGLRAALVAVPPGEGSKSYATFTEVC 89 
                                           6899*******9999999866699************************************************* PP

                             TIGR01357  73 dqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgkNliGafy 145
                                           d+ll++ +er+++++a+GGGvvgDlaGF+A++  RG+r+vq PTtlla+vDssvGGKtgin p+gkNliGaf+
  NCBI__GCF_000022085.1:WP_015927835.1  90 DALLAHRIERRDLVLALGGGVVGDLAGFAASVLRRGVRFVQAPTTLLAQVDSSVGGKTGINSPHGKNLIGAFH 162
                                           ************************************************************************* PP

                             TIGR01357 146 qPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeelikrsievKaevV 218
                                           qP++Vl d++ l tl+ re+r+G+aEv K+gli d ++f+++e n +++ +     a +++++++++ Ka vV
  NCBI__GCF_000022085.1:WP_015927835.1 163 QPSLVLADTAALDTLSAREMRAGYAEVAKYGLIDDPAFFAWCEANFSEIFS--GGPARDRAVASCCRAKAGVV 233
                                           ********************************************9998774..679***************** PP

                             TIGR01357 219 eeDekesglRalLNfGHtlgHaiEallkyk...lsHGeaVaiGmvveaklseklgllkaellerlvallkklg 288
                                            +De+e g RalLN+GHt++Ha+E l+ y+   l HGeaVaiG+++++++s +lgl++ +++ r+++ l  +g
  NCBI__GCF_000022085.1:WP_015927835.1 234 VRDEREDGERALLNLGHTFAHALERLTRYEsarLVHGEAVAIGLALAFRFSARLGLCPGQDAGRVANHLALAG 306
                                           *****************************99999*************************************** PP

                             TIGR01357 289 lptklkk....klsveellkallkDKKnegskiklvlleeiGkaalasev 334
                                           lpt+l++    + ++++ll+a+ +DKK +++ ++++l++ iG+ ++a  +
  NCBI__GCF_000022085.1:WP_015927835.1 307 LPTTLRQvpggCGDADQLLDAMRQDKKVRDGALTFILARGIGRSFIAPGI 356
                                           *******************************************9988655 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (370 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: 00:00:00.00
# Mc/sec: 25.24
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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