Alignments for a candidate for aroB in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Dinoroseobacter shibae DFL-12

Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate 3608203 Dshi_1608 3-dehydroquinate synthase (RefSeq)

Query= SwissProt::U3KRF2
         (445 letters)



>FitnessBrowser__Dino:3608203
          Length = 383

 Score =  274 bits (700), Expect = 4e-78
 Identities = 166/374 (44%), Positives = 218/374 (58%), Gaps = 9/374 (2%)

Query: 74  TKAVSSAPTIVDVDLGDRSYPIYIGSGLLDQPDL-LQRHVHGKRVLVVTNSTVAPIYLDK 132
           T + + AP  V V L DR+Y + IG GLL Q    +   +   +V +V++ TVA ++L  
Sbjct: 2   TMSAAPAPQTVYVPLEDRAYDVVIGPGLLAQAGARISPFLPRPKVAIVSDETVAALHLAT 61

Query: 133 VVGALTNGNPNVSVESVILPDGEKYKNMDTLMKVFDKAIESRLDRRCTFVALGGGVIGDM 192
           +  +L      +   ++ILP GE  K      +  D  +  +++RR   +A GGGVIGD+
Sbjct: 62  LQDSLATAG--IDSTALILPAGEATKGWPEFSRTVDWLLAQKIERRDLVIAFGGGVIGDL 119

Query: 193 CGYAAASFLRGVNFIQIPTTVMAQVDSSVGGKTGINHRLGKNLIGAFYQPQCVLIDTDTL 252
            G+AAA   RGV FIQIPT+++AQVDSSVGGKTGIN   GKNLIGAF+QP+ VL DTD L
Sbjct: 120 VGFAAAVLRRGVGFIQIPTSLLAQVDSSVGGKTGINSVHGKNLIGAFHQPRLVLADTDVL 179

Query: 253 NTLPDRELASGLAEVVKYGLIRDANFFEWQEKNMPALMARDPSALAYAIKRSCENKAEVV 312
            TL  R+  +G  EVVKYGL+ DA+FF W E   P L A D SA   A++RS E KAE+V
Sbjct: 180 GTLTPRDFLAGYGEVVKYGLLGDADFFAWLETEGPRLAAGDGSARVAAVRRSVEMKAEIV 239

Query: 313 SLDEKESGLRATLNLGHTFGHAIETGFGYG-QWLHGEAVAAGMVMAVDMSYRLGWIDESI 371
             DE E G RA LNLGHTF HA+E   GY  + LHGE VA G  +A D+S RLG   +  
Sbjct: 240 VRDETEQGDRALLNLGHTFCHALEAATGYSDRLLHGEGVAIGCALAFDLSARLGLCAQED 299

Query: 372 VNRAHNILQ----QAKLPTAPPETMTVEMFKSVMAVDKKVADGLLRLILLKGPLGNCVFT 427
            +R    LQ    +  L     +    E   ++M  DKKV DG LR IL +G +G    T
Sbjct: 300 PSRVRAHLQTMGMKRDLRDIAGDLPDAEALLNLMGQDKKVMDGTLRFILARG-IGQAFMT 358

Query: 428 GDYDRKALDETLHA 441
            +   +A+   L A
Sbjct: 359 SEVPSEAVLSVLRA 372


Lambda     K      H
   0.318    0.133    0.385 

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: 345
Number of extensions: 11
Number of successful extensions: 3
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: 445
Length of database: 383
Length adjustment: 31
Effective length of query: 414
Effective length of database: 352
Effective search space:   145728
Effective search space used:   145728
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate 3608203 Dshi_1608 (3-dehydroquinate synthase (RefSeq))
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.22205.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.2e-108  349.3   0.0   1.3e-108  349.2   0.0    1.0  1  lcl|FitnessBrowser__Dino:3608203  Dshi_1608 3-dehydroquinate synth


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3608203  Dshi_1608 3-dehydroquinate synthase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  349.2   0.0  1.3e-108  1.3e-108       1     341 [.      21     368 ..      21     371 .. 0.97

  Alignments for each domain:
  == domain 1  score: 349.2 bits;  conditional E-value: 1.3e-108
                         TIGR01357   1 ykvkvgegllkklveelae..kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletvaklldql 75 
                                       y+v++g gll+++ + ++    + k+ +++de+v++l+ ++l++ l+++g+  + l++p+ge +K + ++++++d+l
  lcl|FitnessBrowser__Dino:3608203  21 YDVVIGPGLLAQAGARISPflPRPKVAIVSDETVAALHLATLQDSLATAGIDSTALILPAGEATKGWPEFSRTVDWL 97 
                                       789***************9854589**************************************************** PP

                         TIGR01357  76 leeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgkNliGafyqPkaVli 152
                                       l++k+er+++++a+GGGv+gDl+GF+Aa+  RG+ ++q+PT+lla+vDssvGGKtgin  +gkNliGaf+qP++Vl 
  lcl|FitnessBrowser__Dino:3608203  98 LAQKIERRDLVIAFGGGVIGDLVGFAAAVLRRGVGFIQIPTSLLAQVDSSVGGKTGINSVHGKNLIGAFHQPRLVLA 174
                                       ***************************************************************************** PP

                         TIGR01357 153 dlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeelikrsievKaevVeeDekesglRa 229
                                       d++vl tl+ r + +G++Ev+K+gl+ da++f++le+    l    + +a   +++rs+e+Kae+V +De+e+g Ra
  lcl|FitnessBrowser__Dino:3608203 175 DTDVLGTLTPRDFLAGYGEVVKYGLLGDADFFAWLETEGPRLAA-GDGSARVAAVRRSVEMKAEIVVRDETEQGDRA 250
                                       *************************************9986665.67799999************************ PP

                         TIGR01357 230 lLNfGHtlgHaiEallkyk..lsHGeaVaiGmvveaklseklgllkaellerlvallkklglptklkk....klsve 300
                                       lLN+GHt+ Ha+Ea+++y+  l HGe VaiG ++++ ls +lgl+ +e+ +r++a l+++g++++l++      ++e
  lcl|FitnessBrowser__Dino:3608203 251 LLNLGHTFCHALEAATGYSdrLLHGEGVAIGCALAFDLSARLGLCAQEDPSRVRAHLQTMGMKRDLRDiagdLPDAE 327
                                       ******************999***********************************************9997789** PP

                         TIGR01357 301 ellkallkDKKnegskiklvlleeiGkaalasevteeelle 341
                                       +ll+ + +DKK  +++++++l++ iG+a+++sev++e++l+
  lcl|FitnessBrowser__Dino:3608203 328 ALLNLMGQDKKVMDGTLRFILARGIGQAFMTSEVPSEAVLS 368
                                       ***********************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (383 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: 10.02
//
[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