Aligments for a candidate for aroB in Azospirillum brasilense Sp245

GapMind for Amino acid biosynthesis

Aligments for a candidate for aroB in Azospirillum brasilense Sp245

Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate AZOBR_RS03220 AZOBR_RS03220 3-dehydroquinate synthase

Query= SwissProt::U3KRF2
         (445 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS03220 AZOBR_RS03220
           3-dehydroquinate synthase
          Length = 378

 Score =  289 bits (739), Expect = 1e-82
 Identities = 167/360 (46%), Positives = 227/360 (63%), Gaps = 11/360 (3%)

Query: 81  PTIVD---VDLGDRSYPIYIGSGLLDQPD-LLQRHVHGKRVLVVTNSTVAPIYLDKVVGA 136
           PT +D   +DLG RSY I +G  +LD     +     GK  +VVT+  VAP +L  +   
Sbjct: 7   PTAIDTVRLDLGPRSYDILVGDRVLDGAGPRIAAITRGKAPIVVTDENVAPRHLPTLERT 66

Query: 137 LTNENPNVSVESVILPDGEKYKNMDTLMKVFDKAIESRLDRRCTFVALGGGVIGDMCGYA 196
           L +     + ++++LP GEK K++    ++ D  +   ++R    +ALGGGVIGD+ G+A
Sbjct: 67  LRDAGIEPT-QAIVLPAGEKTKDIAHFERLMDAVLARGIERSAVLLALGGGVIGDITGFA 125

Query: 197 AASFLRGVNFIQIPTTVMAQVDSSVGGKTGINHRLGKNLIGAFYQPQCVLIDTDTLNTLP 256
           AAS LRG++FIQ+PTT+++QVDSSVGGKTGIN   GKNLIGAF+QP+ V+ DT TL+TLP
Sbjct: 126 AASALRGIDFIQVPTTLLSQVDSSVGGKTGINSPHGKNLIGAFHQPRLVIADTATLDTLP 185

Query: 257 DRELASGLAEVVKYGLIRDANFFEWQEKNMPALMARDPSALAYAIKRSCENKAEVVSLDE 316
            RE+ +G AEVVKYGLIR   FF W E+N   ++A D  A  +A+  SC  KA +V +DE
Sbjct: 186 RREVLAGYAEVVKYGLIRLPGFFAWLEENGERVVAGDSDARRHAVTESCRAKAAIVGVDE 245

Query: 317 KESGLRATLNLGHTFGHAIETGFGYG-QWLHGEAVAAGMVMAVDMSYRLGWIDESIVNRA 375
           +ESG RA LNLGHTFGHA+E   G+G + LHGEAV+ GMV+A D+S RLG    +   +A
Sbjct: 246 RESGDRALLNLGHTFGHALEAATGFGSRLLHGEAVSIGMVLAFDLSVRLGLCPAADAEKA 305

Query: 376 HNILQQAKLPTAPPETMTVEM----FKSVMAVDKKVADGLLRLILLKGPLGNCVFTGDYD 431
              L +  LP  P +   VE         MA DKKV DG +  +L++  LG+     D D
Sbjct: 306 RAHLARVGLPVRPTDVPGVEWDIDGLILSMAKDKKVKDGRITFVLVRA-LGDAFTQRDVD 364


Lambda     K      H
   0.317    0.133    0.382 

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: 396
Number of extensions: 15
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: 445
Length of database: 378
Length adjustment: 31
Effective length of query: 414
Effective length of database: 347
Effective search space:   143658
Effective search space used:   143658
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 AZOBR_RS03220 AZOBR_RS03220 (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.23290.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.2e-111  357.8   0.0   3.9e-111  357.5   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS03220  AZOBR_RS03220 3-dehydroquinate s


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS03220  AZOBR_RS03220 3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  357.5   0.0  3.9e-111  3.9e-111       1     336 [.      22     365 ..      22     372 .. 0.95

  Alignments for each domain:
  == domain 1  score: 357.5 bits;  conditional E-value: 3.9e-111
                                 TIGR01357   1 ykvkvgegllkklveelae..kasklvvitdeeveklvaekleealkslgve.vlvlvvpdgeesKsle 66 
                                               y++ vg+ +l+ +   +a   + +  +v+tde+v+  +  +le++l+++g+e ++ +v+p+ge++K+++
  lcl|FitnessBrowser__azobra:AZOBR_RS03220  22 YDILVGDRVLDGAGPRIAAitRGKAPIVVTDENVAPRHLPTLERTLRDAGIEpTQAIVLPAGEKTKDIA 90 
                                               68999999999999999987455999***********************7652778899********** PP

                                 TIGR01357  67 tvaklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlp 135
                                               ++++l+d++l++++er+ vl+a+GGGv+gD++GF+Aa+ lRGi+++qvPTtll++vDssvGGKtgin p
  lcl|FitnessBrowser__azobra:AZOBR_RS03220  91 HFERLMDAVLARGIERSAVLLALGGGVIGDITGFAAASALRGIDFIQVPTTLLSQVDSSVGGKTGINSP 159
                                               ********************************************************************* PP

                                 TIGR01357 136 lgkNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaeleale 204
                                               +gkNliGaf+qP++V+ d+++l tlp+re+ +G+aEv+K+gli    +f++le+n + ++   + +a +
  lcl|FitnessBrowser__azobra:AZOBR_RS03220 160 HGKNLIGAFHQPRLVIADTATLDTLPRREVLAGYAEVVKYGLIRLPGFFAWLEENGERVVAG-DSDARR 227
                                               ********************************************************988875.559*** PP

                                 TIGR01357 205 elikrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk..lsHGeaVaiGmvveaklseklgl 271
                                               +++++s++ Ka +V  De+esg RalLN+GHt+gHa+Ea+++++  l HGeaV+iGmv+++ ls +lgl
  lcl|FitnessBrowser__azobra:AZOBR_RS03220 228 HAVTESCRAKAAIVGVDERESGDRALLNLGHTFGHALEAATGFGsrLLHGEAVSIGMVLAFDLSVRLGL 296
                                               ******************************************9999*********************** PP

                                 TIGR01357 272 lkaellerlvallkklglptklkk....klsveellkallkDKKnegskiklvlleeiGkaalasevte 336
                                               ++a ++e+ +a l ++glp++ ++    +++++ l+ ++ kDKK ++++i++vl++++G+a+++++v+ 
  lcl|FitnessBrowser__azobra:AZOBR_RS03220 297 CPAADAEKARAHLARVGLPVRPTDvpgvEWDIDGLILSMAKDKKVKDGRITFVLVRALGDAFTQRDVDP 365
                                               **********************99999***********************************9987754 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (378 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.46
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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