Alignments for a candidate for aroB in Shewanella loihica PV-4

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Shewanella loihica PV-4

Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate 5207692 Shew_0214 3-dehydroquinate synthase (RefSeq)

Query= BRENDA::P07639
         (362 letters)



>FitnessBrowser__PV4:5207692
          Length = 358

 Score =  421 bits (1083), Expect = e-122
 Identities = 212/357 (59%), Positives = 265/357 (74%), Gaps = 1/357 (0%)

Query: 1   MERIVVTLGERSYPITIASGLFNEPASFLPLKSGEQVMLVTNETLAPLYLDKVRGVLEQA 60
           ME+I V LG RSYPI I   L      F     G+++++VTN+T+APLYL KV+ +L   
Sbjct: 1   MEQIQVELGVRSYPIFIGQNLLENSDYFSSYLQGKKILIVTNDTIAPLYLAKVQALLASY 60

Query: 61  GVNVDSVILPDGEQYKSLAVLDTVFTALLQKPHGRDTTLVALGGGVVGDLTGFAAASYQR 120
               D VILPDGEQYK+L+ +D +FT+LL +  GRD+ L+ALGGGV+GD+TGFAAA YQR
Sbjct: 61  QC-ADPVILPDGEQYKTLSQMDAIFTSLLAQNMGRDSVLIALGGGVIGDMTGFAAACYQR 119

Query: 121 GVRFIQVPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPASVVVDLDCLKTLPPRELAS 180
           GV FIQ+PTTLLSQVDSSVGGKTAVNHP+GKNMIGAFYQP  V +D  CL TLP RE A+
Sbjct: 120 GVDFIQIPTTLLSQVDSSVGGKTAVNHPMGKNMIGAFYQPKMVAIDTACLHTLPAREFAA 179

Query: 181 GLAEVIKYGIILDGAFFNWLEENLDALLRLDGPAMAYCIRRCCELKAEVVAADERETGLR 240
           G+AEVIKYGII DG+FF+WLE+N+ AL  LD  A+ Y I +CC++KA+VVA DE E G+R
Sbjct: 180 GMAEVIKYGIIWDGSFFSWLEQNVAALKSLDEAALTYAIAKCCQIKADVVAQDETEQGVR 239

Query: 241 ALLNLGHTFGHAIEAEMGYGNWLHGEAVAAGMVMAARTSERLGQFSSAETQRIITLLKRA 300
           ALLNLGHTFGHAIEAEMGYG WLHGEAVAAG V+AA+T+ ++G    +   RI  + +  
Sbjct: 240 ALLNLGHTFGHAIEAEMGYGVWLHGEAVAAGTVLAAQTASKMGLVDQSIVCRIEAIFEAF 299

Query: 301 GLPVNGPREMSAQAYLPHMLRDKKVLAGEMRLILPLAIGKSEVRSGVSHELVLNAIA 357
            LP   P  M  + ++ HM RDKKVL G++RL+LP AIG++EV   VS  L+   I+
Sbjct: 300 DLPTEAPEAMDFEQFIKHMRRDKKVLNGKLRLVLPKAIGQAEVYGEVSESLLQEVIS 356


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: 323
Number of extensions: 5
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: 362
Length of database: 358
Length adjustment: 29
Effective length of query: 333
Effective length of database: 329
Effective search space:   109557
Effective search space used:   109557
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 5207692 Shew_0214 (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.11692.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   9.8e-125  402.2   0.0   1.1e-124  402.1   0.0    1.0  1  lcl|FitnessBrowser__PV4:5207692  Shew_0214 3-dehydroquinate synth


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5207692  Shew_0214 3-dehydroquinate synthase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  402.1   0.0  1.1e-124  1.1e-124       1     341 [.      13     353 ..      13     356 .. 0.95

  Alignments for each domain:
  == domain 1  score: 402.1 bits;  conditional E-value: 1.1e-124
                        TIGR01357   1 ykvkvgegllkklveelae..kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletvaklldqll 76 
                                      y++ +g++ll++  +++++  + +k++++t+++++ l+ +k++++l+s  + ++ +++pdge++K+l+++ ++ + ll
  lcl|FitnessBrowser__PV4:5207692  13 YPIFIGQNLLENS-DYFSSylQGKKILIVTNDTIAPLYLAKVQALLAS-YQCADPVILPDGEQYKTLSQMDAIFTSLL 88 
                                      6789999999843.3444444569**********************98.67788999********************* PP

                        TIGR01357  77 eeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgkNliGafyqPkaVlidl 154
                                      ++++ r+svl+a+GGGv+gD++GF+Aa y+RG++++q+PTtll++vDssvGGKt++n+p gkN+iGafyqPk+V id+
  lcl|FitnessBrowser__PV4:5207692  89 AQNMGRDSVLIALGGGVIGDMTGFAAACYQRGVDFIQIPTTLLSQVDSSVGGKTAVNHPMGKNMIGAFYQPKMVAIDT 166
                                      ****************************************************************************** PP

                        TIGR01357 155 kvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeelikrsievKaevVeeDekesglRalLN 232
                                      ++l+tlp re+++GmaEviK+g+i+d ++f++le+n ++l++l +++al+ +i++++++Ka+vV++De+e+g+RalLN
  lcl|FitnessBrowser__PV4:5207692 167 ACLHTLPAREFAAGMAEVIKYGIIWDGSFFSWLEQNVAALKSL-DEAALTYAIAKCCQIKADVVAQDETEQGVRALLN 243
                                      *************************************988865.66******************************** PP

                        TIGR01357 233 fGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgllkaellerlvallkklglptklkkklsveellkallkD 309
                                      +GHt+gHaiEa+++y+ + HGeaVa G v++a+++ k+gl++++++ r++a+++++ lpt+ ++ +++e+++k++ +D
  lcl|FitnessBrowser__PV4:5207692 244 LGHTFGHAIEAEMGYGvWLHGEAVAAGTVLAAQTASKMGLVDQSIVCRIEAIFEAFDLPTEAPEAMDFEQFIKHMRRD 321
                                      ****************************************************************************** PP

                        TIGR01357 310 KKnegskiklvlleeiGkaalasevteeelle 341
                                      KK  ++k++lvl+++iG+a++  ev+e+ l+e
  lcl|FitnessBrowser__PV4:5207692 322 KKVLNGKLRLVLPKAIGQAEVYGEVSESLLQE 353
                                      ********************998887665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (358 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: 7.42
//
[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