Alignments for a candidate for aroB in Marinobacter adhaerens HP15

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Marinobacter adhaerens HP15

Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate GFF492 HP15_480 3-dehydroquinate synthase

Query= SwissProt::U3KRF2
         (445 letters)



>FitnessBrowser__Marino:GFF492
          Length = 364

 Score =  395 bits (1016), Expect = e-115
 Identities = 206/362 (56%), Positives = 260/362 (71%), Gaps = 6/362 (1%)

Query: 84  VDVDLGDRSYPIYIGSGLLDQPDLLQRHVHGKRVLVVTNSTVAPIYLDKVVGALTNGNPN 143
           + V+LG+RSYPI+IG GLL   DL    V G +V++VTN TVAP+YL++         P 
Sbjct: 8   LSVELGERSYPIFIGEGLLGTQDL-SAFVSGAQVMIVTNETVAPLYLERAKACF----PG 62

Query: 144 VSVESVILPDGEKYKNMDTLMKVFDKAIESRLDRRCTFVALGGGVIGDMCGYAAASFLRG 203
             V++V+LPDGEK+K+  TL  +FD  +E R  R+ T VALGGGV+GDM G+AAA + RG
Sbjct: 63  KRVDTVVLPDGEKFKDWQTLNSIFDGLLEHRHTRKTTLVALGGGVVGDMAGFAAACYQRG 122

Query: 204 VNFIQIPTTVMAQVDSSVGGKTGINHRLGKNLIGAFYQPQCVLIDTDTLNTLPDRELASG 263
           V FIQIPTT+++QVDSSVGGKTGINH LGKN+IGAF+QPQ VLIDT +L TLP RE+++G
Sbjct: 123 VPFIQIPTTLLSQVDSSVGGKTGINHPLGKNMIGAFHQPQAVLIDTASLQTLPAREVSAG 182

Query: 264 LAEVVKYGLIRDANFFEWQEKNMPALMARDPSALAYAIKRSCENKAEVVSLDEKESGLRA 323
           LAEV+KYGLIRD  F  W E++M AL++ DP ALA AI RSC  KAE+V+LDE+E G+RA
Sbjct: 183 LAEVIKYGLIRDQGFLGWLEEHMDALVSLDPEALAEAIFRSCACKAEIVALDEREGGIRA 242

Query: 324 TLNLGHTFGHAIETGFGYGQWLHGEAVAAGMVMAVDMSYRLGWIDESIVNRAHNILQQAK 383
            LNLGHTFGHAIET  GYG WLHGEAV  GM+MA ++S   G I     +R + ++ +A 
Sbjct: 243 ILNLGHTFGHAIETYAGYGNWLHGEAVGTGMLMAAELSALEGMISRDDCDRINRLILRAG 302

Query: 384 LPTAPPETMTVEMFKSVMAVDKKVADGLLRLILLKGPLGNCVFTGDYDRKALDETLHAFC 443
           LP  PP  MT + F  +MAVDKK  DGLLRLILL+  +G+ V T +   + L  T   FC
Sbjct: 303 LPDKPPVAMTADDFMGLMAVDKKNVDGLLRLILLRS-VGDAVVTSEASPENLALTFARFC 361

Query: 444 KS 445
            S
Sbjct: 362 SS 363


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: 414
Number of extensions: 19
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: 364
Length adjustment: 31
Effective length of query: 414
Effective length of database: 333
Effective search space:   137862
Effective search space used:   137862
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 GFF492 HP15_480 (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.32739.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   5.5e-118  380.0   0.0   6.2e-118  379.9   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF492  HP15_480 3-dehydroquinate syntha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF492  HP15_480 3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  379.9   0.0  6.2e-118  6.2e-118       1     337 [.      17     351 ..      17     358 .. 0.95

  Alignments for each domain:
  == domain 1  score: 379.9 bits;  conditional E-value: 6.2e-118
                          TIGR01357   1 ykvkvgegllk.klveelaekasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletvaklldql 75 
                                        y++ +gegll  +  +++ +   +++++t+e+v+ l+ e+ ++     g +v+++v+pdge+ K+++t++++ d l
  lcl|FitnessBrowser__Marino:GFF492  17 YPIFIGEGLLGtQDLSAFVS-GAQVMIVTNETVAPLYLERAKACFP--GKRVDTVVLPDGEKFKDWQTLNSIFDGL 89 
                                        57889999998655555553.689*************988888874..8*************************** PP

                          TIGR01357  76 leeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgkNliGafyqPkaVl 151
                                        le+ ++rk++lva+GGGvvgD+aGF+Aa y+RG++++q+PTtll++vDssvGGKtgin+plgkN+iGaf+qP+aVl
  lcl|FitnessBrowser__Marino:GFF492  90 LEHRHTRKTTLVALGGGVVGDMAGFAAACYQRGVPFIQIPTTLLSQVDSSVGGKTGINHPLGKNMIGAFHQPQAVL 165
                                        **************************************************************************** PP

                          TIGR01357 152 idlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeelikrsievKaevVeeDekesgl 227
                                        id++ l+tlp re+++G+aEviK+gli d+ ++ +le++ ++l++l + eal+e+i+rs+ +Kae+V+ De+e g+
  lcl|FitnessBrowser__Marino:GFF492 166 IDTASLQTLPAREVSAGLAEVIKYGLIRDQGFLGWLEEHMDALVSL-DPEALAEAIFRSCACKAEIVALDEREGGI 240
                                        *****************************************99976.55*************************** PP

                          TIGR01357 228 RalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgllkaellerlvallkklglptklkkklsveel 302
                                        Ra+LN+GHt+gHaiE+ ++y+ + HGeaV +Gm ++a+ls   g++++++ +r+ +l+ ++glp k +  ++++ +
  lcl|FitnessBrowser__Marino:GFF492 241 RAILNLGHTFGHAIETYAGYGnWLHGEAVGTGMLMAAELSALEGMISRDDCDRINRLILRAGLPDKPPVAMTADDF 316
                                        **************************************************************************** PP

                          TIGR01357 303 lkallkDKKnegskiklvlleeiGkaalasevtee 337
                                        +  +  DKKn ++ ++l+ll+++G+a+++se + e
  lcl|FitnessBrowser__Marino:GFF492 317 MGLMAVDKKNVDGLLRLILLRSVGDAVVTSEASPE 351
                                        **************************999876554 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (364 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: 8.41
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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