Alignments for a candidate for aroB in Sinorhizobium medicae WSM419

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Sinorhizobium medicae WSM419

Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate YP_001328229.1 Smed_2564 3-dehydroquinate synthase

Query= BRENDA::P07639
         (362 letters)



>NCBI__GCF_000017145.1:YP_001328229.1
          Length = 380

 Score =  280 bits (715), Expect = 6e-80
 Identities = 167/363 (46%), Positives = 222/363 (61%), Gaps = 8/363 (2%)

Query: 3   RIVVTLGERSYPITIASGLFNEPASFLPLK-SGEQVMLVTNETLAPLYLDKVRGVLEQAG 61
           ++ V L ERSY I I  GL       +  +  G ++ ++T+E +AP YL+ +   L  +G
Sbjct: 15  KVRVDLAERSYDILIGPGLIAAAGGEIASRLKGRKMAVITDENVAPRYLEPLMASLAGSG 74

Query: 62  VNVDSVILPDGEQYKSLAVLDTVFTALLQKPHGRDTTLVALGGGVVGDLTGFAAASYQRG 121
           ++  S+ILP GE+ KS   L  V  A+L     R+  ++ALGGGV+GDLTGFAA   +RG
Sbjct: 75  MDPVSLILPAGEKTKSFEHLIPVCEAVLGARIERNDAVIALGGGVIGDLTGFAAGIVRRG 134

Query: 122 VRFIQVPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPASVVVDLDCLKTLPPRELASG 181
            RFIQ+PT+LL+QVDSSVGGKT +N P GKN+IG F+QP  V+ D   L TL PRE  +G
Sbjct: 135 SRFIQIPTSLLAQVDSSVGGKTGINSPHGKNLIGVFHQPDLVLADTAALDTLSPREFRAG 194

Query: 182 LAEVIKYGIILDGAFFNWLEENLDALLRLDGPAMAYCIRRCCELKAEVVAADERETGLRA 241
            AEV+KYG+I    FF WLE+N  A+    GPA    I   C+ KA+VVAADERE GLRA
Sbjct: 195 YAEVVKYGLIDKPDFFEWLEQNWQAVF-AGGPARIEAIAVSCQAKADVVAADERENGLRA 253

Query: 242 LLNLGHTFGHAIEAEMGYGN--WLHGEAVAAGMVMAARTSERLGQFSSAETQRIITLLKR 299
           LLNLGHTFGHA+EA  GY +   +HGE VA GMV+A   S R+   S  + +R+   LK 
Sbjct: 254 LLNLGHTFGHALEAATGYDSKRLVHGEGVAIGMVLAHEFSARMNIASPDDARRVEMHLKT 313

Query: 300 AGLP---VNGPREM-SAQAYLPHMLRDKKVLAGEMRLILPLAIGKSEVRSGVSHELVLNA 355
            GLP    + P  +  A   L  + +DKKV  G+   IL   IG+S +   V    VL+ 
Sbjct: 314 VGLPTRMADIPGMLPPADRLLEAIAQDKKVKGGKFTFILTRGIGQSFIADDVPSSEVLSF 373

Query: 356 IAD 358
           + +
Sbjct: 374 LEE 376


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: 340
Number of extensions: 8
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: 362
Length of database: 380
Length adjustment: 30
Effective length of query: 332
Effective length of database: 350
Effective search space:   116200
Effective search space used:   116200
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 YP_001328229.1 Smed_2564 (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.9394.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-111  357.0   0.0   6.2e-111  356.8   0.0    1.0  1  lcl|NCBI__GCF_000017145.1:YP_001328229.1  Smed_2564 3-dehydroquinate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000017145.1:YP_001328229.1  Smed_2564 3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  356.8   0.0  6.2e-111  6.2e-111       1     341 [.      25     372 ..      25     375 .. 0.97

  Alignments for each domain:
  == domain 1  score: 356.8 bits;  conditional E-value: 6.2e-111
                                 TIGR01357   1 ykvkvgegllkklveelae..kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKslet 67 
                                               y++ +g gl++++  e+a+  k +k+ vitde+v+  + e l + l+  g+    l++p+ge++Ks+e+
  lcl|NCBI__GCF_000017145.1:YP_001328229.1  25 YDILIGPGLIAAAGGEIASrlKGRKMAVITDENVAPRYLEPLMASLAGSGMDPVSLILPAGEKTKSFEH 93 
                                               6899*******999888887666********************************************** PP

                                 TIGR01357  68 vaklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlpl 136
                                               +  + +++l + +er+++++a+GGGv+gDl+GF+A +  RG r++q+PT+lla+vDssvGGKtgin p+
  lcl|NCBI__GCF_000017145.1:YP_001328229.1  94 LIPVCEAVLGARIERNDAVIALGGGVIGDLTGFAAGIVRRGSRFIQIPTSLLAQVDSSVGGKTGINSPH 162
                                               ********************************************************************* PP

                                 TIGR01357 137 gkNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealee 205
                                               gkNliG f+qP++Vl d++ l tl+ re+r+G+aEv+K+gli   ++fe+le+n++++       a  e
  lcl|NCBI__GCF_000017145.1:YP_001328229.1 163 GKNLIGVFHQPDLVLADTAALDTLSPREFRAGYAEVVKYGLIDKPDFFEWLEQNWQAVFA--GGPARIE 229
                                               ********************************************************8884..679999* PP

                                 TIGR01357 206 likrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk...lsHGeaVaiGmvveaklseklgl 271
                                               +i+ s++ Ka+vV++De+e+glRalLN+GHt+gHa+Ea+++y+   l HGe VaiGmv++ ++s ++ +
  lcl|NCBI__GCF_000017145.1:YP_001328229.1 230 AIAVSCQAKADVVAADERENGLRALLNLGHTFGHALEAATGYDskrLVHGEGVAIGMVLAHEFSARMNI 298
                                               ******************************************99999********************** PP

                                 TIGR01357 272 lkaellerlvallkklglptklkk....klsveellkallkDKKnegskiklvlleeiGkaalasevte 336
                                               +++++++r++  lk++glpt++ +       ++ ll+a+ +DKK +g+k +++l + iG+ ++a++v++
  lcl|NCBI__GCF_000017145.1:YP_001328229.1 299 ASPDDARRVEMHLKTVGLPTRMADipgmLPPADRLLEAIAQDKKVKGGKFTFILTRGIGQSFIADDVPS 367
                                               ************************99987899***********************************99 PP

                                 TIGR01357 337 eelle 341
                                               +e+l+
  lcl|NCBI__GCF_000017145.1:YP_001328229.1 368 SEVLS 372
                                               99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (380 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.05
//
[ok]

This GapMind analysis is from Apr 10 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