Alignments for a candidate for aroB in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Sinorhizobium meliloti 1021

Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate SMc00696 SMc00696 3-dehydroquinate synthase

Query= BRENDA::Q3M4V2
         (363 letters)



>FitnessBrowser__Smeli:SMc00696
          Length = 377

 Score =  278 bits (710), Expect = 2e-79
 Identities = 160/364 (43%), Positives = 220/364 (60%), Gaps = 9/364 (2%)

Query: 5   INVNLPTQSYEIAIAPASLDQIGQSLAGLKLGKKVLLVSNPTIFKHFGKVAVDSLEAAGF 64
           + V+L  +SY+I I P  +   G+ +A    G+K+ ++++  +   + +  + SL  +G 
Sbjct: 13  VRVDLAERSYDILIGPGLIAAAGKEIASRLKGRKMAVITDENVAPRYLEPLMASLGESGI 72

Query: 65  QVASYCLPAGERYKTLNSIQKLYDIALENRLERSSTMVALGGGVIGDMTGFAAATWLRGI 124
           +  S  LPAGE+ K+   +  + +  L  R+ER+  ++ALGGGVIGD+TGFAA    RG 
Sbjct: 73  EAVSLILPAGEKTKSFEHLIPVCEAILGARIERNDAVIALGGGVIGDLTGFAAGIVRRGS 132

Query: 125 NVVQVPTTLLAMVDSAIGGKTGVNHPHGKNLIGAFHQPRFVLIDPQVLKTLPVREFRAGM 184
             +Q+PT+LLA VDS++GGKTG+N  HGKNLIG FHQP  VL D   L TL  REFRAG 
Sbjct: 133 RFIQIPTSLLAQVDSSVGGKTGINSAHGKNLIGVFHQPDLVLADTAALDTLSPREFRAGY 192

Query: 185 AEVIKYGVIWDAELFNQLEQSKRLDQLRYIKPELMDAILTRSCQAKADVVGKDEKEGGLR 244
           AEV KYG+I   E F  LE  K    +    P  ++AI   SCQAKADVV  DE+E G R
Sbjct: 193 AEVAKYGLIDKPEFFEWLE--KNWQAVFAGGPARIEAIAV-SCQAKADVVAADERENGRR 249

Query: 245 AILNYGHTVGHAVESLTNY--RLLKHGEAVGIGMVAAGQIAVNLGLWQQADADRQNALIE 302
           A+LN GHT GHA+E+ T+Y  + L HGE V IGMV A + +  + L    DA R  A ++
Sbjct: 250 ALLNLGHTFGHALEAATDYDSKRLVHGEGVAIGMVLAHEFSARMNLASPDDARRVEAHLK 309

Query: 303 KAGLPTKL---PAGL-DIEGIIEALQLDKKVKDGKVRFVLPTQIGVVTVTDEVTSDHIRQ 358
             GLPT+L   P  L   + ++EA+  DKKVK GK+ F+L   IG   V D+V S  +  
Sbjct: 310 TVGLPTRLADIPGALPPADRLMEAIAQDKKVKGGKLTFILTRGIGQSFVADDVPSSEVLS 369

Query: 359 VLQQ 362
            L +
Sbjct: 370 FLTE 373


Lambda     K      H
   0.319    0.136    0.388 

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: 389
Number of extensions: 11
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: 363
Length of database: 377
Length adjustment: 30
Effective length of query: 333
Effective length of database: 347
Effective search space:   115551
Effective search space used:   115551
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate SMc00696 SMc00696 (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.7567.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
     9e-111  356.3   0.0     1e-110  356.1   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc00696  SMc00696 3-dehydroquinate syntha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc00696  SMc00696 3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  356.1   0.0    1e-110    1e-110       1     341 [.      22     369 ..      22     372 .. 0.97

  Alignments for each domain:
  == domain 1  score: 356.1 bits;  conditional E-value: 1e-110
                           TIGR01357   1 ykvkvgegllkklveelae..kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletvaklld 73 
                                         y++ +g gl++++ +e+a+  k +k+ vitde+v+  + e l + l + g+e+  l++p+ge++Ks+e++  + +
  lcl|FitnessBrowser__Smeli:SMc00696  22 YDILIGPGLIAAAGKEIASrlKGRKMAVITDENVAPRYLEPLMASLGESGIEAVSLILPAGEKTKSFEHLIPVCE 96 
                                         6899*******999999997666*********************99999************************** PP

                           TIGR01357  74 qlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgkNliGafyqPk 148
                                         ++l + +er+++++a+GGGv+gDl+GF+A +  RG r++q+PT+lla+vDssvGGKtgin ++gkNliG f+qP+
  lcl|FitnessBrowser__Smeli:SMc00696  97 AILGARIERNDAVIALGGGVIGDLTGFAAGIVRRGSRFIQIPTSLLAQVDSSVGGKTGINSAHGKNLIGVFHQPD 171
                                         *************************************************************************** PP

                           TIGR01357 149 aVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeelikrsievKaevVeeDek 223
                                         +Vl d++ l tl+ re+r+G+aEv K+gli   e+fe+lekn++++       a  e+i+ s++ Ka+vV++De+
  lcl|FitnessBrowser__Smeli:SMc00696 172 LVLADTAALDTLSPREFRAGYAEVAKYGLIDKPEFFEWLEKNWQAVFA--GGPARIEAIAVSCQAKADVVAADER 244
                                         ********************************************8884..679999******************* PP

                           TIGR01357 224 esglRalLNfGHtlgHaiEallkyk...lsHGeaVaiGmvveaklseklgllkaellerlvallkklglptklkk 295
                                         e+g RalLN+GHt+gHa+Ea+++y+   l HGe VaiGmv++ ++s ++ l+++++++r++a lk++glpt+l +
  lcl|FitnessBrowser__Smeli:SMc00696 245 ENGRRALLNLGHTFGHALEAATDYDskrLVHGEGVAIGMVLAHEFSARMNLASPDDARRVEAHLKTVGLPTRLAD 319
                                         ************************99999********************************************** PP

                           TIGR01357 296 ....klsveellkallkDKKnegskiklvlleeiGkaalasevteeelle 341
                                                ++ l++a+ +DKK +g+k++++l + iG+ ++a++v+++e+l+
  lcl|FitnessBrowser__Smeli:SMc00696 320 ipgaLPPADRLMEAIAQDKKVKGGKLTFILTRGIGQSFVADDVPSSEVLS 369
                                         99987899***********************************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (377 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: 8.76
//
[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