Alignments for a candidate for aroG in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Sinorhizobium meliloti 1021

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate SMc00155 SMc00155 DAHP synthetase prtein

Query= BRENDA::P29976
         (525 letters)



>FitnessBrowser__Smeli:SMc00155
          Length = 457

 Score =  531 bits (1367), Expect = e-155
 Identities = 260/454 (57%), Positives = 330/454 (72%), Gaps = 2/454 (0%)

Query: 72  ALKWTPESWKLKKALQLPDYPNANELESVLKTIEAFPPIVFAGEARNLEERLADAAVGKA 131
           A  WTP SW+ K   Q+PDYP+   L+SV   +  +PP+VFAGEAR L+  LA+ A G+ 
Sbjct: 2   AQTWTPNSWRQKPIQQVPDYPDLAVLDSVEARLAKYPPLVFAGEARRLKSALANVAEGRG 61

Query: 132 FLLQGGDCAESFKEFNATNIRDTFRVLLQMSIVLTFGGQVPVIKVGRMAGQFAKPRSDAF 191
           FLLQGGDCAESF E  A  IRD FR  LQM++VLTFG Q PV+KVGR+AGQFAKPRS   
Sbjct: 62  FLLQGGDCAESFAEHGADTIRDFFRAFLQMAVVLTFGAQQPVVKVGRIAGQFAKPRSSGV 121

Query: 192 EEKDGVKLPSYKGDNINGDTFDEKSRIPDPNRMIRAYTQSAATLNLLRAFATGGYAAIQR 251
           E++  V LPSY+GD ING  F E++R+P+P R + AY QSAATLNLLRAFA GGYA ++ 
Sbjct: 122 EKQGDVTLPSYRGDIINGIEFTEEARVPNPERQVMAYRQSAATLNLLRAFAMGGYANLEN 181

Query: 252 VTQWNLDFVEQSEQADRYQELANRVDEALGFMSACGL-GTDHPLMTTTDFYTSHECLLLP 310
           V QW L FV+ S QA+RY++LA+R+ E + FM A G+   +HP +  TDF+TSHE LLL 
Sbjct: 182 VHQWMLGFVKDSPQAERYRKLADRISETMDFMKAIGITAENHPSLRETDFFTSHEALLLG 241

Query: 311 YEQSLTRLDSTSGLYYDCSAHMVWCGERTRQLDGAHVEFLRGIANPLGIKVSNKMDPFEL 370
           YEQ+LTR+DSTSG +Y  S HM+W G+RTRQ D AH+E+ RGI NPLG+K    +    L
Sbjct: 242 YEQALTRVDSTSGDWYATSGHMIWIGDRTRQPDHAHIEYCRGIKNPLGLKCGPSLTADGL 301

Query: 371 VKLVEILNPNNKPGRITVIVRMGAENMRVKLPHLIRAVRRSGQIVTWVCDPMHGNTIKAP 430
           ++L++ILNP N+ GR+T+I R G + +   LP LIRAV R G+ V W CDPMHGNTI   
Sbjct: 302 LELIDILNPANEAGRLTLICRFGHDKVAEHLPRLIRAVEREGKKVVWSCDPMHGNTITLN 361

Query: 431 CGLKTRAFDSILAEVRAFLDVHEQEGSHAGGIHLEMTGQNVTECIGGSRTVTYDDLSSRY 490
              KTR F+ IL+EV +F  +H  EGSH GGIH+EMTG +VTEC GG+R ++ DDL+ RY
Sbjct: 362 -NYKTRPFERILSEVESFFQIHRAEGSHPGGIHIEMTGNDVTECTGGARALSGDDLADRY 420

Query: 491 HTHCDPRLNASQSLELAFIVAERLRKRRTGSQRV 524
           HTHCDPRLNA Q+LELAF++AER++  R   + V
Sbjct: 421 HTHCDPRLNADQALELAFLLAERMKGGRDEKKMV 454


Lambda     K      H
   0.318    0.132    0.389 

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: 651
Number of extensions: 25
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: 525
Length of database: 457
Length adjustment: 34
Effective length of query: 491
Effective length of database: 423
Effective search space:   207693
Effective search space used:   207693
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: 52 (24.6 bits)

Align candidate SMc00155 SMc00155 (DAHP synthetase prtein)
to HMM TIGR01358 (3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54))

# 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/TIGR01358.hmm
# target sequence database:        /tmp/gapView.15022.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01358  [M=443]
Accession:   TIGR01358
Description: DAHP_synth_II: 3-deoxy-7-phosphoheptulonate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
     3e-216  704.0   0.0   3.5e-216  703.8   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc00155  SMc00155 DAHP synthetase prtein


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc00155  SMc00155 DAHP synthetase prtein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  703.8   0.0  3.5e-216  3.5e-216       1     440 [.       5     445 ..       5     448 .. 0.99

  Alignments for each domain:
  == domain 1  score: 703.8 bits;  conditional E-value: 3.5e-216
                           TIGR01358   1 wsleswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesfkevead 75 
                                         w+++swr+kp +q+P+yPd + l++v++ l+++PPlv+age+++lk+ la+va+G++fllqgGdcaesf e  ad
  lcl|FitnessBrowser__Smeli:SMc00155   5 WTPNSWRQKPIQQVPDYPDLAVLDSVEARLAKYPPLVFAGEARRLKSALANVAEGRGFLLQGGDCAESFAEHGAD 79 
                                         89************************************************************************* PP

                           TIGR01358  76 nirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaafdeaarvpdperl 150
                                         +ird +r++lqmavvlt+ga+ PvvkvgriaGq+akPrs+ +e++++vtlpsyrGd+ing +f+e+arvp+per 
  lcl|FitnessBrowser__Smeli:SMc00155  80 TIRDFFRAFLQMAVVLTFGAQQPVVKVGRIAGQFAKPRSSGVEKQGDVTLPSYRGDIINGIEFTEEARVPNPERQ 154
                                         *************************************************************************** PP

                           TIGR01358 151 vrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealrfmsavgvaeae..alkrv 223
                                         v ay +saatlnllra++ gGya+l++vh+W l fvk+sp+++ry+kla++i+e++ fm+a+g++ ++  +l+++
  lcl|FitnessBrowser__Smeli:SMc00155 155 VMAYRQSAATLNLLRAFAMGGYANLENVHQWMLGFVKDSPQAERYRKLADRISETMDFMKAIGITAENhpSLRET 229
                                         ***************************************************************99888799**** PP

                           TIGR01358 224 elytsheallldyeealtrvdskegqlfdlsahllWiGertrqldgahveflrgvknPigikvgpsmeadellkl 298
                                         +++tshealll ye+altrvds++g+++ +s+h++WiG+rtrq d+ah+e+ rg+knP+g+k+gps++ad ll+l
  lcl|FitnessBrowser__Smeli:SMc00155 230 DFFTSHEALLLGYEQALTRVDSTSGDWYATSGHMIWIGDRTRQPDHAHIEYCRGIKNPLGLKCGPSLTADGLLEL 304
                                         *************************************************************************** PP

                           TIGR01358 299 ievldPenePGrltlisrlGaekiaeklPelleavkaaGravvWvtdpmhGntleaasGyktrrfddilsevkef 373
                                         i++l+P ne Grltli r+G +k+ae+lP+l++av+++G++vvW +dpmhGnt++  + yktr f++ilsev++f
  lcl|FitnessBrowser__Smeli:SMc00155 305 IDILNPANEAGRLTLICRFGHDKVAEHLPRLIRAVEREGKKVVWSCDPMHGNTIT-LNNYKTRPFERILSEVESF 378
                                         *****************************************************96.577**************** PP

                           TIGR01358 374 fevhkaeGthpGGvhleltGedvteclGGareitetdlasryetacdPrlnaeqslelaflvaeklr 440
                                         f++h+aeG+hpGG+h+e+tG+dvtec+GGar+++ +dla+ry+t+cdPrlna+q+lelafl+ae+++
  lcl|FitnessBrowser__Smeli:SMc00155 379 FQIHRAEGSHPGGIHIEMTGNDVTECTGGARALSGDDLADRYHTHCDPRLNADQALELAFLLAERMK 445
                                         ****************************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (443 nodes)
Target sequences:                          1  (457 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: 12.43
//
[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