GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroG in Sphingomonas koreensis DSMZ 15582

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate Ga0059261_0258 Ga0059261_0258 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (EC 2.5.1.54)

Query= BRENDA::P29976
         (525 letters)



>FitnessBrowser__Korea:Ga0059261_0258
          Length = 527

 Score =  543 bits (1399), Expect = e-159
 Identities = 265/446 (59%), Positives = 333/446 (74%), Gaps = 1/446 (0%)

Query: 72  ALKWTPESWKLKKALQLPDYPNANELESVLKTIEAFPPIVFAGEARNLEERLADAAVGKA 131
           A+ WTP+SWK  +A QLP YP+   L +    + +FPP+VFAGEAR L + LA  A G+A
Sbjct: 73  AMGWTPDSWKSAEARQLPIYPDTATLAAATTQLSSFPPLVFAGEARALTQELAKVARGEA 132

Query: 132 FLLQGGDCAESFKEFNATNIRDTFRVLLQMSIVLTFGGQVPVIKVGRMAGQFAKPRSDAF 191
           FLLQGGDCAESF EF+  NIRDTFRV+LQM++VLTF  ++P +KVGRMAGQFAKPRS   
Sbjct: 133 FLLQGGDCAESFAEFHPNNIRDTFRVILQMAVVLTFASKLPTVKVGRMAGQFAKPRSADT 192

Query: 192 EEKDGVKLPSYKGDNINGDTFDEKSRIPDPNRMIRAYTQSAATLNLLRAFATGGYAAIQR 251
           E  +GV+LPSY+GDN+N   F  ++RIPDP RMI+ Y+QSAATLNLLRAFA+GGYA + +
Sbjct: 193 ETINGVELPSYRGDNVNDIAFTPEARIPDPQRMIQGYSQSAATLNLLRAFASGGYANLHQ 252

Query: 252 VTQWNLDFVEQSEQADRYQELANRVDEALGFMSACGLGTDH-PLMTTTDFYTSHECLLLP 310
           V +W LDF+ +S  + ++ ++A+R+ EAL FM ACG+  D  P +  TDFYTSHE LLLP
Sbjct: 253 VHKWTLDFMGKSPWSAKFADVADRIGEALDFMQACGIDADSVPQLKGTDFYTSHEALLLP 312

Query: 311 YEQSLTRLDSTSGLYYDCSAHMVWCGERTRQLDGAHVEFLRGIANPLGIKVSNKMDPFEL 370
           YEQ+LTR DS +G +YD SAHM+W G+RTR    AHVEFLRGI NP+G+K    ++P  L
Sbjct: 313 YEQALTRQDSLTGDWYDTSAHMLWIGDRTRFDGSAHVEFLRGIGNPIGMKCGPSLEPDAL 372

Query: 371 VKLVEILNPNNKPGRITVIVRMGAENMRVKLPHLIRAVRRSGQIVTWVCDPMHGNTIKAP 430
           ++L++ LNP   PGR+T+I R G + +   LP L+RAV+R G  V W CDPMHGN +KA 
Sbjct: 373 LRLLDTLNPARTPGRLTLITRYGHDKIEDGLPKLVRAVKREGHPVVWSCDPMHGNVVKAA 432

Query: 431 CGLKTRAFDSILAEVRAFLDVHEQEGSHAGGIHLEMTGQNVTECIGGSRTVTYDDLSSRY 490
            G KTR F+ ILAEVR F  VH  EG++AGGIH EMTGQNVTEC GG   V+  DL+ RY
Sbjct: 433 NGYKTRPFERILAEVRGFFAVHRAEGTYAGGIHAEMTGQNVTECTGGMIDVSEHDLADRY 492

Query: 491 HTHCDPRLNASQSLELAFIVAERLRK 516
           HTHCDPRLNA QSLELAF++AE L +
Sbjct: 493 HTHCDPRLNAGQSLELAFLLAEMLNE 518


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: 723
Number of extensions: 19
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: 525
Length of database: 527
Length adjustment: 35
Effective length of query: 490
Effective length of database: 492
Effective search space:   241080
Effective search space used:   241080
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 Ga0059261_0258 Ga0059261_0258 (3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (EC 2.5.1.54))
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.17367.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.7e-215  699.1   0.0   1.2e-214  698.8   0.0    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_0258  Ga0059261_0258 3-deoxy-D-arabino


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_0258  Ga0059261_0258 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (EC 2.5.
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  698.8   0.0  1.2e-214  1.2e-214       1     441 [.      76     518 ..      76     520 .. 0.99

  Alignments for each domain:
  == domain 1  score: 698.8 bits;  conditional E-value: 1.2e-214
                                 TIGR01358   1 wsleswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesf 69 
                                               w+++sw+s +a qlP yPd+++l a +++l+s+PPlv+age+++l ++la+va+GeafllqgGdcaesf
  lcl|FitnessBrowser__Korea:Ga0059261_0258  76 WTPDSWKSAEARQLPIYPDTATLAAATTQLSSFPPLVFAGEARALTQELAKVARGEAFLLQGGDCAESF 144
                                               89******************************************************************* PP

                                 TIGR01358  70 keveadnirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaaf 138
                                                e++ +nird++rv+lqmavvlt++++lP vkvgr+aGq+akPrs+++e+ +gv+lpsyrGd++n  af
  lcl|FitnessBrowser__Korea:Ga0059261_0258 145 AEFHPNNIRDTFRVILQMAVVLTFASKLPTVKVGRMAGQFAKPRSADTETINGVELPSYRGDNVNDIAF 213
                                               ********************************************************************* PP

                                 TIGR01358 139 deaarvpdperlvrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealr 207
                                               + +ar+pdp+r+++ y++saatlnllra++sgGya+l++vh+W+l+f++ksp +a++ ++a++i+eal 
  lcl|FitnessBrowser__Korea:Ga0059261_0258 214 TPEARIPDPQRMIQGYSQSAATLNLLRAFASGGYANLHQVHKWTLDFMGKSPWSAKFADVADRIGEALD 282
                                               ********************************************************************* PP

                                 TIGR01358 208 fmsavgvaeae..alkrvelytsheallldyeealtrvdskegqlfdlsahllWiGertrqldgahvef 274
                                               fm+a+g++ ++  +lk +++ytshealll+ye+altr+ds +g+++d+sah+lWiG+rtr    ahvef
  lcl|FitnessBrowser__Korea:Ga0059261_0258 283 FMQACGIDADSvpQLKGTDFYTSHEALLLPYEQALTRQDSLTGDWYDTSAHMLWIGDRTRFDGSAHVEF 351
                                               *******9999899**********************************************9889***** PP

                                 TIGR01358 275 lrgvknPigikvgpsmeadellklievldPenePGrltlisrlGaekiaeklPelleavkaaGravvWv 343
                                               lrg+ nPig+k+gps+e+d ll+l++ l+P + PGrltli+r G +ki + lP+l++avk++G+ vvW 
  lcl|FitnessBrowser__Korea:Ga0059261_0258 352 LRGIGNPIGMKCGPSLEPDALLRLLDTLNPARTPGRLTLITRYGHDKIEDGLPKLVRAVKREGHPVVWS 420
                                               ********************************************************************* PP

                                 TIGR01358 344 tdpmhGntleaasGyktrrfddilsevkeffevhkaeGthpGGvhleltGedvteclGGareitetdla 412
                                               +dpmhGn ++aa+Gyktr f++il+ev++ff+vh+aeGt+ GG+h e+tG++vtec+GG  +++e+dla
  lcl|FitnessBrowser__Korea:Ga0059261_0258 421 CDPMHGNVVKAANGYKTRPFERILAEVRGFFAVHRAEGTYAGGIHAEMTGQNVTECTGGMIDVSEHDLA 489
                                               ********************************************************************* PP

                                 TIGR01358 413 sryetacdPrlnaeqslelaflvaeklre 441
                                               +ry+t+cdPrlna qslelafl+ae+l+e
  lcl|FitnessBrowser__Korea:Ga0059261_0258 490 DRYHTHCDPRLNAGQSLELAFLLAEMLNE 518
                                               **************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (443 nodes)
Target sequences:                          1  (527 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: 00:00:00.02
# Mc/sec: 8.58
//
[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:

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:

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:

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:

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