Aligments for a candidate for aroG in Sphingomonas koreensis DSMZ 15582

GapMind for Amino acid biosynthesis

Aligments 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)



>lcl|FitnessBrowser__Korea:Ga0059261_0258 Ga0059261_0258
           3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (EC
           2.5.1.54)
          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.4681.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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.02
# Mc/sec: 8.99
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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