GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroG in Dechlorosoma suillum PS

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate Dsui_3444 Dsui_3444 phospho-2-dehydro-3-deoxyheptonate aldolase

Query= BRENDA::C3TIE2
         (350 letters)



>FitnessBrowser__PS:Dsui_3444
          Length = 365

 Score =  470 bits (1210), Expect = e-137
 Identities = 231/344 (67%), Positives = 276/344 (80%)

Query: 6   DDLRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGPCSIHD 65
           DD+RI+EIKEL+PP  +  ++P +  AA T   AR+ IH+IL G DDRLLVVIGPCSIHD
Sbjct: 16  DDVRIREIKELVPPAHVFREYPVSNRAAQTTYGARQGIHRILHGADDRLLVVIGPCSIHD 75

Query: 66  PVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQINDGLRI 125
             AA EYA RL    E LKD+L +VMRVYFEKPRTTVGWKGLINDP MD SF+IN+GLR+
Sbjct: 76  YEAAMEYAQRLQKEAERLKDDLLVVMRVYFEKPRTTVGWKGLINDPRMDGSFRINEGLRL 135

Query: 126 ARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLSCPVGF 185
           ARK+LLDIN+ GL  A EFLD I+PQY ADL++WGAIGARTTESQVHRELASGLSCPVGF
Sbjct: 136 ARKILLDINELGLSCATEFLDTISPQYTADLIAWGAIGARTTESQVHRELASGLSCPVGF 195

Query: 186 KNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPNYSAKH 245
           KNGTDG +++A+DAI +A APH FLSVTK GHSAIV+T+GN DCH+ILRGGK PNY A  
Sbjct: 196 KNGTDGNVRIAVDAIRSASAPHHFLSVTKGGHSAIVSTAGNEDCHVILRGGKGPNYDAAS 255

Query: 246 VAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVMVESHL 305
           V    + +  AGL A++M+DFSHANSSK+F++Q+DV  DV  Q+A G++ IIGVMVESHL
Sbjct: 256 VDAACKDIAAAGLAARLMVDFSHANSSKKFERQVDVAKDVATQLAAGDERIIGVMVESHL 315

Query: 306 VEGNQSLESGEPLAYGKSITDACIGWEDTDALLRQLANAVKARR 349
           VEG Q +   +PL YGKS+TDACIGWED+  +L  LA AV+ RR
Sbjct: 316 VEGRQDITPDKPLEYGKSVTDACIGWEDSVRVLDILARAVRERR 359


Lambda     K      H
   0.317    0.134    0.397 

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: 450
Number of extensions: 8
Number of successful extensions: 1
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: 350
Length of database: 365
Length adjustment: 29
Effective length of query: 321
Effective length of database: 336
Effective search space:   107856
Effective search space used:   107856
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: 49 (23.5 bits)

Align candidate Dsui_3444 Dsui_3444 (phospho-2-dehydro-3-deoxyheptonate aldolase)
to HMM TIGR00034 (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/TIGR00034.hmm
# target sequence database:        /tmp/gapView.10416.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00034  [M=342]
Accession:   TIGR00034
Description: aroFGH: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   6.1e-171  553.7   0.0     7e-171  553.5   0.0    1.0  1  lcl|FitnessBrowser__PS:Dsui_3444  Dsui_3444 phospho-2-dehydro-3-de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_3444  Dsui_3444 phospho-2-dehydro-3-deoxyheptonate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  553.5   0.0    7e-171    7e-171       1     342 []      16     359 ..      16     359 .. 0.99

  Alignments for each domain:
  == domain 1  score: 553.5 bits;  conditional E-value: 7e-171
                         TIGR00034   1 ddlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakrlkklaek 77 
                                       dd+ri +i+el++P+++ +++p++++aa++   +r+ i++il+G ddrllvviGPcsihd eaa+eya+rl+k ae+
  lcl|FitnessBrowser__PS:Dsui_3444  16 DDVRIREIKELVPPAHVFREYPVSNRAAQTTYGARQGIHRILHGADDRLLVVIGPCSIHDYEAAMEYAQRLQKEAER 92 
                                       799************************************************************************** PP

                         TIGR00034  78 lkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatelldtispqyladllsw 154
                                       lkddl +vmrvyfekPrttvGWkGlindP +++sf++n+Glr+ark+lld++elgl  ate+ldtispqy adl++w
  lcl|FitnessBrowser__PS:Dsui_3444  93 LKDDLLVVMRVYFEKPRTTVGWKGLINDPRMDGSFRINEGLRLARKILLDINELGLSCATEFLDTISPQYTADLIAW 169
                                       ***************************************************************************** PP

                         TIGR00034 155 gaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvtkaGqvaivetkGnedghiilrGG 231
                                       gaiGarttesqvhrelasgls+pvgfkngtdG++++a+dair+a+a+h+flsvtk G++aiv+t+Gned+h+ilrGG
  lcl|FitnessBrowser__PS:Dsui_3444 170 GAIGARTTESQVHRELASGLSCPVGFKNGTDGNVRIAVDAIRSASAPHHFLSVTKGGHSAIVSTAGNEDCHVILRGG 246
                                       ***************************************************************************** PP

                         TIGR00034 232 kkpnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlevaesvveqiaeGekaiiGvmiesnleeGnqsl. 307
                                       k pnyda++v+++++++ +agl ++lm+dfsh+ns+k+++rq++va++v+ q+a G++ iiGvm+es+l+eG+q++ 
  lcl|FitnessBrowser__PS:Dsui_3444 247 KGPNYDAASVDAACKDIAAAGLAARLMVDFSHANSSKKFERQVDVAKDVATQLAAGDERIIGVMVESHLVEGRQDIt 323
                                       ****************************************************************************8 PP

                         TIGR00034 308 .keelkyGksvtdacigwedteallrklaeavkerr 342
                                        +++l+yGksvtdacigwed+ ++l  la+av+err
  lcl|FitnessBrowser__PS:Dsui_3444 324 pDKPLEYGKSVTDACIGWEDSVRVLDILARAVRERR 359
                                       889******************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (365 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: 9.85
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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