Alignments for a candidate for aroG in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Acidovorax sp. GW101-3H11

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate Ac3H11_4034 2-keto-3-deoxy-D-arabino-heptulosonate-7- phosphate synthase I alpha (EC 2.5.1.54)

Query= BRENDA::C3TIE2
         (350 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4034
          Length = 373

 Score =  429 bits (1104), Expect = e-125
 Identities = 215/351 (61%), Positives = 263/351 (74%), Gaps = 5/351 (1%)

Query: 4   QNDDLRIKEIKELLPPVALLEKFPATENAANT-VAHARKAIHKILKGNDDRLLVVIGPCS 62
           Q DD RIK+I  L PP  L+  FP       T +   RK IH I+ G DDRLLV+IGPCS
Sbjct: 21  QTDDERIKDITVLPPPEHLIRFFPIGGTPVETLITQTRKNIHNIMAGKDDRLLVIIGPCS 80

Query: 63  IHDPVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQINDG 122
           IHDP AA +YA RL+A+R +  D LEIVMRVYFEKPRTTVGWKGLINDP++D S++I++G
Sbjct: 81  IHDPAAAVDYARRLMAVRTQYADTLEIVMRVYFEKPRTTVGWKGLINDPYLDESYRIDEG 140

Query: 123 LRIARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLSCP 182
           LRIAR+LL++IN  G+PA  EFLD+I+PQY+ DL+SWGAIGARTTESQVHRELASG+S P
Sbjct: 141 LRIARQLLIEINRLGMPAGSEFLDVISPQYIGDLISWGAIGARTTESQVHRELASGISAP 200

Query: 183 VGFKNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPNYS 242
           +GFKNGTDG I++A DAI +A   H FLSV K G  AIVNT GN DCH+ILRGGK PNY 
Sbjct: 201 IGFKNGTDGNIRIATDAIQSASRGHHFLSVHKNGQVAIVNTKGNKDCHVILRGGKTPNYD 260

Query: 243 AKHVAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVMVE 302
           A  VA   + L  A LPA +M+D SHANSSKQ +KQ++V  DV  Q+AGG +++ G+M+E
Sbjct: 261 AVSVAAACKDLEAAKLPATLMVDCSHANSSKQHEKQLEVARDVAAQLAGGSRSVFGLMIE 320

Query: 303 SHLVEGNQSLESGE----PLAYGKSITDACIGWEDTDALLRQLANAVKARR 349
           SHL  G Q    G+     L YGKSITDAC+GW+D+   L +L++AVKARR
Sbjct: 321 SHLTAGAQKFTPGKDDASKLEYGKSITDACLGWDDSLQALAELSDAVKARR 371


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: 435
Number of extensions: 10
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: 350
Length of database: 373
Length adjustment: 29
Effective length of query: 321
Effective length of database: 344
Effective search space:   110424
Effective search space used:   110424
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 Ac3H11_4034 (2-keto-3-deoxy-D-arabino-heptulosonate-7- phosphate synthase I alpha (EC 2.5.1.54))
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.925.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   1.7e-164  532.5   0.0     2e-164  532.3   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4034  2-keto-3-deoxy-D-arabino-heptulo


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4034  2-keto-3-deoxy-D-arabino-heptulosonate-7- phosphate synthase I alpha
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  532.3   0.0    2e-164    2e-164       1     342 []      23     371 ..      23     371 .. 0.97

  Alignments for each domain:
  == domain 1  score: 532.3 bits;  conditional E-value: 2e-164
                                        TIGR00034   1 ddlrivkidelltPeelkakfpltek.aaekvaksrkeiadilaGkddrllvviGPcsihdp 61 
                                                      dd ri++i  l +Pe+l++ fp+  + +++ ++++rk+i++i+aGkddrllv+iGPcsihdp
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4034  23 DDERIKDITVLPPPEHLIRFFPIGGTpVETLITQTRKNIHNIMAGKDDRLLVIIGPCSIHDP 84 
                                                      7899*******************8762566799***************************** PP

                                        TIGR00034  62 eaaleyakrlkklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriark 123
                                                       aa++ya+rl +++ ++ d leivmrvyfekPrttvGWkGlindP+l+es+++++Glriar+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4034  85 AAAVDYARRLMAVRTQYADTLEIVMRVYFEKPRTTVGWKGLINDPYLDESYRIDEGLRIARQ 146
                                                      ************************************************************** PP

                                        TIGR00034 124 llldlvelglplatelldtispqyladllswgaiGarttesqvhrelasglslpvgfkngtd 185
                                                      ll++++ lg+p+++e+ld+ispqy++dl+swgaiGarttesqvhrelasg+s p+gfkngtd
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4034 147 LLIEINRLGMPAGSEFLDVISPQYIGDLISWGAIGARTTESQVHRELASGISAPIGFKNGTD 208
                                                      ************************************************************** PP

                                        TIGR00034 186 GslkvaidairaaaaehlflsvtkaGqvaivetkGnedghiilrGGkkpnydaedvaevkee 247
                                                      G++++a dai++a++ h+flsv+k+Gqvaiv+tkGn+d+h+ilrGGk+pnyda +va+++++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4034 209 GNIRIATDAIQSASRGHHFLSVHKNGQVAIVNTKGNKDCHVILRGGKTPNYDAVSVAAACKD 270
                                                      ************************************************************** PP

                                        TIGR00034 248 lekaglkeelmidfshgnsnkdykrqlevaesvveqiaeGekaiiGvmiesnleeGnqsl.. 307
                                                      le+a+l ++lm+d+sh+ns+k++++qleva++v++q+a G+++++G+mies+l+ G+q+   
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4034 271 LEAAKLPATLMVDCSHANSSKQHEKQLEVARDVAAQLAGGSRSVFGLMIESHLTAGAQKFtp 332
                                                      **********************************************************9744 PP

                                        TIGR00034 308 .k...eelkyGksvtdacigwedteallrklaeavkerr 342
                                                       k   ++l+yGks+tdac+gw+d+ + l++l++avk+rr
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4034 333 gKddaSKLEYGKSITDACLGWDDSLQALAELSDAVKARR 371
                                                      31333679****************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (373 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.33
//
[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