GapMind for Amino acid biosynthesis

 

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

Align 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; EC 4.3.3.7 (characterized)
to candidate Ac3H11_277 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7)

Query= SwissProt::Q9JZR4
         (291 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_277
          Length = 299

 Score =  323 bits (827), Expect = 4e-93
 Identities = 160/291 (54%), Positives = 208/291 (71%), Gaps = 1/291 (0%)

Query: 2   LQGSLVALITPMNQDGSIHYEQLRDLIDWHIENGTDGIVAVGTTGESATLSVEEHTAVIE 61
           L GS+VAL+TPM+ DGS+ Y  LR LIDWHI  GTD I  VGTTGES T++VEEH  +I 
Sbjct: 8   LTGSIVALVTPMHADGSVDYPALRKLIDWHIAEGTDCIGVVGTTGESPTVNVEEHCEIIR 67

Query: 62  AVVKHVAKRVPVIAGTGANNTVEAIALSQAAEKAGADYTLSVVPYYNKPSQEGIYQHFKT 121
             V+  AKRVP++AG GAN+T EAI L++ A   GAD  L VVPYYNKP+QEG +QHFK 
Sbjct: 68  VAVEQSAKRVPIMAGCGANSTAEAIELAKFARGVGADSQLQVVPYYNKPTQEGQFQHFKA 127

Query: 122 IAEATS-IPMIIYNVPGRTVVSMTNDTILRLAEIPNIVGVKEASGNIGSNIELINRAPEG 180
           IAEAT  +P+++YNVPGR+V  M +DT+LRLA++P I+G+KEA+GNI     LI   P+G
Sbjct: 128 IAEATGDLPIVLYNVPGRSVADMQHDTVLRLAQVPGIIGIKEATGNIERAQWLIRDVPQG 187

Query: 181 FVVLSGDDHTALPFMLCGGHGVITVAANAAPKLFADMCRAALQGDIALARELNDRLIPIY 240
           F V SGDD TA+  MLCGGHG I+V AN AP+L  ++C AAL GD   A E+  +L+P++
Sbjct: 188 FGVYSGDDPTAVALMLCGGHGNISVTANVAPRLMHELCVAALAGDARRAMEIQFKLMPVH 247

Query: 241 DTMFCEPSPAAPKWAVSALGRCEPHVRLPLVPLTENGQAKVRAALKASGQL 291
             +F E +P   KWA++ +G C   +RLP+ PL    +A V AAL++SG L
Sbjct: 248 KNLFVEANPIPVKWAMARMGLCGGTMRLPMTPLASGNEAVVEAALRSSGLL 298


Lambda     K      H
   0.317    0.133    0.386 

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: 315
Number of extensions: 8
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: 291
Length of database: 299
Length adjustment: 26
Effective length of query: 265
Effective length of database: 273
Effective search space:    72345
Effective search space used:    72345
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: 48 (23.1 bits)

Align candidate Ac3H11_277 (4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7))
to HMM TIGR00674 (dapA: 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7))

# 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/TIGR00674.hmm
# target sequence database:        /tmp/gapView.31922.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00674  [M=286]
Accession:   TIGR00674
Description: dapA: 4-hydroxy-tetrahydrodipicolinate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   1.6e-112  361.0   0.0   1.8e-112  360.8   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_277  4-hydroxy-tetrahydrodipicolinate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_277  4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  360.8   0.0  1.8e-112  1.8e-112       1     284 [.      10     293 ..      10     295 .. 0.99

  Alignments for each domain:
  == domain 1  score: 360.8 bits;  conditional E-value: 1.8e-112
                                       TIGR00674   1 gvltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavel 63 
                                                     g+++Al+TP+++dgsvd+ al kli+ +i++g+d i vvGtTGEs+t ++eE+ ++i+vave 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_277  10 GSIVALVTPMHADGSVDYPALRKLIDWHIAEGTDCIGVVGTTGESPTVNVEEHCEIIRVAVEQ 72 
                                                     589************************************************************ PP

                                       TIGR00674  64 vknrvpviaGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeev.el 125
                                                     +++rvp++aG+g+n+t+eaiel+k+a+ +g+d+ l+v+PyYnkPtqeG+++hfkaiae++ +l
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_277  73 SAKRVPIMAGCGANSTAEAIELAKFARGVGADSQLQVVPYYNKPTQEGQFQHFKAIAEATgDL 135
                                                     ***********************************************************99** PP

                                       TIGR00674 126 PiilYnvPsRtgvslepetvkrLaeeveivaiKeasgdlervseikaeakedfkvlsGdDalt 188
                                                     Pi+lYnvP+R++++++ +tv+rLa+ + i++iKea+g++er++ +++ +++ f v+sGdD ++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_277 136 PIVLYNVPGRSVADMQHDTVLRLAQVPGIIGIKEATGNIERAQWLIRDVPQGFGVYSGDDPTA 198
                                                     *************************************************************** PP

                                       TIGR00674 189 leilalGakGviSVasnvapkelkemvkaalegdteeareihqkllklfkalfietNPipvKt 251
                                                      +++++G++G iSV++nvap++++e++ aal+gd ++a ei+ kl++++k lf+e+NPipvK+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_277 199 VALMLCGGHGNISVTANVAPRLMHELCVAALAGDARRAMEIQFKLMPVHKNLFVEANPIPVKW 261
                                                     *************************************************************** PP

                                       TIGR00674 252 alallgliekdelRlPLtelseekkeklkevlk 284
                                                     a+a +gl+ + ++RlP+t+l + ++  ++++l+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_277 262 AMARMGLCGG-TMRLPMTPLASGNEAVVEAALR 293
                                                     **********.****************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (286 nodes)
Target sequences:                          1  (299 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.46
//
[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