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_1501 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7)

Query= SwissProt::Q57695
         (289 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1501
          Length = 309

 Score =  148 bits (373), Expect = 2e-40
 Identities = 90/272 (33%), Positives = 143/272 (52%), Gaps = 2/272 (0%)

Query: 2   FKGVYPAIITPFKNKEVDFDGLEENINFLIENGVSGIVAVGTTGESPTLSHEEHKKVIEK 61
           F G++ A++TPFK+  VD   L      L   GV+G VA G+TGE+  L   E  +V+E 
Sbjct: 23  FSGLWIALVTPFKDGAVDHPALAALTARLRAQGVAGFVACGSTGEAAALDKAEQLQVLET 82

Query: 62  VVDVVNGRVQVIAGAGSNCTEEAIELSVFAEDVGADAVLSITPYYNKPTQEGLRKHFGKV 121
           V+    G   V+  +G +  +   ++   A    A  ++S  P+Y +P+QEGL   F  +
Sbjct: 83  VLQAAQGLPVVMGVSGYHQGQVLQQVQALARYPVAGLLVS-APHYIRPSQEGLLHWFRTL 141

Query: 122 AESINLPIVLYNVPSRTAVNLEPKTVKLLAEEYSNISAVKEANPNLSQVSELIHDAKITV 181
           A++  +P+++Y++P RT   +  +T+  LA  +  I A+K+   + ++   LI D ++ V
Sbjct: 142 ADASAVPLLIYDIPYRTGATITTETLLALAA-HPRIQAIKDCGGSPAKTQALISDGRLQV 200

Query: 182 LSGNDELTLPIIALGGKGVISVVANIVPKEFVEMVNYALEGDFEKAREIHYKLFPLMKAM 241
           L+G D      +ALGG G IS  A+     FVE++     GD  +AR +   L P ++  
Sbjct: 201 LTGEDAQIFHTLALGGAGAISASAHWQTPRFVELMALLRAGDLGEARRVWRALLPWIEVC 260

Query: 242 FIETNPIPVKTALNMMGRPAGELRLPLCEMSE 273
           F E NP P+KT L   G    ELR P+   SE
Sbjct: 261 FAEPNPAPLKTVLAHAGEMCNELRAPMMGASE 292


Lambda     K      H
   0.315    0.135    0.374 

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: 203
Number of extensions: 8
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: 289
Length of database: 309
Length adjustment: 27
Effective length of query: 262
Effective length of database: 282
Effective search space:    73884
Effective search space used:    73884
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: 42 (22.0 bits)
S2: 48 (23.1 bits)

Align candidate Ac3H11_1501 (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.24097.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
    3.3e-68  215.6   0.0      4e-68  215.3   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1501  4-hydroxy-tetrahydrodipicolinate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1501  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 !  215.3   0.0     4e-68     4e-68       3     277 ..      27     296 ..      25     302 .. 0.97

  Alignments for each domain:
  == domain 1  score: 215.3 bits;  conditional E-value: 4e-68
                                        TIGR00674   3 ltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelv 64 
                                                        Al+TPfk+   vd  al+ l  ++ ++gv + v++G+TGE+a+L + E+ +v+e++++ +
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1501  27 WIALVTPFKDGA-VDHPALAALTARLRAQGVAGFVACGSTGEAAALDKAEQLQVLETVLQAA 87 
                                                      679*****9888.************************************************* PP

                                        TIGR00674  65 knrvpviaGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelP 126
                                                      ++ +pv+ G+++    ++++ ++ ++  +v+g+lv++P Y +P+qeGl+++f ++a+++ +P
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1501  88 QG-LPVVMGVSGYHQGQVLQQVQALARYPVAGLLVSAPHYIRPSQEGLLHWFRTLADASAVP 148
                                                      *9.*********************************************************** PP

                                        TIGR00674 127 iilYnvPsRtgvslepetvkrLaeeveivaiKeasgdlervseikaeakedfkvlsGdDalt 188
                                                      +++Y++P Rtg+ ++ et+++La++++i aiK+++g+ ++ + +++  +  ++vl+G+Da  
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1501 149 LLIYDIPYRTGATITTETLLALAAHPRIQAIKDCGGSPAKTQALIS--DGRLQVLTGEDAQI 208
                                                      *******************************************999..557*********** PP

                                        TIGR00674 189 leilalGakGviSVasnvapkelkemvkaalegdteeareihqkllklfkalfietNPipvK 250
                                                       + lalG++G iS  ++  + ++ e+++   +gd  ear + + ll+ +++ f e+NP p+K
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1501 209 FHTLALGGAGAISASAHWQTPRFVELMALLRAGDLGEARRVWRALLPWIEVCFAEPNPAPLK 270
                                                      ************************************************************** PP

                                        TIGR00674 251 talallgliekdelRlPLtelseekke 277
                                                      t+la +g + + elR P++ +se  + 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1501 271 TVLAHAGEMCN-ELRAPMMGASEALNL 296
                                                      *******9999.*******99987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (286 nodes)
Target sequences:                          1  (309 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: 00:00:00.00
# Mc/sec: 10.35
//
[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