GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapA in Pseudomonas fluorescens FW300-N2E3

Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate AO353_17670 AO353_17670 4-hydroxy-tetrahydrodipicolinate synthase

Query= BRENDA::Q9I4W3
         (292 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_17670
          Length = 292

 Score =  479 bits (1233), Expect = e-140
 Identities = 241/291 (82%), Positives = 261/291 (89%)

Query: 1   MIAGSMVALVTPFDAQGRLDWDSLAKLVDFHLQEGTNAIVAVGTTGESATLDVEEHIQVI 60
           MIAGSMVALVTP DAQGRLDWDSL+KLVDFHLQ GT+AIVAVGTTGESATLDV EHI+VI
Sbjct: 1   MIAGSMVALVTPMDAQGRLDWDSLSKLVDFHLQNGTHAIVAVGTTGESATLDVNEHIEVI 60

Query: 61  RRVVDQVKGRIPVIAGTGANSTREAVALTEAAKSGGADACLLVTPYYNKPTQEGMYQHFR 120
           RRVV QV GRIPVIAGTGANSTREA+ LT  AK+ GADACLLVTPYYNKPTQEG+Y HF+
Sbjct: 61  RRVVKQVNGRIPVIAGTGANSTREAIELTTNAKTAGADACLLVTPYYNKPTQEGLYLHFK 120

Query: 121 HIAEAVAIPQILYNVPGRTSCDMLPETVERLSKVPNIIGIKEATGDLQRAKEVIERVGKD 180
            IAEAV IPQILYNVPGRT+CDM  ETV RLS V NIIGIKEATGDL RAK +++ V KD
Sbjct: 121 TIAEAVDIPQILYNVPGRTACDMQAETVIRLSTVKNIIGIKEATGDLSRAKAILDGVSKD 180

Query: 181 FLVYSGDDATAVELMLLGGKGNISVTANVAPRAMSDLCAAAMRGDAAAARAINDRLMPLH 240
           FLV SGDDATAVEL+LLGGKGNISVTANVAPR MSDLC AA+ GDA  ARAI+++LMPL+
Sbjct: 181 FLVISGDDATAVELILLGGKGNISVTANVAPRDMSDLCIAALNGDAVKARAIHEKLMPLN 240

Query: 241 KALFIESNPIPVKWALHEMGLIPEGIRLPLTWLSPRCHEPLRQAMRQTGVL 291
           K LFIESNPIPVKWALHEMGL+P+GIRLPLTWLS  CHEPLRQAMRQ+GVL
Sbjct: 241 KTLFIESNPIPVKWALHEMGLMPDGIRLPLTWLSEACHEPLRQAMRQSGVL 291


Lambda     K      H
   0.319    0.134    0.393 

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: 344
Number of extensions: 6
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: 292
Length of database: 292
Length adjustment: 26
Effective length of query: 266
Effective length of database: 266
Effective search space:    70756
Effective search space used:    70756
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate AO353_17670 AO353_17670 (4-hydroxy-tetrahydrodipicolinate synthase)
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.9696.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   4.9e-117  375.8   0.0   5.5e-117  375.6   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_17670  AO353_17670 4-hydroxy-tetrahydro


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_17670  AO353_17670 4-hydroxy-tetrahydrodipicolinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  375.6   0.0  5.5e-117  5.5e-117       2     284 ..       5     286 ..       4     288 .. 0.99

  Alignments for each domain:
  == domain 1  score: 375.6 bits;  conditional E-value: 5.5e-117
                                     TIGR00674   2 vltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvkn 66 
                                                   +++Al+TP++++g +d ++l+kl+++++++g+ aiv+vGtTGEsatL ++E+++vi+ +v+ v++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_17670   5 SMVALVTPMDAQGRLDWDSLSKLVDFHLQNGTHAIVAVGTTGESATLDVNEHIEVIRRVVKQVNG 69 
                                                   799************************************************************** PP

                                     TIGR00674  67 rvpviaGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYn 131
                                                   r+pviaGtg+n+t+eaielt+ a+ +g+d++l+vtPyYnkPtqeGly hfk+iae+v++P+ilYn
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_17670  70 RIPVIAGTGANSTREAIELTTNAKTAGADACLLVTPYYNKPTQEGLYLHFKTIAEAVDIPQILYN 134
                                                   ***************************************************************** PP

                                     TIGR00674 132 vPsRtgvslepetvkrLaeeveivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGa 196
                                                   vP+Rt+++++ etv+rL++ ++i++iKea+gdl+r++ i   +++df v sGdDa++ e+++lG+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_17670 135 VPGRTACDMQAETVIRLSTVKNIIGIKEATGDLSRAKAILDGVSKDFLVISGDDATAVELILLGG 199
                                                   ***************************************************************** PP

                                     TIGR00674 197 kGviSVasnvapkelkemvkaalegdteeareihqkllklfkalfietNPipvKtalallgliek 261
                                                   kG iSV++nvap+++++++ aal+gd  +ar ih+kl++l k+lfie+NPipvK+al+ +gl+  
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_17670 200 KGNISVTANVAPRDMSDLCIAALNGDAVKARAIHEKLMPLNKTLFIESNPIPVKWALHEMGLMPD 264
                                                   ***************************************************************99 PP

                                     TIGR00674 262 delRlPLtelseekkeklkevlk 284
                                                     +RlPLt lse  +e l+++++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_17670 265 -GIRLPLTWLSEACHEPLRQAMR 286
                                                   .9**********99999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (286 nodes)
Target sequences:                          1  (292 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: 9.60
//
[ok]

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

Links

Downloads

Related tools

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:

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