GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapA in Thermodesulforhabdus norvegica DSM 9990

Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate WP_093396409.1 BM091_RS13075 4-hydroxy-tetrahydrodipicolinate synthase

Query= BRENDA::O67216
         (294 letters)



>NCBI__GCF_900114975.1:WP_093396409.1
          Length = 292

 Score =  318 bits (815), Expect = 9e-92
 Identities = 157/291 (53%), Positives = 212/291 (72%), Gaps = 2/291 (0%)

Query: 1   MFQGSIVALITPFKEGEVDYEALGNLIEFHVDNGTDAILVCGTTGESPTLTFEEHEKVIE 60
           MF+G+ VA++TPFK+G+VD +AL  LI++ ++ GT  I+ CGTTGES TL+FEEHE+V+E
Sbjct: 1   MFKGAFVAIVTPFKDGKVDEDALRKLIDYQIEQGTHGIVPCGTTGESATLSFEEHERVVE 60

Query: 61  FAVKRAAGRIKVIAGTGGNATHEAVHLTAHAKEVGADGALVVVPYYNKPTQRGLYEHFKT 120
             V+    R+ V+AGTG N T EA+ LT HA++VGADGAL++ PYYNKPTQ GLY HF+ 
Sbjct: 61  ITVEHVNKRVPVLAGTGSNNTAEAIRLTRHAEKVGADGALMISPYYNKPTQEGLYRHFEK 120

Query: 121 VAQEVDIPIIIYNIPSRTCVEISVDTMFKLASECENIVASKESTPNMDRISEIVKRLGES 180
           VA  V+IPII+YNIP RT V I  +TM +L S  ENIV  KE++ ++ ++ EI+ R GE+
Sbjct: 121 VAASVNIPIIVYNIPGRTAVNIEPETMERL-SRIENIVGVKEASGSIKQVMEIIARCGEN 179

Query: 181 FSVLSGDDSLTLPMMALGAKGVISVANNVMPREVKELIRAALEGDFRRAREIHYYLHDLF 240
           F VLSG+D +T P+++LG KGVISV +NV PR++ ++   ALEG +  AR +HY L  L 
Sbjct: 180 FDVLSGEDYITFPLLSLGGKGVISVVSNVAPRDMADMCNFALEGKWDEARSLHYKLLPLC 239

Query: 241 KVLFIETNPIPVKTACWMLG-MCEKEFRLPLTEMSPENENKLREVLKKYNL 290
            +LF ETNP+PVK A  M+G +   E RLPL  +S  N NKL+ VLK+Y L
Sbjct: 240 NILFCETNPVPVKAALHMMGKIPSDEVRLPLAPLSENNRNKLQSVLKQYGL 290


Lambda     K      H
   0.318    0.136    0.390 

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: 273
Number of extensions: 4
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: 294
Length of database: 292
Length adjustment: 26
Effective length of query: 268
Effective length of database: 266
Effective search space:    71288
Effective search space used:    71288
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 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate WP_093396409.1 BM091_RS13075 (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.2851039.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.5e-126  405.0   0.0   7.3e-126  404.8   0.0    1.0  1  NCBI__GCF_900114975.1:WP_093396409.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900114975.1:WP_093396409.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  404.8   0.0  7.3e-126  7.3e-126       3     286 .]       6     288 ..       4     288 .. 0.99

  Alignments for each domain:
  == domain 1  score: 404.8 bits;  conditional E-value: 7.3e-126
                             TIGR00674   3 ltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpviaGtg 75 
                                            +A++TPfk+ + vd +al kli++qie+g+ +iv++GtTGEsatLs+eE+++v+e++ve v++rvpv+aGtg
  NCBI__GCF_900114975.1:WP_093396409.1   6 FVAIVTPFKDGK-VDEDALRKLIDYQIEQGTHGIVPCGTTGESATLSFEEHERVVEITVEHVNKRVPVLAGTG 77 
                                           79******9988.************************************************************ PP

                             TIGR00674  76 snateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvslepetvkrL 148
                                           sn+t+eai+lt++aek+g+dg+l+++PyYnkPtqeGly+hf+++a++v++Pii+Yn+P+Rt+v++epet+ rL
  NCBI__GCF_900114975.1:WP_093396409.1  78 SNNTAEAIRLTRHAEKVGADGALMISPYYNKPTQEGLYRHFEKVAASVNIPIIVYNIPGRTAVNIEPETMERL 150
                                           ************************************************************************* PP

                             TIGR00674 149 aeeveivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnvapkelkemvkaaleg 221
                                           ++ ++iv++Keasg++++v+ei+a+ +e+f vlsG+D +t ++l+lG+kGviSV+snvap+++++m++ aleg
  NCBI__GCF_900114975.1:WP_093396409.1 151 SRIENIVGVKEASGSIKQVMEIIARCGENFDVLSGEDYITFPLLSLGGKGVISVVSNVAPRDMADMCNFALEG 223
                                           ************************************************************************* PP

                             TIGR00674 222 dteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekkeklkevlkel 286
                                           + +ear +h+kll+l+++lf+etNP+pvK+al+++g i +de+RlPL++lse++++kl++vlk++
  NCBI__GCF_900114975.1:WP_093396409.1 224 KWDEARSLHYKLLPLCNILFCETNPVPVKAALHMMGKIPSDEVRLPLAPLSENNRNKLQSVLKQY 288
                                           **************************************************************985 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 12.99
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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