GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapA in Lentibacillus jeotgali Grbi

Align dihydrodipicolinate synthase subunit (EC 4.3.3.7) (characterized)
to candidate WP_010531457.1 ON01_RS12820 4-hydroxy-tetrahydrodipicolinate synthase

Query= metacyc::MONOMER-6565
         (289 letters)



>NCBI__GCF_000224785.1:WP_010531457.1
          Length = 295

 Score =  368 bits (945), Expect = e-107
 Identities = 175/286 (61%), Positives = 234/286 (81%)

Query: 1   MNFGNIATAMVTPFDKNENIDFQKLSKLIDYLLNNGTDSLVVAGTTGESPTLSEEEKVAL 60
           MNFG + TAMVTPFD+N +IDF     L++YL+ NG+D LVVAGTTGESPTL+  EK+ L
Sbjct: 1   MNFGQVLTAMVTPFDQNGDIDFNATRTLVNYLIANGSDGLVVAGTTGESPTLTNNEKLDL 60

Query: 61  IQYSVKEAAGRAPIIAGTGSNNTKASIKLTKKAEEAGADAVMLVTPYYNKPSQEGMYRHF 120
            ++  + A GRA +IAGTGSN+T ASI+LT++AE  G DA+ML TPYYNKPSQEG+Y+H+
Sbjct: 61  FRFVAQVADGRAAVIAGTGSNSTWASIELTQQAEATGIDAIMLTTPYYNKPSQEGLYQHY 120

Query: 121 RAIAEETSLPVMLYNVPGRTAASLAPETTIRLAEIPNIIAIKEASGDLDAITKIVAETPE 180
           +AIA+ TSLPVMLYNVPGR+A ++APETTIRL+EI NI+++KEASG+LDA+T+IV++T +
Sbjct: 121 KAIAQATSLPVMLYNVPGRSAVAIAPETTIRLSEISNIVSVKEASGNLDAMTEIVSKTSD 180

Query: 181 DFAVYSGDDSLTLPALSVGARGIVSVASHIIGPEMQEMIKHYTEGNTAQAALIHQKLLPL 240
           +F +YSGDDSLTLPAL++G  G++SVASHIIG +M+EM + +  G+   AA IHQKLLP 
Sbjct: 181 EFTLYSGDDSLTLPALTIGGSGVISVASHIIGSDMKEMAQSFKNGDVQNAAFIHQKLLPT 240

Query: 241 MKGLFAAPNPSPLKTALQLKGLDVGSVRLPLIPLNEDERLRLSSLM 286
           M+ LFA P+PSP+K AL + G+ VG VRLP+IPL+ +E+ +L  ++
Sbjct: 241 MQALFAQPSPSPVKAALNMMGIYVGDVRLPMIPLSSEEKQQLRQML 286


Lambda     K      H
   0.313    0.131    0.357 

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: 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: 289
Length of database: 295
Length adjustment: 26
Effective length of query: 263
Effective length of database: 269
Effective search space:    70747
Effective search space used:    70747
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate WP_010531457.1 ON01_RS12820 (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.3921554.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.1e-115  369.9   0.2   3.8e-115  369.6   0.2    1.0  1  NCBI__GCF_000224785.1:WP_010531457.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000224785.1:WP_010531457.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  369.6   0.2  3.8e-115  3.8e-115       2     283 ..       6     286 ..       5     288 .. 0.99

  Alignments for each domain:
  == domain 1  score: 369.6 bits;  conditional E-value: 3.8e-115
                             TIGR00674   2 vltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpviaGt 74 
                                           vltA++TPf+++g++df+a  +l++++i++g+d++vv+GtTGEs+tL+ +Ek ++++++++++++r  viaGt
  NCBI__GCF_000224785.1:WP_010531457.1   6 VLTAMVTPFDQNGDIDFNATRTLVNYLIANGSDGLVVAGTTGESPTLTNNEKLDLFRFVAQVADGRAAVIAGT 78 
                                           89*********************************************************************** PP

                             TIGR00674  75 gsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvslepetvkr 147
                                           gsn+t  +ielt++ae +g+d+++++tPyYnkP+qeGly+h+kaia++++lP++lYnvP+R++v ++pet++r
  NCBI__GCF_000224785.1:WP_010531457.1  79 GSNSTWASIELTQQAEATGIDAIMLTTPYYNKPSQEGLYQHYKAIAQATSLPVMLYNVPGRSAVAIAPETTIR 151
                                           ************************************************************************* PP

                             TIGR00674 148 LaeeveivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnvapkelkemvkaale 220
                                           L+e  +iv++Keasg+l+ ++ei+++++++f+++sGdD+ltl+ l++G++GviSVas+++++++kem + + +
  NCBI__GCF_000224785.1:WP_010531457.1 152 LSEISNIVSVKEASGNLDAMTEIVSKTSDEFTLYSGDDSLTLPALTIGGSGVISVASHIIGSDMKEMAQSFKN 224
                                           ************************************************************************* PP

                             TIGR00674 221 gdteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekkeklkevl 283
                                           gd+++a+ ihqkll++++alf ++ P pvK+al+++g+ ++ ++RlP+ +ls+e+k++l+++l
  NCBI__GCF_000224785.1:WP_010531457.1 225 GDVQNAAFIHQKLLPTMQALFAQPSPSPVKAALNMMGIYVG-DVRLPMIPLSSEEKQQLRQML 286
                                           *****************************************.9****************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (286 nodes)
Target sequences:                          1  (295 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: 21.31
//
[ok]

This GapMind analysis is from Jul 26 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