GapMind for Amino acid biosynthesis

 

Alignments for a candidate for DAPtransferase in Synechococcus elongatus PCC 7942

Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate Synpcc7942_0853 Synpcc7942_0853 L,L-diaminopimelate aminotransferase

Query= BRENDA::Q3MAL4
         (411 letters)



>FitnessBrowser__SynE:Synpcc7942_0853
          Length = 411

 Score =  708 bits (1827), Expect = 0.0
 Identities = 342/405 (84%), Positives = 376/405 (92%)

Query: 1   MATINDNYLKLKAGYLFPEIARRVNAFAEANPDAKIIRLGIGDVTEPLPEACRTAMIQAV 60
           MATINDNYLKLKAGYLFPEIARRVNAFA++NP+A IIRLGIGDVTEPLP ACR AMIQAV
Sbjct: 1   MATINDNYLKLKAGYLFPEIARRVNAFAQSNPEAAIIRLGIGDVTEPLPVACRQAMIQAV 60

Query: 61  EEMGDRSSFKGYGPEQGYAWLREKIATQDFQARGADVDASEIFISDGSKCDTGNILDIFG 120
           E+MG R +FKGYGPEQGYAWLREKIA  DFQ+RG +VDASEIFISDGSKCD GNILDIFG
Sbjct: 61  EDMGQRENFKGYGPEQGYAWLREKIAAHDFQSRGCEVDASEIFISDGSKCDCGNILDIFG 120

Query: 121 DNNIIAVTDPVYPVYVDTNVMAGHTGVANDKGEFEGLVYLPVTAENNFTAEIPSQKVDLI 180
           +NN IAVTDPVYPVYVDTNVMAGHTG AND+GE++GLVYLP++AENNFTAEIPS+KVDLI
Sbjct: 121 NNNRIAVTDPVYPVYVDTNVMAGHTGDANDRGEYDGLVYLPISAENNFTAEIPSEKVDLI 180

Query: 181 YLCFPNNPTGATATKEHLQAWVDYAKAHNSIIFFDAAYESYITDPSLPHSIYEIEGAREV 240
           YLCFPNNPTGA A++E+LQAWVDYA+A+ +II FDAAYE++ITDP++PHSI+EI GAR+ 
Sbjct: 181 YLCFPNNPTGAVASREYLQAWVDYARANGAIILFDAAYEAFITDPAIPHSIFEIPGARDC 240

Query: 241 AIEFRSFSKNAGFTGTRCALTVVPKTLKAKAADGSDVELWKLWNRRQSTKFNGVSYIVQR 300
           AIEFRSFSKNAGFTGTRCA TVVPK LK KAADGS+VELW LWNRRQSTKFNGVSYIVQR
Sbjct: 241 AIEFRSFSKNAGFTGTRCAFTVVPKGLKGKAADGSEVELWGLWNRRQSTKFNGVSYIVQR 300

Query: 301 GAEAVYSEAGQAQVKALVSFYLDNAKIIREKLTAAGLSVYGGVNAPYVWVKTPNGLSSWD 360
           GAEAVYS  GQAQ+K LV+FYL+NA+IIRE+LTAAGL V+GGVNAPYVWVKTP GL+SWD
Sbjct: 301 GAEAVYSAEGQAQIKELVAFYLENARIIREELTAAGLDVHGGVNAPYVWVKTPAGLTSWD 360

Query: 361 FFDKLLQTVNVVGTPGSGFGAAGEGYFRISAFNSRENVEEAMQRI 405
           FFDKLLQ  NVVGTPGSGFGAAGEGYFRISAFNSRENV  AMQRI
Sbjct: 361 FFDKLLQVCNVVGTPGSGFGAAGEGYFRISAFNSRENVVTAMQRI 405


Lambda     K      H
   0.317    0.134    0.397 

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: 665
Number of extensions: 21
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: 411
Length of database: 411
Length adjustment: 31
Effective length of query: 380
Effective length of database: 380
Effective search space:   144400
Effective search space used:   144400
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: 50 (23.9 bits)

Align candidate Synpcc7942_0853 Synpcc7942_0853 (L,L-diaminopimelate aminotransferase)
to HMM TIGR03542 (LL-diaminopimelate aminotransferase (EC 2.6.1.83))

# 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/TIGR03542.hmm
# target sequence database:        /tmp/gapView.10141.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03542  [M=402]
Accession:   TIGR03542
Description: DAPAT_plant: LL-diaminopimelate aminotransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.3e-189  613.7   0.0   8.4e-189  613.5   0.0    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_0853  Synpcc7942_0853 L,L-diaminopimel


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_0853  Synpcc7942_0853 L,L-diaminopimelate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  613.5   0.0  8.4e-189  8.4e-189       2     400 ..       3     407 ..       2     409 .. 0.98

  Alignments for each domain:
  == domain 1  score: 613.5 bits;  conditional E-value: 8.4e-189
                                 TIGR03542   2 kvnehflklkssylfseiakkvkefrkknpeadiirlgiGdvtqPlakaviealkeaveelaseetfrG 70 
                                               ++n+++lklk++ylf+eia++v+ f+++npea iirlgiGdvt+Pl+ a+ +a+ +ave++ ++e+f+G
  lcl|FitnessBrowser__SynE:Synpcc7942_0853   3 TINDNYLKLKAGYLFPEIARRVNAFAQSNPEAAIIRLGIGDVTEPLPVACRQAMIQAVEDMGQRENFKG 71 
                                               68******************************************************************* PP

                                 TIGR03542  71 yGpeqGldllreaiaeeeykgr...idpeeifisdGakcdvarllelfgsdktvavqdPvyPvyvdsav 136
                                               yGpeqG+ +lre+ia +++++r   +d++eifisdG+kcd++++l++fg+++ +av+dPvyPvyvd++v
  lcl|FitnessBrowser__SynE:Synpcc7942_0853  72 YGPEQGYAWLREKIAAHDFQSRgceVDASEIFISDGSKCDCGNILDIFGNNNRIAVTDPVYPVYVDTNV 140
                                               ***********************9********************************************* PP

                                 TIGR03542 137 laGragvldddgkykkivylpctkenefiPelpeekkvdiiylCsPnnPtGtvltkeqlkelvdyaken 205
                                               +aG++g ++d g+y  +vylp  +en+f  e+p+ek vd+iylC+PnnPtG+v+++e l+++vdya++n
  lcl|FitnessBrowser__SynE:Synpcc7942_0853 141 MAGHTGDANDRGEYDGLVYLPISAENNFTAEIPSEK-VDLIYLCFPNNPTGAVASREYLQAWVDYARAN 208
                                               ***********************************9.******************************** PP

                                 TIGR03542 206 dslilfdaayeafisdpslPksiyeiegakecaieirsfsktlGftGvrlgytvvPkelkvedg....e 270
                                               +++ilfdaayeafi+dp++P+si+ei+ga+ caie+rsfsk++GftG+r+++tvvPk lk + +     
  lcl|FitnessBrowser__SynE:Synpcc7942_0853 209 GAIILFDAAYEAFITDPAIPHSIFEIPGARDCAIEFRSFSKNAGFTGTRCAFTVVPKGLKGKAAdgseV 277
                                               ***********************************************************9765555666 PP

                                 TIGR03542 271 slkklWerllctkfnGaslivqraaeavlakeglqqikeaisyymenarilrkaleaaglkvyGGenaP 339
                                               +l  lW+r+++tkfnG+s+ivqr+aeav++ eg+ qike+++ y+enari+r++l+aagl v+GG+naP
  lcl|FitnessBrowser__SynE:Synpcc7942_0853 278 ELWGLWNRRQSTKFNGVSYIVQRGAEAVYSAEGQAQIKELVAFYLENARIIREELTAAGLDVHGGVNAP 346
                                               7889***************************************************************** PP

                                 TIGR03542 340 ylWvklpegissedffdkllkeaevvgtPGsGfGssGeGfvrlsalgkredivealerike 400
                                               y+Wvk+p+g++s+dffdkll+ ++vvgtPGsGfG++GeG++r+sa+++re++v+a++ri++
  lcl|FitnessBrowser__SynE:Synpcc7942_0853 347 YVWVKTPAGLTSWDFFDKLLQVCNVVGTPGSGFGAAGEGYFRISAFNSRENVVTAMQRIRS 407
                                               ***********************************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (402 nodes)
Target sequences:                          1  (411 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.88
//
[ok]

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

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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