GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdh in Sinorhizobium meliloti 1021

Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate SMc01564 SMc01564 L-threonine 3-dehydrogenase

Query= BRENDA::P07913
         (341 letters)



>FitnessBrowser__Smeli:SMc01564
          Length = 344

 Score =  513 bits (1322), Expect = e-150
 Identities = 240/340 (70%), Positives = 282/340 (82%)

Query: 1   MKALSKLKAEEGIWMTDVPVPELGHNDLLIKIRKTAICGTDVHIYNWDEWSQKTIPVPMV 60
           MKAL K K E G+WM  VPVPE+G ND+LI++RK+AICGTDVHI+NWD+W++KTIPVPMV
Sbjct: 5   MKALVKTKPEVGLWMERVPVPEIGPNDVLIRVRKSAICGTDVHIWNWDQWAEKTIPVPMV 64

Query: 61  VGHEYVGEVVGIGQEVKGFKIGDRVSGEGHITCGHCRNCRGGRTHLCRNTIGVGVNRPGC 120
           VGHE++GEVV +G  V    +G+RVSGEGHI CG CRNCR GR HLCRNT+GVGVNRPG 
Sbjct: 65  VGHEFMGEVVEVGPAVSKHHVGERVSGEGHIVCGKCRNCRAGRGHLCRNTLGVGVNRPGS 124

Query: 121 FAEYLVIPAFNAFKIPDNISDDLAAIFDPFGNAVHTALSFDLVGEDVLVSGAGPIGIMAA 180
           FAE++ +P +N   IPD++ D++AAIFDPFGNAVHTALSFDLVGEDVLV+GAGPIGIM A
Sbjct: 125 FAEFVCLPEYNVVSIPDDVPDEIAAIFDPFGNAVHTALSFDLVGEDVLVTGAGPIGIMGA 184

Query: 181 AVAKHVGARNVVITDVNEYRLELARKMGITRAVNVAKENLNDVMAELGMTEGFDVGLEMS 240
            VAK  GAR VVITD+N  RL+LARK+GI   V+ +KE L DVM  +GMTEGFDVGLEMS
Sbjct: 185 MVAKRCGARKVVITDINPVRLDLARKLGIDHVVDASKEKLADVMRVIGMTEGFDVGLEMS 244

Query: 241 GAPPAFRTMLDTMNHGGRIAMLGIPPSDMSIDWTKVIFKGLFIKGIYGREMFETWYKMAA 300
           GA PAFR M+D MN+GG+IA+LGI P+   IDW KVIFK L +KGIYGREMFETWYKM A
Sbjct: 245 GAAPAFRDMIDKMNNGGKIAILGIAPAGFEIDWNKVIFKMLNLKGIYGREMFETWYKMIA 304

Query: 301 LIQSGLDLSPIITHRFSIDDFQKGFDAMRSGQSGKVILSW 340
            +Q GLDLSPIITHR  IDDF+ GF+AMRSG SGKV++ W
Sbjct: 305 FVQGGLDLSPIITHRIGIDDFRDGFEAMRSGNSGKVVMDW 344


Lambda     K      H
   0.322    0.140    0.433 

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: 525
Number of extensions: 20
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: 341
Length of database: 344
Length adjustment: 29
Effective length of query: 312
Effective length of database: 315
Effective search space:    98280
Effective search space used:    98280
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 (21.9 bits)
S2: 49 (23.5 bits)

Align candidate SMc01564 SMc01564 (L-threonine 3-dehydrogenase)
to HMM TIGR00692 (tdh: L-threonine 3-dehydrogenase (EC 1.1.1.103))

# 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.carbon/TIGR00692.hmm
# target sequence database:        /tmp/gapView.24478.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00692  [M=340]
Accession:   TIGR00692
Description: tdh: L-threonine 3-dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   6.1e-158  511.2   1.8   6.9e-158  511.0   1.8    1.0  1  lcl|FitnessBrowser__Smeli:SMc01564  SMc01564 L-threonine 3-dehydroge


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc01564  SMc01564 L-threonine 3-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  511.0   1.8  6.9e-158  6.9e-158       1     339 [.       7     343 ..       7     344 .] 0.99

  Alignments for each domain:
  == domain 1  score: 511.0 bits;  conditional E-value: 6.9e-158
                           TIGR00692   1 almkkkaeeGavltevpvpelgknevlikvkatsicGtdvhiynwdewaqkrikvpqvlGhevaGevvgiGeeve 75 
                                         al+k+k+e G ++  vpvpe+g+n+vli+v++++icGtdvhi+nwd+wa+k+i+vp+v+Ghe+ Gevv++G+ v+
  lcl|FitnessBrowser__Smeli:SMc01564   7 ALVKTKPEVGLWMERVPVPEIGPNDVLIRVRKSAICGTDVHIWNWDQWAEKTIPVPMVVGHEFMGEVVEVGPAVS 81 
                                         799************************************************************************ PP

                           TIGR00692  76 gvkvGdyvsaethivcGkcvacrrGkshvcrntkivGvdtaGvfaeyvvvpadnifknpkdidpelaaiqeplGn 150
                                           +vG++vs+e+hivcGkc++cr+G+ h+crnt +vGv+++G fae+v +p  n+  +p+d+++e+aai++p+Gn
  lcl|FitnessBrowser__Smeli:SMc01564  82 KHHVGERVSGEGHIVCGKCRNCRAGRGHLCRNTLGVGVNRPGSFAEFVCLPEYNVVSIPDDVPDEIAAIFDPFGN 156
                                         *************************************************************************** PP

                           TIGR00692 151 avdtvlesdlaGesvlvsGaGpiGllavavakaaGasqvivsdkneyrlelakkvGatrvvnvakedlvkvvael 225
                                         av+t+l++dl+Ge+vlv+GaGpiG++++ vak +Ga++v+++d n  rl+la+k+G+++vv+  ke+l +v+  +
  lcl|FitnessBrowser__Smeli:SMc01564 157 AVHTALSFDLVGEDVLVTGAGPIGIMGAMVAKRCGARKVVITDINPVRLDLARKLGIDHVVDASKEKLADVMRVI 231
                                         *************************************************************************** PP

                           TIGR00692 226 tsgeGvdvvlelsGapkaleqgldavangGrvallglpeskvtidltnkvifkgltikGitGrklfetwykvsrl 300
                                         +++eG+dv+le+sGa +a+++++d ++ngG++a+lg+ ++   id++ kvifk l +kGi+Gr++fetwyk+ ++
  lcl|FitnessBrowser__Smeli:SMc01564 232 GMTEGFDVGLEMSGAAPAFRDMIDKMNNGGKIAILGIAPAGFEIDWN-KVIFKMLNLKGIYGREMFETWYKMIAF 305
                                         **********************************************9.*************************** PP

                           TIGR00692 301 iqsnkldlapiithkfkldefekgfelmrsGksGkvili 339
                                         +q  +ldl+piith+  +d+f++gfe+mrsG+sGkv++ 
  lcl|FitnessBrowser__Smeli:SMc01564 306 VQG-GLDLSPIITHRIGIDDFRDGFEAMRSGNSGKVVMD 343
                                         **8.9********************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (344 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: 7.52
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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