GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdh in Phyllobacterium brassicacearum STM 196

Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate WP_106713900.1 CU102_RS25640 L-threonine 3-dehydrogenase

Query= BRENDA::P07913
         (341 letters)



>NCBI__GCF_003010955.1:WP_106713900.1
          Length = 345

 Score =  515 bits (1327), Expect = e-151
 Identities = 246/341 (72%), Positives = 281/341 (82%)

Query: 1   MKALSKLKAEEGIWMTDVPVPELGHNDLLIKIRKTAICGTDVHIYNWDEWSQKTIPVPMV 60
           MKAL K KAE GIWM  VPVPE G ND+LI+++K+AICGTDVHIYNWD+W+Q TIPVPMV
Sbjct: 5   MKALVKAKAEPGIWMERVPVPEPGPNDVLIRVKKSAICGTDVHIYNWDKWAQATIPVPMV 64

Query: 61  VGHEYVGEVVGIGQEVKGFKIGDRVSGEGHITCGHCRNCRGGRTHLCRNTIGVGVNRPGC 120
           VGHE+ GE+  IG  V  +K+G RVSGEGHI CG CRNCR GR HLCRNT+GVGV+RPG 
Sbjct: 65  VGHEFSGEIAEIGSAVTKYKVGQRVSGEGHIVCGTCRNCRAGRGHLCRNTLGVGVHRPGS 124

Query: 121 FAEYLVIPAFNAFKIPDNISDDLAAIFDPFGNAVHTALSFDLVGEDVLVSGAGPIGIMAA 180
           F EY+ IP  N   IPD+++D++AAIFDPFGNAVHTALSFDLVGEDVLV+GAGPIGIM A
Sbjct: 125 FGEYVCIPEANVVPIPDDVADEIAAIFDPFGNAVHTALSFDLVGEDVLVTGAGPIGIMGA 184

Query: 181 AVAKHVGARNVVITDVNEYRLELARKMGITRAVNVAKENLNDVMAELGMTEGFDVGLEMS 240
            VAK  GAR VVITD+N  RL LARK+GI   V+ + +NL DVM E+GMTEGFDVGLEMS
Sbjct: 185 LVAKRSGARKVVITDINPARLALARKLGIDYVVDASSQNLTDVMREIGMTEGFDVGLEMS 244

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

Query: 301 LIQSGLDLSPIITHRFSIDDFQKGFDAMRSGQSGKVILSWD 341
            +Q GLDLS IITHR SIDDFQ GFDAMRSG SGKV+LSW+
Sbjct: 305 FVQGGLDLSQIITHRLSIDDFQAGFDAMRSGSSGKVVLSWN 345


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: 534
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: 341
Length of database: 345
Length adjustment: 29
Effective length of query: 312
Effective length of database: 316
Effective search space:    98592
Effective search space used:    98592
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 WP_106713900.1 CU102_RS25640 (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.2456229.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.2e-157  508.1   0.9   5.9e-157  507.9   0.9    1.0  1  NCBI__GCF_003010955.1:WP_106713900.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010955.1:WP_106713900.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  507.9   0.9  5.9e-157  5.9e-157       1     340 []       7     344 ..       7     344 .. 1.00

  Alignments for each domain:
  == domain 1  score: 507.9 bits;  conditional E-value: 5.9e-157
                             TIGR00692   1 almkkkaeeGavltevpvpelgknevlikvkatsicGtdvhiynwdewaqkrikvpqvlGhevaGevvgiGee 73 
                                           al+k kae G+++  vpvpe+g+n+vli+vk+++icGtdvhiynwd+waq +i+vp+v+Ghe++Ge+ +iG  
  NCBI__GCF_003010955.1:WP_106713900.1   7 ALVKAKAEPGIWMERVPVPEPGPNDVLIRVKKSAICGTDVHIYNWDKWAQATIPVPMVVGHEFSGEIAEIGSA 79 
                                           799********************************************************************** PP

                             TIGR00692  74 vegvkvGdyvsaethivcGkcvacrrGkshvcrntkivGvdtaGvfaeyvvvpadnifknpkdidpelaaiqe 146
                                           v   kvG++vs+e+hivcG c++cr+G+ h+crnt +vGv+++G f eyv +p  n+  +p+d+ +e+aai++
  NCBI__GCF_003010955.1:WP_106713900.1  80 VTKYKVGQRVSGEGHIVCGTCRNCRAGRGHLCRNTLGVGVHRPGSFGEYVCIPEANVVPIPDDVADEIAAIFD 152
                                           ************************************************************************* PP

                             TIGR00692 147 plGnavdtvlesdlaGesvlvsGaGpiGllavavakaaGasqvivsdkneyrlelakkvGatrvvnvakedlv 219
                                           p+Gnav+t+l++dl+Ge+vlv+GaGpiG++++ vak +Ga++v+++d n  rl la+k+G+++vv+   ++l+
  NCBI__GCF_003010955.1:WP_106713900.1 153 PFGNAVHTALSFDLVGEDVLVTGAGPIGIMGALVAKRSGARKVVITDINPARLALARKLGIDYVVDASSQNLT 225
                                           ************************************************************************* PP

                             TIGR00692 220 kvvaeltsgeGvdvvlelsGapkaleqgldavangGrvallglpeskvtidltnkvifkgltikGitGrklfe 292
                                           +v+ e++++eG+dv+le+sGa +a+++++d ++ngG++a+lg+ ++   id++ kvifk l +kGi+Gr++fe
  NCBI__GCF_003010955.1:WP_106713900.1 226 DVMREIGMTEGFDVGLEMSGAAPAFRDMIDKMNNGGKIAILGIAPTGFEIDWN-KVIFKMLNLKGIYGREMFE 297
                                           ****************************************************9.******************* PP

                             TIGR00692 293 twykvsrliqsnkldlapiithkfkldefekgfelmrsGksGkvilil 340
                                           twyk+ +++q  +ldl+ iith+ ++d+f+ gf++mrsG sGkv+l++
  NCBI__GCF_003010955.1:WP_106713900.1 298 TWYKMIAFVQG-GLDLSQIITHRLSIDDFQAGFDAMRSGSSGKVVLSW 344
                                           **********8.9*********************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (345 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: 17.54
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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