GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ilvE in Limnohabitans curvus MWH-C5

Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate WP_108402105.1 B9Z44_RS07660 branched-chain amino acid transaminase

Query= reanno::BFirm:BPHYT_RS16285
         (307 letters)



>NCBI__GCF_003063475.1:WP_108402105.1
          Length = 313

 Score =  446 bits (1148), Expect = e-130
 Identities = 210/307 (68%), Positives = 258/307 (84%), Gaps = 2/307 (0%)

Query: 2   SMADRDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHTK 61
           SM+DRDGKIWMDG+++DWRDAKIHVL+HTLHYG G FEGVRAYKT + GTAIFRLQEHT 
Sbjct: 8   SMSDRDGKIWMDGQMVDWRDAKIHVLSHTLHYGCGAFEGVRAYKT-EQGTAIFRLQEHTD 66

Query: 62  RLLNSAKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIHV 121
           RL NSAKI +M++PF  E +  AQC VVREN LES Y+RP+ W+G +KLGVS +GN IHV
Sbjct: 67  RLFNSAKILRMNMPFTKEQINNAQCAVVRENNLESGYIRPLTWIGDKKLGVSPRGNDIHV 126

Query: 122 AIAAWPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADGY 181
            +AAW WGAYLGE+G+ +GIRVKTSS+TRHHVN++M +AKA   Y NSILAN E   +GY
Sbjct: 127 MVAAWTWGAYLGEEGMKRGIRVKTSSYTRHHVNITMTQAKAVSNYTNSILANMEVTDEGY 186

Query: 182 DEALLLDVDGYVSEGSGENFFLVNNGKLYTPDLSS-CLDGITRDTVITLARDAGIQVIEK 240
           DEALLLD  G+VSEG+GEN F+V +G +YTPDLS+  L+GITR+TV  +A+D G+++++K
Sbjct: 187 DEALLLDTSGFVSEGAGENIFVVKDGVIYTPDLSAGALNGITRNTVFHIAKDLGLEIVQK 246

Query: 241 RITRDEVYTCDEAFFTGTAAEVTPIRELDNRTIGSGARGPITEKLQSGFFDIVNGKSDKY 300
           RITRDE+Y  DEAFFTGTAAEVTPIRELD   +G G+RGPITEK+Q+ FFDIVNG++ KY
Sbjct: 247 RITRDEIYIADEAFFTGTAAEVTPIRELDRIQLGEGSRGPITEKIQTAFFDIVNGRNPKY 306

Query: 301 ANWLTKI 307
           A+WLTK+
Sbjct: 307 AHWLTKV 313


Lambda     K      H
   0.319    0.136    0.411 

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: 378
Number of extensions: 8
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: 307
Length of database: 313
Length adjustment: 27
Effective length of query: 280
Effective length of database: 286
Effective search space:    80080
Effective search space used:    80080
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 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate WP_108402105.1 B9Z44_RS07660 (branched-chain amino acid transaminase)
to HMM TIGR01122 (ilvE: branched-chain amino acid aminotransferase (EC 2.6.1.42))

# 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/TIGR01122.hmm
# target sequence database:        /tmp/gapView.3993170.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01122  [M=298]
Accession:   TIGR01122
Description: ilvE_I: branched-chain amino acid 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.7e-141  456.0   0.3     3e-141  455.8   0.3    1.0  1  NCBI__GCF_003063475.1:WP_108402105.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003063475.1:WP_108402105.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  455.8   0.3    3e-141    3e-141       1     298 []      17     313 .]      17     313 .] 0.99

  Alignments for each domain:
  == domain 1  score: 455.8 bits;  conditional E-value: 3e-141
                             TIGR01122   1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskeelvev 73 
                                           w+dG++vd++dak+hvl+h+lhYG g feG+RaY+t++g+aifrl+eh++Rl++sakilr+++p++ke+++++
  NCBI__GCF_003063475.1:WP_108402105.1  17 WMDGQMVDWRDAKIHVLSHTLHYGCGAFEGVRAYKTEQGTAIFRLQEHTDRLFNSAKILRMNMPFTKEQINNA 89 
                                           9************************************************************************ PP

                             TIGR01122  74 tkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavnsi 146
                                           +  v+r+nnl+s YiRpl ++G+++lg++p+ + +++v++aaw+wgaylgee++++Gi+vk+ss++r++vn+ 
  NCBI__GCF_003063475.1:WP_108402105.1  90 QCAVVRENNLESGYIRPLTWIGDKKLGVSPRGN-DIHVMVAAWTWGAYLGEEGMKRGIRVKTSSYTRHHVNIT 161
                                           ******************************765.9************************************** PP

                             TIGR01122 147 ptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdavik 219
                                           +t+aka++nY ns+la++e + +Gydea+lLd++G+v+eG+Genif+vkdgv++tP++s  +L+gitr++v +
  NCBI__GCF_003063475.1:WP_108402105.1 162 MTQAKAVSNYTNSILANMEVTDEGYDEALLLDTSGFVSEGAGENIFVVKDGVIYTPDLSAGALNGITRNTVFH 234
                                           ************************************************************************* PP

                             TIGR01122 220 lakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlvegktekke 292
                                           +ak+lg+e++++ri+r+e+y+aDe+f+tGtaaevtPire+D +++geg+rGp+t+k+q+affd+v+g+++k++
  NCBI__GCF_003063475.1:WP_108402105.1 235 IAKDLGLEIVQKRITRDEIYIADEAFFTGTAAEVTPIRELDRIQLGEGSRGPITEKIQTAFFDIVNGRNPKYA 307
                                           ************************************************************************* PP

                             TIGR01122 293 ewltyv 298
                                           +wlt+v
  NCBI__GCF_003063475.1:WP_108402105.1 308 HWLTKV 313
                                           ***987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (313 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 20.30
//
[ok]

This GapMind analysis is from Sep 24 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