GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Caldicellulosiruptor kronotskyensis 2002

Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_013430883.1 CALKRO_RS09925 branched-chain-amino-acid transaminase

Query= BRENDA::A0A1B1L2T7
         (298 letters)



>NCBI__GCF_000166775.1:WP_013430883.1
          Length = 293

 Score =  352 bits (902), Expect = e-102
 Identities = 169/293 (57%), Positives = 221/293 (75%)

Query: 1   MNEQWIFLNGEFVPKDEAKVSVYDHGYLYGDGVFEGIRVYSGNVFRLREHLVRLYESAKS 60
           M E+ I+++G+F  K EAK+SV+DHG+LYGDGVFEGIRVY+G +F+ +EH+ RLY++AK+
Sbjct: 1   MEEKLIYIDGKFYKKSEAKISVFDHGFLYGDGVFEGIRVYNGKIFKCKEHVDRLYQAAKA 60

Query: 61  ILLEIPYSLDEVTNIVVETIRQNKLSNGYIRLVVSRGAGNLGLDPDSCKKPNVVVIAEQL 120
           I +EIP S +E+   + +T R N +  GYIRLVVSRG G+LGL P  C KP +V+IA+ +
Sbjct: 61  IYMEIPISKEEMIEALKKTCRVNNIREGYIRLVVSRGVGDLGLSPTKCPKPTIVIIADSI 120

Query: 121 SLFPQEYYEKGIPVVTVATRRNRPDVLSPQVKSLNYLNNILVRIEAKLAGVQEALMLNDQ 180
            L+PQE YEKG+ V+T +TRRN P  + PQ+KSLNYLNNIL +IEA  AGV EA+ML   
Sbjct: 121 VLYPQEMYEKGMKVITASTRRNSPQCVDPQIKSLNYLNNILAKIEANRAGVPEAIMLTQD 180

Query: 181 GYVAEGSGDNVFIVKGNKLITPPSSAGALEGITRNAILEIGEKLGYDVREELFTRHDVYV 240
           GYV E +GDN+FIVK  +LITPP   GAL+GITR  ++ + + LG  V E++FT +++Y 
Sbjct: 181 GYVTECTGDNIFIVKDGELITPPVYLGALDGITRRTVMALAKDLGIPVYEKVFTLYNLYN 240

Query: 241 ADEVFLTGTAAEVIAVTTVDGRTIGLGQTGPHTNRLLEEFRKLVVEDGEKIYE 293
           ADE F TGTAAEVIAVT VDGR IG G+ GP T +L+EEF+KL   DG  IYE
Sbjct: 241 ADECFFTGTAAEVIAVTEVDGRKIGNGEVGPITKKLMEEFKKLTQIDGVDIYE 293


Lambda     K      H
   0.317    0.138    0.389 

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: 311
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: 298
Length of database: 293
Length adjustment: 26
Effective length of query: 272
Effective length of database: 267
Effective search space:    72624
Effective search space used:    72624
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 (21.6 bits)
S2: 48 (23.1 bits)

Align candidate WP_013430883.1 CALKRO_RS09925 (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.aa/TIGR01122.hmm
# target sequence database:        /tmp/gapView.242078.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.1e-109  352.2   0.3   1.4e-109  351.9   0.3    1.0  1  NCBI__GCF_000166775.1:WP_013430883.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000166775.1:WP_013430883.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  351.9   0.3  1.4e-109  1.4e-109       1     285 [.       7     285 ..       7     292 .. 0.96

  Alignments for each domain:
  == domain 1  score: 351.9 bits;  conditional E-value: 1.4e-109
                             TIGR01122   1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskeelvev 73 
                                           ++dG++ +  +ak++v++h+++YG+gvfeGiR+Y++     if+ kehv+Rly++ak++ +eip+skee++e+
  NCBI__GCF_000166775.1:WP_013430883.1   7 YIDGKFYKKSEAKISVFDHGFLYGDGVFEGIRVYNG----KIFKCKEHVDRLYQAAKAIYMEIPISKEEMIEA 75 
                                           89**********************************....9******************************** PP

                             TIGR01122  74 tkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavnsi 146
                                            k++ r+nn+++ YiR +v +G++dlgl+p    k++++i+a ++  y   e +ekG+kv+++s rr++++ +
  NCBI__GCF_000166775.1:WP_013430883.1  76 LKKTCRVNNIREGYIRLVVSRGVGDLGLSPTKCPKPTIVIIADSIVLYPQ-EMYEKGMKVITASTRRNSPQCV 147
                                           ******************************63337777788877776665.68******************** PP

                             TIGR01122 147 ptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdavik 219
                                            +++k+ + Yln++lak+ea+raG+ eai+L ++Gyv+e +G+nifivkdg+l+tPpv+  +L+gitr +v+ 
  NCBI__GCF_000166775.1:WP_013430883.1 148 DPQIKSLN-YLNNILAKIEANRAGVPEAIMLTQDGYVTECTGDNIFIVKDGELITPPVYLGALDGITRRTVMA 219
                                           *******9.**************************************************************** PP

                             TIGR01122 220 lakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlve 285
                                           lak+lgi v e+++++++ly aDe f+tGtaaev+ ++evDgrkig+g++Gp+tkkl+e+f++l++
  NCBI__GCF_000166775.1:WP_013430883.1 220 LAKDLGIPVYEKVFTLYNLYNADECFFTGTAAEVIAVTEVDGRKIGNGEVGPITKKLMEEFKKLTQ 285
                                           **************************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (293 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: 25.24
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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