Alignments for a candidate for leuB in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuB in Echinicola vietnamensis KMM 6221, DSM 17526

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate Echvi_2062 Echvi_2062 3-isopropylmalate dehydrogenase

Query= BRENDA::P54354
         (353 letters)



>FitnessBrowser__Cola:Echvi_2062
          Length = 353

 Score =  416 bits (1070), Expect = e-121
 Identities = 210/352 (59%), Positives = 263/352 (74%), Gaps = 5/352 (1%)

Query: 5   IAVLAGDGIGPEISVQGVEVMSAVCEKFGHKVNYEYAICGADAIDKVGDPFPEETYRVCK 64
           IA+L GDGIGPE+  Q V+V+ AV +KFGH + ++ A+ GA AID  G+P+P+ET+ +C 
Sbjct: 3   IALLPGDGIGPEVIEQTVKVVKAVGKKFGHTITFKEAVVGAAAIDATGNPYPDETHEICL 62

Query: 65  NADAVLFSAVGDPKFDNDPTAKVRPEQGLLAMRKKLGLFANIRPVQTFKCLVHKSPLRAE 124
            ADAVLF A+GDPK+DNDP AKVRPEQGLLAMRKKLGLF+N+RP  TF  L+HKSPL+ E
Sbjct: 63  QADAVLFGAIGDPKYDNDPKAKVRPEQGLLAMRKKLGLFSNVRPTFTFPSLIHKSPLKKE 122

Query: 125 LVEGADFLCIRELTGGMYFGEKYQDND---KAYDTNMYTRPEIERILKVGFEYAMKRRKH 181
            +EG D + +RELTGG+YFGE    N+   KA+DTN+YT+ EI R+ ++GFE+A KRRK 
Sbjct: 123 RIEGTDLVFLRELTGGIYFGEPRGRNEQGTKAFDTNVYTKEEITRLARMGFEFAQKRRKL 182

Query: 182 LTVVDKANVLASSRLWRQIAQEMAPQYPEVTTDYMFVDNAAMKMIQEPKFFDVMVTENTF 241
           LT VDKANVLA+SRLWR+  QE+ P+YP+V  +Y FVD  AM++IQ PK +DV++TEN F
Sbjct: 183 LTCVDKANVLATSRLWRETVQELEPEYPDVKVEYEFVDAVAMRLIQWPKAYDVLITENLF 242

Query: 242 GDILTDEGSVISGSMGLLPSASTGESTPVFEPIHGSWPQAKGLNIANPLAQILSVAMLFE 301
           GDILTDE SVISGSMGL+PSAS G    +FEPIHGS+PQA G +IANPLA +LS AM+FE
Sbjct: 243 GDILTDEASVISGSMGLMPSASLGTDVKLFEPIHGSYPQAAGKDIANPLATVLSAAMMFE 302

Query: 302 Y-FDCKAEGALIRKAVDASLDANVRTPEIQVEGGEKFGTKEVGAWIVDYIRK 352
           Y FD K E   I   V+ SL   V T +I  E  +   T EVG W+   I K
Sbjct: 303 YAFDLKDEAKAISDVVNLSLAEGVVTEDI-AEESKPSKTSEVGDWLAAQILK 353


Lambda     K      H
   0.319    0.136    0.403 

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: 432
Number of extensions: 14
Number of successful extensions: 2
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: 353
Length of database: 353
Length adjustment: 29
Effective length of query: 324
Effective length of database: 324
Effective search space:   104976
Effective search space used:   104976
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: 49 (23.5 bits)

Align candidate Echvi_2062 Echvi_2062 (3-isopropylmalate dehydrogenase)
to HMM TIGR00169 (leuB: 3-isopropylmalate dehydrogenase (EC 1.1.1.85))

# 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/TIGR00169.hmm
# target sequence database:        /tmp/gapView.29196.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00169  [M=349]
Accession:   TIGR00169
Description: leuB: 3-isopropylmalate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
     9e-145  468.0   0.0     1e-144  467.8   0.0    1.0  1  lcl|FitnessBrowser__Cola:Echvi_2062  Echvi_2062 3-isopropylmalate deh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_2062  Echvi_2062 3-isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  467.8   0.0    1e-144    1e-144       1     347 [.       2     345 ..       2     347 .. 0.98

  Alignments for each domain:
  == domain 1  score: 467.8 bits;  conditional E-value: 1e-144
                            TIGR00169   1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGGp 74 
                                          +ia+LpGDgiGpev+++ +kv+kav ++f++ ++f+ea +G aaidatg+P p+et + c +adavL+ga+G p
  lcl|FitnessBrowser__Cola:Echvi_2062   2 NIALLPGDGIGPEVIEQTVKVVKAVGKKFGHTITFKEAVVGAAAIDATGNPYPDETHEICLQADAVLFGAIGDP 75 
                                          69************************************************************************ PP

                            TIGR00169  75 kWdnlpr.dvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYfGepkeree 147
                                          k+dn p+ +vrPe+gLL++rk+l+lf+n+rP+  f+sL++ splk+e ++g+Dlv +reLtgGiYfGep++r+e
  lcl|FitnessBrowser__Cola:Echvi_2062  76 KYDNDPKaKVRPEQGLLAMRKKLGLFSNVRPTFTFPSLIHKSPLKKERIEGTDLVFLRELTGGIYFGEPRGRNE 149
                                          ****986379**************************************************************99 PP

                            TIGR00169 148 aeeekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPdvelehlyiDn 221
                                            + +ka+dt +Ytkeei r+ar++fe a+krrk +t vDkanvL++srlWr+tv+e+  eyPdv++e  ++D+
  lcl|FitnessBrowser__Cola:Echvi_2062 150 --QGTKAFDTNVYTKEEITRLARMGFEFAQKRRKLLTCVDKANVLATSRLWRETVQELEPEYPDVKVEYEFVDA 221
                                          ..6899******************************************************************** PP

                            TIGR00169 222 aamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvhgsapdiagkgianpiaai 295
                                          +am+L++ P+ +dv++t+nlfGDil Deasvi+Gs+Gl+Psasl+ + ++lfep+hgs p+ agk+ianp+a++
  lcl|FitnessBrowser__Cola:Echvi_2062 222 VAMRLIQWPKAYDVLITENLFGDILTDEASVISGSMGLMPSASLG-TDVKLFEPIHGSYPQAAGKDIANPLATV 294
                                          *********************************************.6789************************ PP

                            TIGR00169 296 lsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstkevee 347
                                          lsaa++ +y+++l+++a+ai ++v+  l+eg  ted+a+e+ + + t+ev++
  lcl|FitnessBrowser__Cola:Echvi_2062 295 LSAAMMFEYAFDLKDEAKAISDVVNLSLAEGVVTEDIAEES-KPSKTSEVGD 345
                                          **************************************999.8888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (353 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: 7.62
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis