Alignments for a candidate for leuB in Bacteroides thetaiotaomicron VPI-5482

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuB in Bacteroides thetaiotaomicron VPI-5482

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate 351385 BT1857 3-isopropylmalate dehydrogenase (NCBI ptt file)

Query= BRENDA::P54354
         (353 letters)



>FitnessBrowser__Btheta:351385
          Length = 353

 Score =  679 bits (1751), Expect = 0.0
 Identities = 335/353 (94%), Positives = 341/353 (96%)

Query: 1   MDFKIAVLAGDGIGPEISVQGVEVMSAVCEKFGHKVNYEYAICGADAIDKVGDPFPEETY 60
           MDFKIAVLAGDGIGPEISVQGV+VMSAVCEKFGHKV+YEYAICGADAIDKVGDPFPEETY
Sbjct: 1   MDFKIAVLAGDGIGPEISVQGVDVMSAVCEKFGHKVSYEYAICGADAIDKVGDPFPEETY 60

Query: 61  RVCKNADAVLFSAVGDPKFDNDPTAKVRPEQGLLAMRKKLGLFANIRPVQTFKCLVHKSP 120
            VCKNADAVLFSAVGDPKFDNDPTAKVRPEQGLLAMRKKLGLFANIRPVQTFKCL+HKSP
Sbjct: 61  EVCKNADAVLFSAVGDPKFDNDPTAKVRPEQGLLAMRKKLGLFANIRPVQTFKCLIHKSP 120

Query: 121 LRAELVEGADFLCIRELTGGMYFGEKYQDNDKAYDTNMYTRPEIERILKVGFEYAMKRRK 180
           LRAELVE ADF+CIRELTGGMYFGEKYQDNDKAYDTN YTRPEIERILKV FEYAMKRRK
Sbjct: 121 LRAELVENADFICIRELTGGMYFGEKYQDNDKAYDTNYYTRPEIERILKVAFEYAMKRRK 180

Query: 181 HLTVVDKANVLASSRLWRQIAQEMAPQYPEVTTDYMFVDNAAMKMIQEPKFFDVMVTENT 240
           HLTVVDKANVLASSRLWRQIAQEMAP YPEVTTDYMFVDNAAMKMIQEP FFDVMVTENT
Sbjct: 181 HLTVVDKANVLASSRLWRQIAQEMAPNYPEVTTDYMFVDNAAMKMIQEPAFFDVMVTENT 240

Query: 241 FGDILTDEGSVISGSMGLLPSASTGESTPVFEPIHGSWPQAKGLNIANPLAQILSVAMLF 300
           FGDILTDEGSVISGSMGLLPSASTGESTPVFEPIHGSWPQAKGLNIANPLAQILSVAMLF
Sbjct: 241 FGDILTDEGSVISGSMGLLPSASTGESTPVFEPIHGSWPQAKGLNIANPLAQILSVAMLF 300

Query: 301 EYFDCKAEGALIRKAVDASLDANVRTPEIQVEGGEKFGTKEVGAWIVDYIRKA 353
           EYFDCK EGALIRKAVDASLD NVRTPEIQV  G K+GTKEVG WIVDYI+KA
Sbjct: 301 EYFDCKEEGALIRKAVDASLDENVRTPEIQVADGAKYGTKEVGQWIVDYIKKA 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: 626
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: 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 351385 BT1857 (3-isopropylmalate dehydrogenase (NCBI ptt file))
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.2475523.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                      -----------
   1.7e-132  427.6   0.0   1.9e-132  427.5   0.0    1.0  1  FitnessBrowser__Btheta:351385  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Btheta:351385  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  427.5   0.0  1.9e-132  1.9e-132       1     347 [.       4     344 ..       4     346 .. 0.98

  Alignments for each domain:
  == domain 1  score: 427.5 bits;  conditional E-value: 1.9e-132
                      TIGR00169   1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGGpkWdnlp 80 
                                    kiavL+GDgiGpe+  + ++v+ av e+f++k+ +e+a  G  aid++g+P+peet + ck+adavL++avG pk+dn p
  FitnessBrowser__Btheta:351385   4 KIAVLAGDGIGPEISVQGVDVMSAVCEKFGHKVSYEYAICGADAIDKVGDPFPEETYEVCKNADAVLFSAVGDPKFDNDP 83 
                                    79****************************************************************************98 PP

                      TIGR00169  81 r.dvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYfGepkereeaeeekkaldtek 159
                                    + +vrPe+gLL++rk+l+lfan+rP++ fk L++ spl++e+v++ D++++reLtgG+YfGe+ ++++     ka+dt  
  FitnessBrowser__Btheta:351385  84 TaKVRPEQGLLAMRKKLGLFANIRPVQTFKCLIHKSPLRAELVENADFICIRELTGGMYFGEKYQDND-----KAYDTNY 158
                                    6379**********************************************************999888.....8****** PP

                      TIGR00169 160 YtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPdvelehlyiDnaamqLvksPeqldvvvts 239
                                    Yt++eieri +vafe a+krrk++t vDkanvL+ssrlWr++++e+a +yP+v+ + +++Dnaam+++++P+ +dv+vt+
  FitnessBrowser__Btheta:351385 159 YTRPEIERILKVAFEYAMKRRKHLTVVDKANVLASSRLWRQIAQEMAPNYPEVTTDYMFVDNAAMKMIQEPAFFDVMVTE 238
                                    ******************************************************************************** PP

                      TIGR00169 240 nlfGDilsDeasvitGslGlLPsaslsskglalfepvhgsapdiagkgianpiaailsaalllryslnleeaaeaieaav 319
                                    n fGDil De svi+Gs+GlLPsas + + + +fep+hgs p+  g +ianp+a+ils+a+l +y ++ +e+ + i +av
  FitnessBrowser__Btheta:351385 239 NTFGDILTDEGSVISGSMGLLPSASTG-ESTPVFEPIHGSWPQAKGLNIANPLAQILSVAMLFEY-FDCKEEGALIRKAV 316
                                    **************************9.8899******************************998.89999999****** PP

                      TIGR00169 320 kkvleegkrtedlaseattavstkevee 347
                                    +  l+e  rt++++  ++++ +tkev++
  FitnessBrowser__Btheta:351385 317 DASLDENVRTPEIQVADGAKYGTKEVGQ 344
                                    *****************9******9986 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 14.46
//
[ok]

This GapMind analysis is from Jul 25 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:

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