Alignments for a candidate for leuB in Burkholderia phytofirmans PsJN

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuB in Burkholderia phytofirmans PsJN

Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 (characterized)
to candidate BPHYT_RS33900 BPHYT_RS33900 3-isopropylmalate dehydrogenase

Query= SwissProt::Q56268
         (358 letters)



>FitnessBrowser__BFirm:BPHYT_RS33900
          Length = 355

 Score =  400 bits (1029), Expect = e-116
 Identities = 213/358 (59%), Positives = 266/358 (74%), Gaps = 10/358 (2%)

Query: 3   KIAIFAGDGIGPEIVAAARQVLDAVDQAAHLGLRCTEGLVGGAALDASDDPLPAASLQLA 62
           KIA+  GDGIGPEIV  A +VL+ + +   L     E  VGGA  +A   PLP ++L LA
Sbjct: 2   KIAVLPGDGIGPEIVKEAVKVLNVLGEKFEL----EEAPVGGAGYEAKGHPLPDSTLALA 57

Query: 63  MAADAVILGAVGGPRWDAYPPAKRPEQGLLRLRKGLDLYANLRPAQIFPQLLDASPLRPE 122
             ADA++ GAVG  ++D+   A RPEQ +L LRK L L+AN RPA  +PQL  AS L+ E
Sbjct: 58  KEADAILFGAVGDWKYDSLERALRPEQAILGLRKHLQLFANFRPAICYPQLTGASSLKEE 117

Query: 123 LVRDVDILVVRELTGDIYFGQPRGLE-----VIDGKRRGFNTMVYDEDEIRRIAHVAFRA 177
           +V  +DIL+VREL GDIYFG PRG+      + +G + GF+TM Y E E+RRIAHVAF+A
Sbjct: 118 IVSGLDILIVRELNGDIYFGAPRGVRSSPDGLFEGAKEGFDTMRYSEPEVRRIAHVAFQA 177

Query: 178 AQGRRKQLCSVDKANVLETTRLWREVVTEVARDYPDVRLSHMYVDNAAMQLIRAPAQFDV 237
           AQ R+K+L SVDKANVLET++ WR+V+ +V+++Y DV LSHMYVDNAAMQL++AP  FDV
Sbjct: 178 AQKRQKKLTSVDKANVLETSQFWRDVMIDVSKEYADVELSHMYVDNAAMQLVKAPKAFDV 237

Query: 238 LLTGNMFGDILSDEASQLTGSIGMLPSASLGE-GRAMYEPIHGSAPDIAGQDKANPLATI 296
           ++TGNMFGDILSDEA+ LTGSIGMLPSASL +  + +YEP HGSAPDIAG+  ANPLATI
Sbjct: 238 VVTGNMFGDILSDEAAMLTGSIGMLPSASLDKNNKGLYEPSHGSAPDIAGKGVANPLATI 297

Query: 297 LSVAMMLRHSLNAEPWAQRVEAAVQRVLDQGLRTADIAAPGTPVIGTKAMGAAVVNAL 354
           LS AMMLR+SLN    A R+E+AV++VL+QG RT DI  PG   +GT AMG AVV AL
Sbjct: 298 LSAAMMLRYSLNKAEQADRIESAVKKVLEQGYRTGDILTPGCKQVGTVAMGDAVVAAL 355


Lambda     K      H
   0.320    0.137    0.396 

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: 391
Number of extensions: 10
Number of successful extensions: 4
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: 358
Length of database: 355
Length adjustment: 29
Effective length of query: 329
Effective length of database: 326
Effective search space:   107254
Effective search space used:   107254
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 BPHYT_RS33900 BPHYT_RS33900 (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.8110.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
     1e-150  487.6   0.0   1.1e-150  487.4   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS33900  BPHYT_RS33900 3-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS33900  BPHYT_RS33900 3-isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  487.4   0.0  1.1e-150  1.1e-150       1     348 [.       2     350 ..       2     351 .. 0.97

  Alignments for each domain:
  == domain 1  score: 487.4 bits;  conditional E-value: 1.1e-150
                                TIGR00169   1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlga 70 
                                              kiavLpGDgiGpe+v+ea+kvL+++ e+    +e eea +GGa  +a+g+Plp+ tl+ +keada+L+ga
  lcl|FitnessBrowser__BFirm:BPHYT_RS33900   2 KIAVLPGDGIGPEIVKEAVKVLNVLGEK----FELEEAPVGGAGYEAKGHPLPDSTLALAKEADAILFGA 67 
                                              79*********************99885....6789********************************** PP

                                TIGR00169  71 vGGpkWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYfG 140
                                              vG  k+d+l r  rPe+++L lrk+l+lfan+rPa  +++L+ +s+lkeeiv+g+D+++vreL g iYfG
  lcl|FitnessBrowser__BFirm:BPHYT_RS33900  68 VGDWKYDSLERALRPEQAILGLRKHLQLFANFRPAICYPQLTGASSLKEEIVSGLDILIVRELNGDIYFG 137
                                              ********************************************************************** PP

                                TIGR00169 141 epkereea....ee.ekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveei 205
                                               p++ + +     e  k+++dt++Y+++e++ria+vaf++a+kr+kk+tsvDkanvLe+s++Wr+++ ++
  lcl|FitnessBrowser__BFirm:BPHYT_RS33900 138 APRGVRSSpdglFEgAKEGFDTMRYSEPEVRRIAHVAFQAAQKRQKKLTSVDKANVLETSQFWRDVMIDV 207
                                              ***988752222124899**************************************************** PP

                                TIGR00169 206 akeyPdvelehlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfep 275
                                               key dvel+h+y+DnaamqLvk+P+ +dvvvt+n+fGDilsDea+++tGs+G+LPsasl ++ ++l+ep
  lcl|FitnessBrowser__BFirm:BPHYT_RS33900 208 SKEYADVELSHMYVDNAAMQLVKAPKAFDVVVTGNMFGDILSDEAAMLTGSIGMLPSASLDKNNKGLYEP 277
                                              ********************************************************************** PP

                                TIGR00169 276 vhgsapdiagkgianpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstkev 345
                                               hgsapdiagkg+anp+a+ilsaa++lrysln+ e+a++ie+avkkvle+g+rt d+ + ++++v+t ++
  lcl|FitnessBrowser__BFirm:BPHYT_RS33900 278 SHGSAPDIAGKGVANPLATILSAAMMLRYSLNKAEQADRIESAVKKVLEQGYRTGDILTPGCKQVGTVAM 347
                                              *******************************************************************999 PP

                                TIGR00169 346 eee 348
                                              ++ 
  lcl|FitnessBrowser__BFirm:BPHYT_RS33900 348 GDA 350
                                              876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (355 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: 8.23
//
[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