Alignments for a candidate for leuB in Pseudomonas fluorescens FW300-N1B4

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuB in Pseudomonas fluorescens FW300-N1B4

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate Pf1N1B4_12 3-isopropylmalate dehydrogenase (EC 1.1.1.85)

Query= BRENDA::P96197
         (360 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_12
          Length = 360

 Score =  520 bits (1340), Expect = e-152
 Identities = 283/372 (76%), Positives = 304/372 (81%), Gaps = 24/372 (6%)

Query: 1   MSKQILVLPGDGIGPEIMAEAVKVLQLANEKYQLGFVLGYDELGGAAVDKYGVPLADETL 60
           MSKQIL+LPGDGIGPEIMAEAVKVL+LAN+KY LGF L +D +GGAA+DK+GVPLADETL
Sbjct: 1   MSKQILILPGDGIGPEIMAEAVKVLELANDKYSLGFELSHDVIGGAAIDKHGVPLADETL 60

Query: 61  ERARR------------RCHPARRRRRSEMGRHRPGHPPGARPAENPFATGPVRQPAPGV 108
            RAR             +     R  R E G  +     G          G +R   P +
Sbjct: 61  ARARAADAVLLGAVGGPKWDTIERDIRPERGLLKIRAQLGL--------FGNLR---PAI 109

Query: 109 LYPQLAEASTLRPEVVAGLDILIVRELTGGIYFGAPRESRLLANGERMAYDTLPYSESEI 168
           LYPQLAEAS+L+ E+VAGLDILIVRELTGGIYFGAPR  R L NGER AYDTLPYSE+EI
Sbjct: 110 LYPQLAEASSLKAEIVAGLDILIVRELTGGIYFGAPRGVRELENGERQAYDTLPYSETEI 169

Query: 169 RRIAKVGFDMARVRGKKLCSVDKANVLASSQLWRAVVEEVAKDYPDVVLSHMYVDNAAMQ 228
           RRIA+VGFDMARVRGKKLCSVDKANVLASSQLWR VVE+VAKDYPDV LSHMYVDNAAMQ
Sbjct: 170 RRIARVGFDMARVRGKKLCSVDKANVLASSQLWREVVEQVAKDYPDVELSHMYVDNAAMQ 229

Query: 229 LVRAPKQFDVIVTDNMFGDILSDEASMLTGSIGMLPSASLDADNKGMYEPCHGSRRPDIA 288
           LVRAPKQFDVIVTDN+FGDILSDEASMLTGSIGMLPSASLDA+NKGMYEPCHGS  PDIA
Sbjct: 230 LVRAPKQFDVIVTDNLFGDILSDEASMLTGSIGMLPSASLDANNKGMYEPCHGS-APDIA 288

Query: 289 GKGIANPLATILSVSMMLRYSFGQVEAANAIEQAVSKVLDQGLRTGDIWSEGCRKVGTAE 348
           GKGIANPLATILSVSMMLRYSF   +AA+AIEQAVS VLDQGLRTGDIWS GC KVGT E
Sbjct: 289 GKGIANPLATILSVSMMLRYSFNLQDAADAIEQAVSLVLDQGLRTGDIWSAGCTKVGTQE 348

Query: 349 MGDAVVAALATL 360
           MGDAVVAAL  L
Sbjct: 349 MGDAVVAALRNL 360


Lambda     K      H
   0.318    0.135    0.393 

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: 477
Number of extensions: 5
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 360
Length of database: 360
Length adjustment: 29
Effective length of query: 331
Effective length of database: 331
Effective search space:   109561
Effective search space used:   109561
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate Pf1N1B4_12 (3-isopropylmalate dehydrogenase (EC 1.1.1.85))
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.3468809.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   1.1e-165  536.8   0.0   1.3e-165  536.6   0.0    1.0  1  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_12  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__pseudo1_N1B4:Pf1N1B4_12  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  536.6   0.0  1.3e-165  1.3e-165       1     348 [.       4     352 ..       4     353 .. 0.99

  Alignments for each domain:
  == domain 1  score: 536.6 bits;  conditional E-value: 1.3e-165
                                TIGR00169   1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlga 70 
                                              +i +LpGDgiGpe++aea+kvL+  ++++ l +e ++  iGGaaid++g Pl++etl+ +++adavLlga
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_12   4 QILILPGDGIGPEIMAEAVKVLELANDKYSLGFELSHDVIGGAAIDKHGVPLADETLARARAADAVLLGA 73 
                                              589******************************************************************* PP

                                TIGR00169  71 vGGpkWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYfG 140
                                              vGGpkWd+  rd+rPe+gLLk+r +l+lf nLrPa l+++L ++s+lk+eiv g+D+++vreLtgGiYfG
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_12  74 VGGPKWDTIERDIRPERGLLKIRAQLGLFGNLRPAILYPQLAEASSLKAEIVAGLDILIVRELTGGIYFG 143
                                              ********************************************************************** PP

                                TIGR00169 141 epkereeaee.ekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakey 209
                                               p++ +e e+ e++a+dt  Y+++ei+riarv+f +ar r kk++svDkanvL+ss+lWr++ve++ak+y
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_12 144 APRGVRELENgERQAYDTLPYSETEIRRIARVGFDMARVRGKKLCSVDKANVLASSQLWREVVEQVAKDY 213
                                              *******9999*********************************************************** PP

                                TIGR00169 210 PdvelehlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvhgs 279
                                              Pdvel+h+y+DnaamqLv++P+q+dv+vt+nlfGDilsDeas++tGs+G+LPsasl  + ++++ep hgs
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_12 214 PDVELSHMYVDNAAMQLVRAPKQFDVIVTDNLFGDILSDEASMLTGSIGMLPSASLDANNKGMYEPCHGS 283
                                              ********************************************************************** PP

                                TIGR00169 280 apdiagkgianpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstkeveee 348
                                              apdiagkgianp+a+ils++++lrys+nl++aa+aie+av+ vl++g rt d+ s ++t+v+t+e+++ 
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_12 284 APDIAGKGIANPLATILSVSMMLRYSFNLQDAADAIEQAVSLVLDQGLRTGDIWSAGCTKVGTQEMGDA 352
                                              ******************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (360 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: 00:00:00.00
# Mc/sec: 15.04
//
[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