Alignments for a candidate for leuB in Desulfovibrio vulgaris Hildenborough

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuB in Desulfovibrio vulgaris Hildenborough

Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 (characterized)
to candidate 208498 DVU2985 3-isopropylmalate dehydrogenase

Query= SwissProt::Q56268
         (358 letters)



>MicrobesOnline__882:208498
          Length = 357

 Score =  432 bits (1110), Expect = e-126
 Identities = 218/353 (61%), Positives = 271/353 (76%), Gaps = 2/353 (0%)

Query: 4   IAIFAGDGIGPEIVAAARQVLDAVDQAAHLGLRCTEGLVGGAALDASDDPLPAASLQLAM 63
           I +  GDGIGPEIVA   +VLDAV +     +  +  L+GGAA+DA+  PLP A+++   
Sbjct: 5   ICLLPGDGIGPEIVAQGTKVLDAVARRFGHTVSTSSALIGGAAIDATGSPLPDATVEACR 64

Query: 64  AADAVILGAVGGPRWDAYPPAKRPEQGLLRLRKGLDLYANLRPAQIFPQLLDASPLRPEL 123
            +DAV+LGAVGGP+WD  P  KRPE+GLL +RK L L+ANLRPA +FP+L  A  LR ++
Sbjct: 65  TSDAVLLGAVGGPKWDDLPSEKRPEKGLLGIRKALGLFANLRPAALFPELAGACLLRADI 124

Query: 124 VR-DVDILVVRELTGDIYFGQPRGLEVIDGKRRGFNTMVYDEDEIRRIAHVAFRAAQGRR 182
               +D++VVRELTGD+YFGQP G+E  DG R GFNTM+YDEDE+RRIA VAF  A+ R+
Sbjct: 125 AAAGLDLVVVRELTGDVYFGQPAGIETRDGLRTGFNTMIYDEDEVRRIARVAFDTARARK 184

Query: 183 KQLCSVDKANVLETTRLWREVVTEVARDYPDVRLSHMYVDNAAMQLIRAPAQFDVLLTGN 242
           +++CSVDKANVL T+RLWREVV EVARDYPDV LSHMYVDNAAMQL+R PAQFDV++TGN
Sbjct: 185 RRVCSVDKANVLATSRLWREVVEEVARDYPDVELSHMYVDNAAMQLVRWPAQFDVIVTGN 244

Query: 243 MFGDILSDEASQLTGSIGMLPSASLGE-GRAMYEPIHGSAPDIAGQDKANPLATILSVAM 301
           +FGDILSDEA+ +TGSIGMLPSAS+G  G A++EPIHGSAPDIAGQDKANP+ATILSV M
Sbjct: 245 LFGDILSDEAAVITGSIGMLPSASMGSGGPALFEPIHGSAPDIAGQDKANPIATILSVGM 304

Query: 302 MLRHSLNAEPWAQRVEAAVQRVLDQGLRTADIAAPGTPVIGTKAMGAAVVNAL 354
           MLR        A  ++AAV+RVL +G RT DI   G  ++GT +MG  +   +
Sbjct: 305 MLRLGFGLAAEADAIDAAVRRVLAEGYRTGDIMENGRTLVGTVSMGNLIAERI 357


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: 449
Number of extensions: 10
Number of successful extensions: 3
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: 357
Length adjustment: 29
Effective length of query: 329
Effective length of database: 328
Effective search space:   107912
Effective search space used:   107912
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 208498 DVU2985 (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.10003.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   6.5e-160  517.8   0.0   7.4e-160  517.6   0.0    1.0  1  lcl|MicrobesOnline__882:208498  DVU2985 3-isopropylmalate dehydr


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:208498  DVU2985 3-isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  517.6   0.0  7.4e-160  7.4e-160       1     347 [.       4     351 ..       4     353 .. 0.99

  Alignments for each domain:
  == domain 1  score: 517.6 bits;  conditional E-value: 7.4e-160
                       TIGR00169   1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGGpkWdnl 79 
                                     +i +LpGDgiGpe+va+ +kvL+av+ rf++ + +++aliGGaaidatg+Plp++t++ac+ +davLlgavGGpkWd+l
  lcl|MicrobesOnline__882:208498   4 NICLLPGDGIGPEIVAQGTKVLDAVARRFGHTVSTSSALIGGAAIDATGSPLPDATVEACRTSDAVLLGAVGGPKWDDL 82 
                                     699**************************************************************************** PP

                       TIGR00169  80 prdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeiv.kgvDlvvvreLtgGiYfGepkereeaeeekkaldt 157
                                     p+++rPekgLL +rk l+lfanLrPa lf++L  ++ l+++i+  g+DlvvvreLtg +YfG+p ++e  +  +++++t
  lcl|MicrobesOnline__882:208498  83 PSEKRPEKGLLGIRKALGLFANLRPAALFPELAGACLLRADIAaAGLDLVVVRELTGDVYFGQPAGIETRDGLRTGFNT 161
                                     ******************************************989************************999******* PP

                       TIGR00169 158 ekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPdvelehlyiDnaamqLvksPeqldvv 236
                                     + Y ++e++riarvaf +ar+r+++v+svDkanvL++srlWr++vee+a++yPdvel+h+y+DnaamqLv+ P+q+dv+
  lcl|MicrobesOnline__882:208498 162 MIYDEDEVRRIARVAFDTARARKRRVCSVDKANVLATSRLWREVVEEVARDYPDVELSHMYVDNAAMQLVRWPAQFDVI 240
                                     ******************************************************************************* PP

                       TIGR00169 237 vtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvhgsapdiagkgianpiaailsaalllryslnleeaaeai 315
                                     vt+nlfGDilsDea+vitGs+G+LPsas++s g alfep+hgsapdiag++ anpia+ils+ ++lr +++l  +a+ai
  lcl|MicrobesOnline__882:208498 241 VTGNLFGDILSDEAAVITGSIGMLPSASMGSGGPALFEPIHGSAPDIAGQDKANPIATILSVGMMLRLGFGLAAEADAI 319
                                     ******************************************************************************* PP

                       TIGR00169 316 eaavkkvleegkrtedlaseattavstkevee 347
                                     +aav++vl+eg+rt d+++++ t v+t ++++
  lcl|MicrobesOnline__882:208498 320 DAAVRRVLAEGYRTGDIMENGRTLVGTVSMGN 351
                                     *************************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (357 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: 00:00:00.01
# Mc/sec: 11.01
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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