Alignments for a candidate for leuB in Dechlorosoma suillum PS

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuB in Dechlorosoma suillum PS

Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 (characterized)
to candidate Dsui_3198 Dsui_3198 3-isopropylmalate dehydrogenase

Query= SwissProt::Q56268
         (358 letters)



>FitnessBrowser__PS:Dsui_3198
          Length = 354

 Score =  432 bits (1111), Expect = e-126
 Identities = 227/357 (63%), Positives = 278/357 (77%), Gaps = 9/357 (2%)

Query: 3   KIAIFAGDGIGPEIVAAARQVLDAVDQAAHLGLRCTEGLVGGAALDASDDPLPAASLQLA 62
           KI +  GDGIGPEI+A A +VL+A++    LG      L+GG A+DA+ +P P AS +LA
Sbjct: 2   KICVLPGDGIGPEIMAEAVRVLEALN----LGFEMETALLGGCAVDATGNPYPEASQKLA 57

Query: 63  MAADAVILGAVGGPRWDAYPPAKRPEQGLLRLRKGLDLYANLRPAQIFPQLLDASPLRPE 122
            AADAV+LGAVGGP+WD  P  +RPE+GLL +RK L+L+ANLRPA ++P+L +AS L+PE
Sbjct: 58  QAADAVLLGAVGGPQWDTLPREQRPERGLLGIRKQLNLFANLRPAILYPELANASTLKPE 117

Query: 123 LVRDVDILVVRELTGDIYFGQPRGLEV--IDGKRR--GFNTMVYDEDEIRRIAHVAFRAA 178
           +V  +DIL+VRELTGDIYFGQPRG+E   IDG+++  GFNTM Y E EIRRI  VAF AA
Sbjct: 118 VVAGLDILIVRELTGDIYFGQPRGIEEREIDGQKQRFGFNTMHYSESEIRRILRVAFEAA 177

Query: 179 QGRRKQLCSVDKANVLETTRLWREVVTEVARDYPDVRLSHMYVDNAAMQLIRAPAQFDVL 238
           + R K+LCSVDK NVLETT+LWR++  E+A +YPDV LSHM VDNAAMQL+R P QFDV+
Sbjct: 178 RKRNKKLCSVDKMNVLETTQLWRDIANELAPEYPDVELSHMLVDNAAMQLVRNPKQFDVM 237

Query: 239 LTGNMFGDILSDEASQLTGSIGMLPSASL-GEGRAMYEPIHGSAPDIAGQDKANPLATIL 297
           +TGNMFGDILSDEAS LTGSIGMLPSASL    + +YEP HGSAPDIAG+  ANPLATIL
Sbjct: 238 VTGNMFGDILSDEASMLTGSIGMLPSASLDANNKGLYEPSHGSAPDIAGKGVANPLATIL 297

Query: 298 SVAMMLRHSLNAEPWAQRVEAAVQRVLDQGLRTADIAAPGTPVIGTKAMGAAVVNAL 354
           S AMMLR++ N E  A +VE AV++VL QG RT DI  PGT  +GT+ MG AV+ AL
Sbjct: 298 SAAMMLRYTFNMEEAAVKVENAVKKVLAQGYRTGDIYEPGTTKVGTRQMGDAVLAAL 354


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: 407
Number of extensions: 14
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: 354
Length adjustment: 29
Effective length of query: 329
Effective length of database: 325
Effective search space:   106925
Effective search space used:   106925
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 Dsui_3198 Dsui_3198 (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.9712.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.9e-160  519.0   0.0   3.3e-160  518.8   0.0    1.0  1  lcl|FitnessBrowser__PS:Dsui_3198  Dsui_3198 3-isopropylmalate dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_3198  Dsui_3198 3-isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  518.8   0.0  3.3e-160  3.3e-160       1     348 [.       2     349 ..       2     350 .. 0.97

  Alignments for each domain:
  == domain 1  score: 518.8 bits;  conditional E-value: 3.3e-160
                         TIGR00169   1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGGpkWd 77 
                                       ki vLpGDgiGpe++aea++vL+a+    +l +e+e+al+GG a+datg+P pe++ k +++adavLlgavGGp+Wd
  lcl|FitnessBrowser__PS:Dsui_3198   2 KICVLPGDGIGPEIMAEAVRVLEAL----NLGFEMETALLGGCAVDATGNPYPEASQKLAQAADAVLLGAVGGPQWD 74 
                                       79********************986....7999******************************************** PP

                         TIGR00169  78 nlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYfGepkereeaee.... 150
                                       +lpr++rPe+gLL +rk+l+lfanLrPa l+++L ++s+lk+e+v g+D+++vreLtg iYfG+p+++ee e     
  lcl|FitnessBrowser__PS:Dsui_3198  75 TLPREQRPERGLLGIRKQLNLFANLRPAILYPELANASTLKPEVVAGLDILIVRELTGDIYFGQPRGIEEREIdgqk 151
                                       ******************************************************************99986532224 PP

                         TIGR00169 151 ekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPdvelehlyiDnaamqLv 227
                                       ++ +++t++Y+++ei+ri rvafe+arkr+kk++svDk nvLe+++lWr++++e+a eyPdvel+h+++DnaamqLv
  lcl|FitnessBrowser__PS:Dsui_3198 152 QRFGFNTMHYSESEIRRILRVAFEAARKRNKKLCSVDKMNVLETTQLWRDIANELAPEYPDVELSHMLVDNAAMQLV 228
                                       6779************************************************************************* PP

                         TIGR00169 228 ksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvhgsapdiagkgianpiaailsaalllry 304
                                       ++P+q+dv+vt+n+fGDilsDeas++tGs+G+LPsasl  + ++l+ep hgsapdiagkg+anp+a+ilsaa++lry
  lcl|FitnessBrowser__PS:Dsui_3198 229 RNPKQFDVMVTGNMFGDILSDEASMLTGSIGMLPSASLDANNKGLYEPSHGSAPDIAGKGVANPLATILSAAMMLRY 305
                                       ***************************************************************************** PP

                         TIGR00169 305 slnleeaaeaieaavkkvleegkrtedlaseattavstkeveee 348
                                       ++n+eeaa ++e+avkkvl++g+rt d+++ +tt+v+t+++++ 
  lcl|FitnessBrowser__PS:Dsui_3198 306 TFNMEEAAVKVENAVKKVLAQGYRTGDIYEPGTTKVGTRQMGDA 349
                                       *****************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (354 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: 00:00:00.01
# Mc/sec: 7.85
//
[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