Alignments for a candidate for leuB in Sphingomonas koreensis DSMZ 15582

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuB in Sphingomonas koreensis DSMZ 15582

Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 (characterized)
to candidate Ga0059261_3190 Ga0059261_3190 3-isopropylmalate dehydrogenase

Query= SwissProt::Q56268
         (358 letters)



>FitnessBrowser__Korea:Ga0059261_3190
          Length = 348

 Score =  397 bits (1019), Expect = e-115
 Identities = 210/355 (59%), Positives = 260/355 (73%), Gaps = 9/355 (2%)

Query: 1   MKKIAIFAGDGIGPEIVAAARQVLDAVDQAAHLGLRCTEGLVGGAALDASDDPLPAASLQ 60
           M  IAI  GDGIGPE+ A AR+VLDA+D    LGL   E  VGGAA  +   PLPA +L 
Sbjct: 1   MPLIAILPGDGIGPEVTAQARRVLDALD----LGLSFEEAPVGGAAYFSDGHPLPARTLD 56

Query: 61  LAMAADAVILGAVGGPRWDAYPPAKRPEQGLLRLRKGLDLYANLRPAQIFPQLLDASPLR 120
           LA  ADA++ GAVG PR D      RPEQ +L LRK L+L+ANLRPA++FP L DAS L+
Sbjct: 57  LAKRADALLFGAVGDPRCDGLDRHLRPEQAILGLRKELELFANLRPARLFPGLEDASALK 116

Query: 121 PELVRDVDILVVRELTGDIYFGQPRGLEVIDGKRRGFNTMVYDEDEIRRIAHVAFRAAQG 180
           PE+   +D+++VREL GD+YFG+        G+R G++ M Y+EDE+ RIA V F  AQ 
Sbjct: 117 PEVAGAIDMVIVRELNGDVYFGEKGMRTTASGRREGYDIMSYNEDEVARIARVGFETAQV 176

Query: 181 RRKQLCSVDKANVLETTRLWREVVTEVARDYPDVRLSHMYVDNAAMQLIRAPAQFDVLLT 240
           R ++LCSVDKANVLET++LWR+VV EV+ ++PDV L+HMYVDNAAMQL+R P QFDV++T
Sbjct: 177 RNRKLCSVDKANVLETSQLWRDVVIEVSAEFPDVELTHMYVDNAAMQLVRNPGQFDVIVT 236

Query: 241 GNMFGDILSDEASQLTGSIGMLPSASL-GEGRAMYEPIHGSAPDIAGQDKANPLATILSV 299
           GN+FGDILSD+AS   GSIGMLPSA+L G G+ +YEPIHGSAPDIAGQ KANP ATILS 
Sbjct: 237 GNLFGDILSDQASMCAGSIGMLPSAALNGSGKGLYEPIHGSAPDIAGQGKANPCATILSA 296

Query: 300 AMMLRHSLNAEPWAQRVEAAVQRVLDQGLRTADIAAPGTPVIGTKAMGAAVVNAL 354
           AM+LR+SL+ E  A +VEAAV   L  G RTAD+       + T+AMG AV+ AL
Sbjct: 297 AMLLRYSLDMEAAADKVEAAVTAALAGGARTADLGG----ALSTEAMGDAVLKAL 347


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: 13
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: 348
Length adjustment: 29
Effective length of query: 329
Effective length of database: 319
Effective search space:   104951
Effective search space used:   104951
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 Ga0059261_3190 Ga0059261_3190 (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.985.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.5e-142  459.5   0.0     4e-142  459.3   0.0    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_3190  Ga0059261_3190 3-isopropylmalate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_3190  Ga0059261_3190 3-isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  459.3   0.0    4e-142    4e-142       2     346 ..       4     344 ..       3     347 .. 0.98

  Alignments for each domain:
  == domain 1  score: 459.3 bits;  conditional E-value: 4e-142
                                 TIGR00169   2 iavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlga 70 
                                               ia+LpGDgiGpev+a+a +vL+a+    +l l feea +GGaa  + g+Plp+ tl+ +k+ada+L+ga
  lcl|FitnessBrowser__Korea:Ga0059261_3190   4 IAILPGDGIGPEVTAQARRVLDAL----DLGLSFEEAPVGGAAYFSDGHPLPARTLDLAKRADALLFGA 68 
                                               89*******************987....699************************************** PP

                                 TIGR00169  71 vGGpkWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYf 139
                                               vG p+ d l r+ rPe+++L lrkel+lfanLrPa+lf++Le++s+lk+e++  +D+v+vreL g +Yf
  lcl|FitnessBrowser__Korea:Ga0059261_3190  69 VGDPRCDGLDRHLRPEQAILGLRKELELFANLRPARLFPGLEDASALKPEVAGAIDMVIVRELNGDVYF 137
                                               ********************************************************************* PP

                                 TIGR00169 140 GepkereeaeeekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiake 208
                                               Ge+  r+ a+ +++++d ++Y+++e+ riarv+fe+a+ r++k++svDkanvLe+s+lWr++v e+  e
  lcl|FitnessBrowser__Korea:Ga0059261_3190 138 GEKGMRTTASGRREGYDIMSYNEDEVARIARVGFETAQVRNRKLCSVDKANVLETSQLWRDVVIEVSAE 206
                                               **999999888********************************************************** PP

                                 TIGR00169 209 yPdvelehlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvh 277
                                               +Pdvel h+y+DnaamqLv++P q+dv+vt+nlfGDilsD+as+ +Gs+G+LPsa+l+++g++l+ep+h
  lcl|FitnessBrowser__Korea:Ga0059261_3190 207 FPDVELTHMYVDNAAMQLVRNPGQFDVIVTGNLFGDILSDQASMCAGSIGMLPSAALNGSGKGLYEPIH 275
                                               ********************************************************************* PP

                                 TIGR00169 278 gsapdiagkgianpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstkeve 346
                                               gsapdiag+g anp+a+ilsaa+llrysl++e aa+++eaav  +l+ g rt+dl++  +t+++ ++v 
  lcl|FitnessBrowser__Korea:Ga0059261_3190 276 GSAPDIAGQGKANPCATILSAAMLLRYSLDMEAAADKVEAAVTAALAGGARTADLGGALSTEAMGDAVL 344
                                               ********************************************************9999888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (348 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.66
//
[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