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.13791.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.98
//
[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:

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:

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:

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:

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