GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Klebsiella michiganensis M5al

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate BWI76_RS04675 BWI76_RS04675 3-isopropylmalate dehydrogenase

Query= BRENDA::P30125
         (363 letters)



>FitnessBrowser__Koxy:BWI76_RS04675
          Length = 363

 Score =  673 bits (1736), Expect = 0.0
 Identities = 336/363 (92%), Positives = 348/363 (95%)

Query: 1   MSKNYHIAVLPGDGIGPEVMTQALKVLDAVRNRFAMRITTSHYDVGGAAIDNHGQPLPPA 60
           MSKNYHIAVLPGDGIGPEVM QALKVL+AVR+RF MRITTS +DVGG AID  G PLP +
Sbjct: 1   MSKNYHIAVLPGDGIGPEVMNQALKVLEAVRHRFDMRITTSQHDVGGIAIDRQGTPLPQS 60

Query: 61  TVEGCEQADAVLFGSVGGPKWEHLPPDQQPERGALLPLRKHFKLFSNLRPAKLYQGLEAF 120
           TVEGCEQADA+LFGSVGGPKWEHLPP +QPERGALLPLRKHFKLFSNLRPAKLYQGLE F
Sbjct: 61  TVEGCEQADAILFGSVGGPKWEHLPPAEQPERGALLPLRKHFKLFSNLRPAKLYQGLEEF 120

Query: 121 CPLRADIAANGFDILCVRELTGGIYFGQPKGREGSGQYEKAFDTEVYHRFEIERIARIAF 180
           CPLRADIAANGFDILCVRELTGGIYFGQPKGREGSGQ+EKAFDTEVYHRFEIERIA IAF
Sbjct: 121 CPLRADIAANGFDILCVRELTGGIYFGQPKGREGSGQHEKAFDTEVYHRFEIERIAHIAF 180

Query: 181 ESARKRRHKVTSIDKANVLQSSILWREIVNEIATEYPDVELAHMYIDNATMQLIKDPSQF 240
           ESARKRRHKVTSIDKANVLQSSILWREIV+EI+ +YPDVEL+HMYIDNATMQLIKDPSQF
Sbjct: 181 ESARKRRHKVTSIDKANVLQSSILWREIVSEISKQYPDVELSHMYIDNATMQLIKDPSQF 240

Query: 241 DVLLCSNLFGDILSDECAMITGSMGMLPSASLNEQGFGLYEPAGGSAPDIAGKNIANPIA 300
           DVLLCSNLFGDILSDECAMITGSMGMLPSASLNEQGFGLYEPAGGSAPDIAGKNIANPIA
Sbjct: 241 DVLLCSNLFGDILSDECAMITGSMGMLPSASLNEQGFGLYEPAGGSAPDIAGKNIANPIA 300

Query: 301 QILSLALLLRYSLDADDAACAIERAINRALEEGIRTGDLARGAAAVSTDEMGDIIARYVA 360
           QILSLALLLRYSLDAD AA AIE AINRALEEG+RTGDLARGAAAVSTDEMGDIIARYVA
Sbjct: 301 QILSLALLLRYSLDADSAATAIENAINRALEEGVRTGDLARGAAAVSTDEMGDIIARYVA 360

Query: 361 EGV 363
           EGV
Sbjct: 361 EGV 363


Lambda     K      H
   0.320    0.137    0.405 

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: 559
Number of extensions: 10
Number of successful extensions: 1
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: 363
Length of database: 363
Length adjustment: 29
Effective length of query: 334
Effective length of database: 334
Effective search space:   111556
Effective search space used:   111556
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 BWI76_RS04675 BWI76_RS04675 (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.23567.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   2.3e-172  558.7   0.0   2.6e-172  558.6   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS04675  BWI76_RS04675 3-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS04675  BWI76_RS04675 3-isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  558.6   0.0  2.6e-172  2.6e-172       1     348 [.       6     354 ..       6     355 .. 0.99

  Alignments for each domain:
  == domain 1  score: 558.6 bits;  conditional E-value: 2.6e-172
                               TIGR00169   1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgav 71 
                                             +iavLpGDgiGpev+++alkvL+av++rf+++++++++++GG aid++g+Plp+ t+++c++ada+L+g+v
  lcl|FitnessBrowser__Koxy:BWI76_RS04675   6 HIAVLPGDGIGPEVMNQALKVLEAVRHRFDMRITTSQHDVGGIAIDRQGTPLPQSTVEGCEQADAILFGSV 76 
                                             69********************************************************************* PP

                               TIGR00169  72 GGpkWdnlprdvrPek.gLLklrkeldlfanLrPaklfksLeklsplkeeiv.kgvDlvvvreLtgGiYfG 140
                                             GGpkW++lp+  +Pe+ +LL+lrk+++lf+nLrPakl+++Le+++pl+++i+ +g+D+++vreLtgGiYfG
  lcl|FitnessBrowser__Koxy:BWI76_RS04675  77 GGPKWEHLPPAEQPERgALLPLRKHFKLFSNLRPAKLYQGLEEFCPLRADIAaNGFDILCVRELTGGIYFG 147
                                             ****************88*********************************989***************** PP

                               TIGR00169 141 epkereeaeeekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPd 211
                                             +pk+re++++++ka+dte+Y++ eieria++afe+arkrr+kvts+DkanvL+ss+lWr++v+ei k+yPd
  lcl|FitnessBrowser__Koxy:BWI76_RS04675 148 QPKGREGSGQHEKAFDTEVYHRFEIERIAHIAFESARKRRHKVTSIDKANVLQSSILWREIVSEISKQYPD 218
                                             *********************************************************************** PP

                               TIGR00169 212 velehlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvhgsapd 282
                                             vel+h+yiDna+mqL+k+P+q+dv+++snlfGDilsDe+++itGs+G+LPsasl+++g++l+ep++gsapd
  lcl|FitnessBrowser__Koxy:BWI76_RS04675 219 VELSHMYIDNATMQLIKDPSQFDVLLCSNLFGDILSDECAMITGSMGMLPSASLNEQGFGLYEPAGGSAPD 289
                                             *********************************************************************** PP

                               TIGR00169 283 iagkgianpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstkeveee 348
                                             iagk+ianpia+ils+alllrysl+++ aa+aie+a++++leeg rt dla+ a +avst+e+++ 
  lcl|FitnessBrowser__Koxy:BWI76_RS04675 290 IAGKNIANPIAQILSLALLLRYSLDADSAATAIENAINRALEEGVRTGDLARGA-AAVSTDEMGDI 354
                                             ****************************************************99.999***99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (363 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: 10.61
//
[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