Alignments for a candidate for leuB in Klebsiella michiganensis M5al

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.10879.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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.47
//
[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