Alignments for a candidate for ilvC in Klebsiella michiganensis M5al

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvC in Klebsiella michiganensis M5al

Align ketol-acid reductoisomerase (NADP+) (EC 1.1.1.86) (characterized)
to candidate BWI76_RS00990 BWI76_RS00990 ketol-acid reductoisomerase

Query= BRENDA::A6TGG1
         (491 letters)



>FitnessBrowser__Koxy:BWI76_RS00990
          Length = 491

 Score =  959 bits (2478), Expect = 0.0
 Identities = 484/491 (98%), Positives = 485/491 (98%)

Query: 1   MANYFNTLNLRQQLAQLGKCRFMARDEFADGASYLQGKKVVIVGCGAQGLNQGLNMRDSG 60
           MANYFNTLNLRQQLAQLGKCRFM RDEFADGASYLQGKKVVIVGCGAQGLNQGLNMRDSG
Sbjct: 1   MANYFNTLNLRQQLAQLGKCRFMGRDEFADGASYLQGKKVVIVGCGAQGLNQGLNMRDSG 60

Query: 61  LDISYALRKEAIAEKRASWRKATENGFKVGTYEELIPQADLVVNLTPDKQHSDVVRSVQP 120
           LDISYALRKEAIAEKRASWRKATENGFKVGTYEELIPQADLVVNLTPDKQHSDVVRSVQP
Sbjct: 61  LDISYALRKEAIAEKRASWRKATENGFKVGTYEELIPQADLVVNLTPDKQHSDVVRSVQP 120

Query: 121 LMKDGAALGYSHGFNIVEVGEQIRKDITVVMVAPKCPGTEVREEYKRGFGVPTLIAVHPE 180
           LMKDGAALGYSHGFNIVEVGEQIRKDITVVMVAPKCPGTEVREEYKRGFGVPTLIAVHPE
Sbjct: 121 LMKDGAALGYSHGFNIVEVGEQIRKDITVVMVAPKCPGTEVREEYKRGFGVPTLIAVHPE 180

Query: 181 NDPKGEGMAIAKAWAAATGGHRAGVLESSFVAEVKSDLMGEQTILCGMLQAGSLLCFDKL 240
           NDPKGEGMAIAKAWAAATGGHRAGVLESSFVAEVKSDLMGEQTILCGMLQAGSLLCFDKL
Sbjct: 181 NDPKGEGMAIAKAWAAATGGHRAGVLESSFVAEVKSDLMGEQTILCGMLQAGSLLCFDKL 240

Query: 241 VAEGTDPAYAEKLIQFGWETITEALKQGGITLMMDRLSNPAKLRAYALSEQLKEIMAPLF 300
           V EGTDPAYAEKLIQFGWETITEALKQGGITLMMDRLSNPAKLRAYALSEQLK IMAPLF
Sbjct: 241 VEEGTDPAYAEKLIQFGWETITEALKQGGITLMMDRLSNPAKLRAYALSEQLKTIMAPLF 300

Query: 301 QKHMDDIISGEFSSGMMADWANDDKKLLTWREETGKTAFETAPQYEGKIGEQEYFDKGVL 360
           QKHMDDIISGEFSSGMMADWANDDKKLLTWREETGKTAFETAPQ+EGKIGEQEYFDKGVL
Sbjct: 301 QKHMDDIISGEFSSGMMADWANDDKKLLTWREETGKTAFETAPQFEGKIGEQEYFDKGVL 360

Query: 361 MIAMVKAGVELAFETMVASGIIEESAYYESLHELPLIANTIARKRLYEMNVVISDTAEYG 420
           MIAMVKAGVELAFETMV SGIIEESAYYESLHELPLIANTIARKRLYEMNVVISDTAEYG
Sbjct: 361 MIAMVKAGVELAFETMVDSGIIEESAYYESLHELPLIANTIARKRLYEMNVVISDTAEYG 420

Query: 421 NYLFSYACVPLLKEFMTTLQTGDLGTAIAEGAVDNAQLRDVNEAIRSHAIEQVGKKLRGY 480
           NYLFSYACVPLLKEFMTTLQTGDLG AIAEGAVDNAQLRDVNEAIR HAIEQVGKKLRGY
Sbjct: 421 NYLFSYACVPLLKEFMTTLQTGDLGKAIAEGAVDNAQLRDVNEAIRGHAIEQVGKKLRGY 480

Query: 481 MTDMKRIAVAG 491
           MTDMKRIAVAG
Sbjct: 481 MTDMKRIAVAG 491


Lambda     K      H
   0.317    0.134    0.384 

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: 928
Number of extensions: 23
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: 491
Length of database: 491
Length adjustment: 34
Effective length of query: 457
Effective length of database: 457
Effective search space:   208849
Effective search space used:   208849
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate BWI76_RS00990 BWI76_RS00990 (ketol-acid reductoisomerase)
to HMM TIGR00465 (ilvC: ketol-acid reductoisomerase (EC 1.1.1.86))

# 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/TIGR00465.hmm
# target sequence database:        /tmp/gapView.31803.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00465  [M=314]
Accession:   TIGR00465
Description: ilvC: ketol-acid reductoisomerase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   7.5e-155  500.6   0.9     3e-140  452.6   0.1    2.0  2  lcl|FitnessBrowser__Koxy:BWI76_RS00990  BWI76_RS00990 ketol-acid reducto


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS00990  BWI76_RS00990 ketol-acid reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  452.6   0.1    3e-140    3e-140       1     313 [.      35     368 ..      35     369 .. 0.98
   2 !   50.8   0.1   6.1e-18   6.1e-18     188     311 ..     364     482 ..     364     485 .. 0.93

  Alignments for each domain:
  == domain 1  score: 452.6 bits;  conditional E-value: 3e-140
                               TIGR00465   1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkea.....aswkkAeedGfkvltveeaikkadlimiL 66 
                                             l+gkkv+i+G+G+qG +q+ln+rdsgl+++++lrkea     asw+kA+e+Gfkv t+ee+i++adl+++L
  lcl|FitnessBrowser__Koxy:BWI76_RS00990  35 LQGKKVVIVGCGAQGLNQGLNMRDSGLDISYALRKEAiaekrASWRKATENGFKVGTYEELIPQADLVVNL 105
                                             79********************************************************************* PP

                               TIGR00465  67 lpDevqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsli 137
                                             +pD+ q+++++++++pl+k+g+al++sHGfniv+++++i+kd++vv+vAPK+pG++vReeyk+g+Gvp+li
  lcl|FitnessBrowser__Koxy:BWI76_RS00990 106 TPDK-QHSDVVRSVQPLMKDGAALGYSHGFNIVEVGEQIRKDITVVMVAPKCPGTEVREEYKRGFGVPTLI 175
                                             ****.99999999********************************************************** PP

                               TIGR00465 138 Aveqd..vtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyq 206
                                             Av+++  ++ge+++iA+a+A+a+Gg+ragvle++F++Ev+sDL+GEq++LcG+l+a+++++fd+Lve+G++
  lcl|FitnessBrowser__Koxy:BWI76_RS00990 176 AVHPEndPKGEGMAIAKAWAAATGGHRAGVLESSFVAEVKSDLMGEQTILCGMLQAGSLLCFDKLVEEGTD 246
                                             **98877**************************************************************** PP

                               TIGR00465 207 pelAyfeivhelklivdllkekGlelmrdavsntAklgalelreilkeelkkemqkilkeiqnGefak... 274
                                             p++A+++i++++++i+++lk++G++lm+d++sn+Akl+a++l+e+lk  +++ +qk++++i++Gef++   
  lcl|FitnessBrowser__Koxy:BWI76_RS00990 247 PAYAEKLIQFGWETITEALKQGGITLMMDRLSNPAKLRAYALSEQLKTIMAPLFQKHMDDIISGEFSSgmm 317
                                             *******************************************************************9999 PP

                               TIGR00465 275 .ewalek........eagkpafeearkke...keqeiekvGkelralvkae 313
                                              +wa+++        e+gk+afe+a++ e    eqe++++G+ ++a+vka+
  lcl|FitnessBrowser__Koxy:BWI76_RS00990 318 aDWANDDkklltwreETGKTAFETAPQFEgkiGEQEYFDKGVLMIAMVKAG 368
                                             9*****9**********************9999***************975 PP

  == domain 2  score: 50.8 bits;  conditional E-value: 6.1e-18
                               TIGR00465 188 glealikaafdtLveaGyqpelAyfeivhelklivdllkekGlelmrdavsntAklgalelreilkeelkk 258
                                             +++a++++af+t+v+ G  +e Ay e +hel li++ + +k l +m   +s+tA++g++     ++ +  +
  lcl|FitnessBrowser__Koxy:BWI76_RS00990 364 MVKAGVELAFETMVDSGIIEESAYYESLHELPLIANTIARKRLYEMNVVISDTAEYGNYL----FSYACVP 430
                                             7999*****************************************************985....6677889 PP

                               TIGR00465 259 emqkilkeiqnGefakewalekeagkpafeearkkekeqeiekvGkelralvk 311
                                              +++ +  +q+G+  k  + e +++++++++ +++ + + ie+vGk+lr  + 
  lcl|FitnessBrowser__Koxy:BWI76_RS00990 431 LLKEFMTTLQTGDLGK-AIAEGAVDNAQLRDVNEAIRGHAIEQVGKKLRGYMT 482
                                             999999**********.777888**************************8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (314 nodes)
Target sequences:                          1  (491 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: 0.06u 0.01s 00:00:00.06 Elapsed: 00:00:00.06
# Mc/sec: 2.32
//
[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