Alignments for a candidate for ilvI in Klebsiella variicola At-22

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Klebsiella variicola At-22

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_012968940.1 KVAR_RS21435 acetolactate synthase 3 large subunit

Query= BRENDA::P00893
         (574 letters)



>NCBI__GCF_000025465.1:WP_012968940.1
          Length = 574

 Score = 1063 bits (2749), Expect = 0.0
 Identities = 524/574 (91%), Positives = 545/574 (94%)

Query: 1   MEMLSGAEMVVRSLIDQGVKQVFGYPGGAVLDIYDALHTVGGIDHVLVRHEQAAVHMADG 60
           MEMLSGAEMVV+SL+DQGVKQVFGYPGGAVLDIYDALHT+GGIDHVLVRHEQAAVHMADG
Sbjct: 1   MEMLSGAEMVVQSLVDQGVKQVFGYPGGAVLDIYDALHTLGGIDHVLVRHEQAAVHMADG 60

Query: 61  LARATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLIGYDAFQECDMVG 120
           LARATGEVGVVLVTSGPGATNAITGIATAYMDSIPLV+LSGQVATSLIGYDAFQECDMVG
Sbjct: 61  LARATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVILSGQVATSLIGYDAFQECDMVG 120

Query: 121 ISRPVVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDILNPANKLPYVWPESV 180
           ISRPVVKHSFLVKQTEDIP VLKKAFWLAASGRPGPVVVDLPKDILNPA KLPY WPE+V
Sbjct: 121 ISRPVVKHSFLVKQTEDIPGVLKKAFWLAASGRPGPVVVDLPKDILNPAKKLPYAWPEAV 180

Query: 181 SMRSYNPTTTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVEALNLPVVCS 240
           SMRSYNPTT+GHKGQIKRALQTLVAA KPVVYVGGGAI A C  QL+E VE L LPV  S
Sbjct: 181 SMRSYNPTTSGHKGQIKRALQTLVAASKPVVYVGGGAINAHCEPQLRELVEKLKLPVASS 240

Query: 241 LMGLGAFPATHRQALGMLGMHGTYEANMTMHNADVIFAVGVRFDDRTTNNLAKYCPNATV 300
           LMGLGAFPATH QALGMLGMHGTYEANM MH++DVIFAVGVRFDDRTTNNLAKYCPNATV
Sbjct: 241 LMGLGAFPATHPQALGMLGMHGTYEANMAMHHSDVIFAVGVRFDDRTTNNLAKYCPNATV 300

Query: 301 LHIDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQESAHQPLDEIRDWWQQIEQWRAR 360
           LHIDIDPTSISKTV AD+PIVGDAR VLEQMLELL QE   QPLD+IRDWWQQIEQWRAR
Sbjct: 301 LHIDIDPTSISKTVPADVPIVGDARLVLEQMLELLDQEETQQPLDDIRDWWQQIEQWRAR 360

Query: 361 QCLKYDTHSEKIKPQAVIETLWRLTKGDAYVTSDVGQHQMFAALYYPFDKPRRWINSGGL 420
            CL+YD  S+KIKPQAVIET+WRLT+GDAYVTSDVGQHQMFAALYYPFDKPRRWINSGGL
Sbjct: 361 HCLRYDDRSDKIKPQAVIETIWRLTQGDAYVTSDVGQHQMFAALYYPFDKPRRWINSGGL 420

Query: 421 GTMGFGLPAALGVKMALPEETVVCVTGDGSIQMNIQELSTALQYELPVLVVNLNNRYLGM 480
           GTMGFGLPAALGVKMALP+E VVCVTGDGSIQMNIQELSTALQYELPVLV+NLNNRYLGM
Sbjct: 421 GTMGFGLPAALGVKMALPDEMVVCVTGDGSIQMNIQELSTALQYELPVLVLNLNNRYLGM 480

Query: 481 VKQWQDMIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHELESKLSEALEQVRNNRL 540
           VKQWQDM+YSGRHSQSYM+SLPDFVRLAEAYGHVGI+IS P ELESKL+EALEQVR  RL
Sbjct: 481 VKQWQDMLYSGRHSQSYMESLPDFVRLAEAYGHVGIRISEPQELESKLAEALEQVRQRRL 540

Query: 541 VFVDVTVDGSEHVYPMQIRGGGMDEMWLSKTERT 574
           VFVDVTVDGSEHVYPMQIRGGGMDEMWLSKTERT
Sbjct: 541 VFVDVTVDGSEHVYPMQIRGGGMDEMWLSKTERT 574


Lambda     K      H
   0.319    0.135    0.403 

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: 1220
Number of extensions: 32
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: 574
Length of database: 574
Length adjustment: 36
Effective length of query: 538
Effective length of database: 538
Effective search space:   289444
Effective search space used:   289444
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: 53 (25.0 bits)

Align candidate WP_012968940.1 KVAR_RS21435 (acetolactate synthase 3 large subunit)
to HMM TIGR00118 (ilvB: acetolactate synthase, large subunit, biosynthetic type (EC 2.2.1.6))

# 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/TIGR00118.hmm
# target sequence database:        /tmp/gapView.8359.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00118  [M=557]
Accession:   TIGR00118
Description: acolac_lg: acetolactate synthase, large subunit, biosynthetic type
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.3e-283  926.1   0.1   3.9e-283  925.9   0.1    1.0  1  lcl|NCBI__GCF_000025465.1:WP_012968940.1  KVAR_RS21435 acetolactate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025465.1:WP_012968940.1  KVAR_RS21435 acetolactate synthase 3 large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  925.9   0.1  3.9e-283  3.9e-283       1     556 [.       4     569 ..       4     570 .. 0.98

  Alignments for each domain:
  == domain 1  score: 925.9 bits;  conditional E-value: 3.9e-283
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 
                                               l+gae++v+sl ++gv++vfGyPGGavl+iydal+  ++++h+lvrheqaa+h+adG+ara+G+vGvvl
  lcl|NCBI__GCF_000025465.1:WP_012968940.1   4 LSGAEMVVQSLVDQGVKQVFGYPGGAVLDIYDALHtLGGIDHVLVRHEQAAVHMADGLARATGEVGVVL 72 
                                               68*********************************99******************************** PP

                                 TIGR00118  69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137
                                               +tsGPGatn++tgiatay+ds+Plv+l+GqvatsliG+dafqe+d++Gi++pv+khsflvk++ed+p +
  lcl|NCBI__GCF_000025465.1:WP_012968940.1  73 VTSGPGATNAITGIATAYMDSIPLVILSGQVATSLIGYDAFQECDMVGISRPVVKHSFLVKQTEDIPGV 141
                                               ********************************************************************* PP

                                 TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleve..ekvelpgykptvkghklqikkaleliekakkPv 204
                                               lk+af++a++GrPGPv+vdlPkd+ +++ +l++   e v++++y+pt++ghk qik+al+++ +a kPv
  lcl|NCBI__GCF_000025465.1:WP_012968940.1 142 LKKAFWLAASGRPGPVVVDLPKDILNPAKKLPYAwpEAVSMRSYNPTTSGHKGQIKRALQTLVAASKPV 210
                                               ******************************999988********************************* PP

                                 TIGR00118 205 llvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliav 273
                                               ++vGgG+i a+++ +l+el+e+lk+pv+++l+GlGafp++hp+algmlGmhGt+ean+a++++d+++av
  lcl|NCBI__GCF_000025465.1:WP_012968940.1 211 VYVGGGAINAHCEPQLRELVEKLKLPVASSLMGLGAFPATHPQALGMLGMHGTYEANMAMHHSDVIFAV 279
                                               ********************************************************************* PP

                                 TIGR00118 274 GarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke 338
                                               G+rfddr+t+nlak++p+a+++hididP++i+k+v +d+pivGda+ vle++l+ l +e      ++++
  lcl|NCBI__GCF_000025465.1:WP_012968940.1 280 GVRFDDRTTNNLAKYCPNATVLHIDIDPTSISKTVPADVPIVGDARLVLEQMLELLDQEetqqPLDDIR 348
                                               ******************************************************999885554446777 PP

                                 TIGR00118 339 .WlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfits 406
                                                W+++ie+w+++++l++d ++++ikPq+vi+++++l++++a+vt+dvGqhqm+aa +y+++kpr++i+s
  lcl|NCBI__GCF_000025465.1:WP_012968940.1 349 dWWQQIEQWRARHCLRYDDRSDKIKPQAVIETIWRLTQGDAYVTSDVGQHQMFAALYYPFDKPRRWINS 417
                                               8******************************************************************** PP

                                 TIGR00118 407 gGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqe 475
                                               gGlGtmGfGlPaalG+k+a p+e vv+vtGdgs+qmn+qelst+ +y++pv +++lnn++lGmvkqWq+
  lcl|NCBI__GCF_000025465.1:WP_012968940.1 418 GGLGTMGFGLPAALGVKMALPDEMVVCVTGDGSIQMNIQELSTALQYELPVLVLNLNNRYLGMVKQWQD 486
                                               ********************************************************************* PP

                                 TIGR00118 476 lfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk...epvlldvevdkeeevl 541
                                               ++y++r+s+++++s lpdfv+laeayG++giri++p+ele+kl+eale+    ++v++dv+vd +e+v+
  lcl|NCBI__GCF_000025465.1:WP_012968940.1 487 MLYSGRHSQSYMES-LPDFVRLAEAYGHVGIRISEPQELESKLAEALEQVrqrRLVFVDVTVDGSEHVY 554
                                               *************5.******************************9886544599************** PP

                                 TIGR00118 542 PmvapGagldelvee 556
                                               Pm+++G+g+de++ +
  lcl|NCBI__GCF_000025465.1:WP_012968940.1 555 PMQIRGGGMDEMWLS 569
                                               ************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (574 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 11.74
//
[ok]

This GapMind analysis is from Apr 10 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