Alignments for a candidate for ilvI in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Shewanella oneidensis MR-1

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate 201429 SO2279 acetolactate synthase III, large subunit (NCBI ptt file)

Query= BRENDA::P00893
         (574 letters)



>FitnessBrowser__MR1:201429
          Length = 572

 Score =  885 bits (2287), Expect = 0.0
 Identities = 425/573 (74%), Positives = 492/573 (85%), Gaps = 2/573 (0%)

Query: 1   MEMLSGAEMVVRSLIDQGVKQVFGYPGGAVLDIYDALHTVGGIDHVLVRHEQAAVHMADG 60
           ME LSGA M+VRSLID+GVK +FGYPGG+VLDIYDALH + GI+H+LVRHEQAAVHMADG
Sbjct: 1   MEKLSGASMIVRSLIDEGVKHIFGYPGGSVLDIYDALHLIPGIEHILVRHEQAAVHMADG 60

Query: 61  LARATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLIGYDAFQECDMVG 120
            ARATG+VGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQV ++LIG DAFQECDM+G
Sbjct: 61  YARATGKVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVPSNLIGNDAFQECDMIG 120

Query: 121 ISRPVVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDILNPANKLPYVWPESV 180
           ISRPVVKHSFLV+    IP+++KKAF++A++GRPGPVVVDLPKD LNPA    Y++PES+
Sbjct: 121 ISRPVVKHSFLVQDPTQIPEIIKKAFYIASTGRPGPVVVDLPKDCLNPALLHDYIYPESI 180

Query: 181 SMRSYNPTTTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVEALNLPVVCS 240
            MRSYNPTT+GHKGQI+R LQ L+AAKKPV+YVGGGAI +G  +Q+    E LN+PV+ +
Sbjct: 181 KMRSYNPTTSGHKGQIRRGLQALLAAKKPVLYVGGGAIISGSEKQILTLAEKLNIPVIST 240

Query: 241 LMGLGAFPATHRQALGMLGMHGTYEANMTMHNADVIFAVGVRFDDRTTNNLAKYCPNATV 300
           LMGLGAFP TH+ +LGMLGMHG YEANM MHN D+IF +GVRFDDRTTNN+ KYCPNAT+
Sbjct: 241 LMGLGAFPGTHKNSLGMLGMHGRYEANMAMHNCDLIFGIGVRFDDRTTNNIEKYCPNATI 300

Query: 301 LHIDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQESAHQPLDEIRDWWQQIEQWRAR 360
           LHIDIDP+SISKTV  DIPIVG A  VL+ +L LL + S       I  WWQ+I  WR R
Sbjct: 301 LHIDIDPSSISKTVRVDIPIVGSADIVLDSILALLDEASETNDFVAINQWWQEITTWRNR 360

Query: 361 QCLKYDTHSEKIKPQAVIETLWRLTKGDAYVTSDVGQHQMFAALYYPFDKPRRWINSGGL 420
           QCL YD  S +IKPQ VIETL++LT G+AYV SDVGQHQMFAALYYPFDKPRRWINSGGL
Sbjct: 361 QCLAYDKESNRIKPQQVIETLYKLTNGEAYVASDVGQHQMFAALYYPFDKPRRWINSGGL 420

Query: 421 GTMGFGLPAALGVKMALPEETVVCVTGDGSIQMNIQELSTALQYELPVLVVNLNNRYLGM 480
           GTMGFGLPAA+GVKMA+P+ETVVCVTGDGSIQMNIQELSTALQY+ PV ++NLNNR+LGM
Sbjct: 421 GTMGFGLPAAMGVKMAMPDETVVCVTGDGSIQMNIQELSTALQYDTPVKIINLNNRFLGM 480

Query: 481 VKQWQDMIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHELESKLSEALEQVRNNRL 540
           VKQWQDMIYSGRHS SYM S+P+F ++AEAYGHVG+ IS P ELESK++EAL     +RL
Sbjct: 481 VKQWQDMIYSGRHSHSYMDSVPNFAKIAEAYGHVGMTISDPAELESKMAEAL--AMKDRL 538

Query: 541 VFVDVTVDGSEHVYPMQIRGGGMDEMWLSKTER 573
           VF+D+ VD +EHVYPM IRGG M+EMWLSKTE+
Sbjct: 539 VFIDIMVDETEHVYPMLIRGGAMNEMWLSKTEK 571


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: 1088
Number of extensions: 30
Number of successful extensions: 2
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: 572
Length adjustment: 36
Effective length of query: 538
Effective length of database: 536
Effective search space:   288368
Effective search space used:   288368
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 201429 SO2279 (acetolactate synthase III, large subunit (NCBI ptt file))
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.24330.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   5.5e-277  905.6   0.5   6.4e-277  905.4   0.5    1.0  1  lcl|FitnessBrowser__MR1:201429  SO2279 acetolactate synthase III


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:201429  SO2279 acetolactate synthase III, large subunit (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  905.4   0.5  6.4e-277  6.4e-277       1     556 [.       4     567 ..       4     568 .. 0.97

  Alignments for each domain:
  == domain 1  score: 905.4 bits;  conditional E-value: 6.4e-277
                       TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGPGatnl 78 
                                     l+ga+++v+sl +egv+++fGyPGG+vl+iydal+   ++ehilvrheqaa+h+adGyara+GkvGvvl+tsGPGatn+
  lcl|FitnessBrowser__MR1:201429   4 LSGASMIVRSLIDEGVKHIFGYPGGSVLDIYDALHlIPGIEHILVRHEQAAVHMADGYARATGKVGVVLVTSGPGATNA 82 
                                     689********************************999***************************************** PP

                       TIGR00118  79 vtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGrPGPvlvdl 157
                                     +tgiatay+ds+Plvvl+Gqv+++liG+dafqe+d++Gi++pv+khsflv+++ ++pei+k+af+iastGrPGPv+vdl
  lcl|FitnessBrowser__MR1:201429  83 ITGIATAYMDSIPLVVLSGQVPSNLIGNDAFQECDMIGISRPVVKHSFLVQDPTQIPEIIKKAFYIASTGRPGPVVVDL 161
                                     ******************************************************************************* PP

                       TIGR00118 158 Pkdvteaei..eleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeaseelkelaerlkipvttt 234
                                     Pkd  ++++  ++ ++e++++++y+pt++ghk qi++ l+++ +akkPvl+vGgG+ii+++++++  lae+l+ipv++t
  lcl|FitnessBrowser__MR1:201429 162 PKDCLNPALlhDYIYPESIKMRSYNPTTSGHKGQIRRGLQALLAAKKPVLYVGGGAIISGSEKQILTLAEKLNIPVIST 240
                                     ******9972255666*************************************************************** PP

                       TIGR00118 235 llGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihididPaeigknvkvdip 313
                                     l+GlGafp +h+++lgmlGmhG++ean+a++++dl++++G+rfddr+t+n++k++p+a+i+hididP++i+k+v+vdip
  lcl|FitnessBrowser__MR1:201429 241 LMGLGAFPGTHKNSLGMLGMHGRYEANMAMHNCDLIFGIGVRFDDRTTNNIEKYCPNATILHIDIDPSSISKTVRVDIP 319
                                     ******************************************************************************* PP

                       TIGR00118 314 ivGdakkvleellkklkee.ekke....keWlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqh 387
                                     ivG a  vl+ +l+ l e  e+++    ++W+++i+ w+++++l++d+e++ ikPq+vi++l+kl+++ea+v++dvGqh
  lcl|FitnessBrowser__MR1:201429 320 IVGSADIVLDSILALLDEAsETNDfvaiNQWWQEITTWRNRQCLAYDKESNRIKPQQVIETLYKLTNGEAYVASDVGQH 398
                                     **************9999843333333246************************************************* PP

                       TIGR00118 388 qmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnel 466
                                     qm+aa +y+++kpr++i+sgGlGtmGfGlPaa+G+k+a+p+etvv+vtGdgs+qmn+qelst+ +yd+pvki++lnn++
  lcl|FitnessBrowser__MR1:201429 399 QMFAALYYPFDKPRRWINSGGLGTMGFGLPAAMGVKMAMPDETVVCVTGDGSIQMNIQELSTALQYDTPVKIINLNNRF 477
                                     ******************************************************************************* PP

                       TIGR00118 467 lGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevlPmv 544
                                     lGmvkqWq+++y++r+s++++ s +p+f+k+aeayG++g++i++p+ele+k++eal++k ++v++d+ vd++e+v+Pm+
  lcl|FitnessBrowser__MR1:201429 478 LGMVKQWQDMIYSGRHSHSYMDS-VPNFAKIAEAYGHVGMTISDPAELESKMAEALAMKdRLVFIDIMVDETEHVYPML 555
                                     **********************5.********************************988799***************** PP

                       TIGR00118 545 apGagldelvee 556
                                     ++G++++e++ +
  lcl|FitnessBrowser__MR1:201429 556 IRGGAMNEMWLS 567
                                     *********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (572 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: 11.54
//
[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