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.491210.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 13.65
//
[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