GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Shewanella loihica PV-4

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate 5209298 Shew_1776 acetolactate synthase 3 catalytic subunit (RefSeq)

Query= BRENDA::P00893
         (574 letters)



>FitnessBrowser__PV4:5209298
          Length = 573

 Score =  868 bits (2242), Expect = 0.0
 Identities = 422/575 (73%), Positives = 488/575 (84%), Gaps = 3/575 (0%)

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

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

Query: 121 ISRPVVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDILNPANKLPYVWPESV 180
           ISRPVVKHSFLV   +DIP ++KKAF++A++GRPGPVVVD+PKD LNP     Y +P+ +
Sbjct: 121 ISRPVVKHSFLVTDAKDIPAIIKKAFYIASTGRPGPVVVDIPKDCLNPQILHEYQYPDEI 180

Query: 181 SMRSYNPTTTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVEALNLPVVCS 240
           +MRSYNPTTTGHKGQI+R LQ L+ AKKPV+YVGGGA+ +G  QQ+ +  + L LPVV +
Sbjct: 181 NMRSYNPTTTGHKGQIRRGLQALLKAKKPVLYVGGGAVISGADQQILKLSDRLGLPVVST 240

Query: 241 LMGLGAFPATHRQALGMLGMHGTYEANMTMHNADVIFAVGVRFDDRTTNNLAKYCPNATV 300
           LMGLGAFP TH  ++GMLGMHG YEANM MHNAD+IF +GVRFDDRTTNN+ KYCPNAT+
Sbjct: 241 LMGLGAFPGTHANSVGMLGMHGCYEANMAMHNADLIFGIGVRFDDRTTNNVEKYCPNATI 300

Query: 301 LHIDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQE-SAHQPLDEIRDWWQQIEQWRA 359
           LHIDIDP+SISKTV  DIPIVG A  VL+ ML LL  E S       I  WW +I QWR+
Sbjct: 301 LHIDIDPSSISKTVRVDIPIVGSADSVLDDMLALLDDEPSMKNDEGAIDYWWSEINQWRS 360

Query: 360 RQCLKYDTHSEKIKPQAVIETLWRLTKGDAYVTSDVGQHQMFAALYYPFDKPRRWINSGG 419
           R  L YD  SE+IKPQ VIETL +LT GDAYV SDVGQHQMFAALYYPF+KPRRWINSGG
Sbjct: 361 RNSLAYDKSSERIKPQQVIETLHKLTNGDAYVASDVGQHQMFAALYYPFNKPRRWINSGG 420

Query: 420 LGTMGFGLPAALGVKMALPEETVVCVTGDGSIQMNIQELSTALQYELPVLVVNLNNRYLG 479
           LGTMGFGLPAA+GVKMA P+ETV+CVTGDGSIQMNIQELSTALQY+ PV ++NLNNR+LG
Sbjct: 421 LGTMGFGLPAAMGVKMAKPDETVICVTGDGSIQMNIQELSTALQYDTPVKIINLNNRFLG 480

Query: 480 MVKQWQDMIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHELESKLSEALEQVRNNR 539
           MVKQWQDMIYSGRHS SYM S+P+F ++AEAYGHVG+ IS P ELE+ L +AL     ++
Sbjct: 481 MVKQWQDMIYSGRHSHSYMDSVPNFAKIAEAYGHVGMTISDPAELEAGLEKAL--AMKDK 538

Query: 540 LVFVDVTVDGSEHVYPMQIRGGGMDEMWLSKTERT 574
           LVFVD++VD +EHVYPMQIRGGGM+EMWLSKTE++
Sbjct: 539 LVFVDISVDETEHVYPMQIRGGGMNEMWLSKTEKS 573


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: 1087
Number of extensions: 33
Number of successful extensions: 3
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: 573
Length adjustment: 36
Effective length of query: 538
Effective length of database: 537
Effective search space:   288906
Effective search space used:   288906
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 5209298 Shew_1776 (acetolactate synthase 3 catalytic subunit (RefSeq))
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.25759.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   2.4e-278  910.1   0.9   2.8e-278  909.9   0.9    1.0  1  lcl|FitnessBrowser__PV4:5209298  Shew_1776 acetolactate synthase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5209298  Shew_1776 acetolactate synthase 3 catalytic subunit (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  909.9   0.9  2.8e-278  2.8e-278       1     556 [.       4     568 ..       4     569 .. 0.98

  Alignments for each domain:
  == domain 1  score: 909.9 bits;  conditional E-value: 2.8e-278
                        TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGPGatn 77 
                                      l+ga+++v+sl +egv+++fGyPGG+vl+iydal+ +s++ehilvrheqaa+h+adGyara+GkvGvvl+tsGPGatn
  lcl|FitnessBrowser__PV4:5209298   4 LSGASMIVRSLIDEGVKHIFGYPGGSVLDIYDALHqKSGIEHILVRHEQAAVHMADGYARATGKVGVVLVTSGPGATN 81 
                                      689********************************99***************************************** PP

                        TIGR00118  78 lvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGrPGPvlv 155
                                      ++tgiatay+ds+Plvvl+Gqv+++liG+dafqe+d++Gi++pv+khsflv++a+d+p+i+k+af+iastGrPGPv+v
  lcl|FitnessBrowser__PV4:5209298  82 AITGIATAYMDSIPLVVLSGQVPSNLIGNDAFQECDMIGISRPVVKHSFLVTDAKDIPAIIKKAFYIASTGRPGPVVV 159
                                      ****************************************************************************** PP

                        TIGR00118 156 dlPkdvteaeieleve..ekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeaseelkelaerlkipv 231
                                      d+Pkd  +++i  e++  +++++++y+pt++ghk qi++ l+++ kakkPvl+vGgG++i++a++++ +l++rl +pv
  lcl|FitnessBrowser__PV4:5209298 160 DIPKDCLNPQILHEYQypDEINMRSYNPTTTGHKGQIRRGLQALLKAKKPVLYVGGGAVISGADQQILKLSDRLGLPV 237
                                      ********9987666656************************************************************ PP

                        TIGR00118 232 tttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihididPaeigknvk 309
                                      ++tl+GlGafp +h +++gmlGmhG++ean+a+++adl++++G+rfddr+t+n++k++p+a+i+hididP++i+k+v+
  lcl|FitnessBrowser__PV4:5209298 238 VSTLMGLGAFPGTHANSVGMLGMHGCYEANMAMHNADLIFGIGVRFDDRTTNNVEKYCPNATILHIDIDPSSISKTVR 315
                                      ****************************************************************************** PP

                        TIGR00118 310 vdipivGdakkvleellkklkee.....ekkeke.WlekieewkkeyilkldeeeesikPqkvikelskllkdeaivt 381
                                      vdipivG a +vl+++l+ l +e     ++  ++ W+++i++w++++ l++d+++e ikPq+vi++l+kl++++a+v+
  lcl|FitnessBrowser__PV4:5209298 316 VDIPIVGSADSVLDDMLALLDDEpsmknDEGAIDyWWSEINQWRSRNSLAYDKSSERIKPQQVIETLHKLTNGDAYVA 393
                                      *******************9998876433333458******************************************* PP

                        TIGR00118 382 tdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvki 459
                                      +dvGqhqm+aa +y+++kpr++i+sgGlGtmGfGlPaa+G+k+akp+etv++vtGdgs+qmn+qelst+ +yd+pvki
  lcl|FitnessBrowser__PV4:5209298 394 SDVGQHQMFAALYYPFNKPRRWINSGGLGTMGFGLPAAMGVKMAKPDETVICVTGDGSIQMNIQELSTALQYDTPVKI 471
                                      ****************************************************************************** PP

                        TIGR00118 460 vilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdk 536
                                      ++lnn++lGmvkqWq+++y++r+s++++ s +p+f+k+aeayG++g++i++p+ele+ l++al++k ++v++d++vd+
  lcl|FitnessBrowser__PV4:5209298 472 INLNNRFLGMVKQWQDMIYSGRHSHSYMDS-VPNFAKIAEAYGHVGMTISDPAELEAGLEKALAMKdKLVFVDISVDE 548
                                      *****************************5.********************************988799********* PP

                        TIGR00118 537 eeevlPmvapGagldelvee 556
                                      +e+v+Pm+++G+g++e++ +
  lcl|FitnessBrowser__PV4:5209298 549 TEHVYPMQIRGGGMNEMWLS 568
                                      *****************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (573 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: 11.87
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Links

Downloads

Related tools

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