Aligments for a candidate for ilvH in Shewanella loihica PV-4

GapMind for Amino acid biosynthesis

Aligments for a candidate for ilvH 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)



>lcl|FitnessBrowser__PV4:5209298 Shew_1776 acetolactate synthase 3
           catalytic subunit (RefSeq)
          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.605.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: 0.03u 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 7.57
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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