Alignments for a candidate for ilvI in Marinobacter adhaerens HP15

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Marinobacter adhaerens HP15

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate GFF543 HP15_531 acetolactate synthase, large subunit, biosynthetic type

Query= BRENDA::P00893
         (574 letters)



>FitnessBrowser__Marino:GFF543
          Length = 572

 Score =  749 bits (1935), Expect = 0.0
 Identities = 353/573 (61%), Positives = 446/573 (77%), Gaps = 2/573 (0%)

Query: 1   MEMLSGAEMVVRSLIDQGVKQVFGYPGGAVLDIYDALHTVGGIDHVLVRHEQAAVHMADG 60
           ME+LSGA+M++RSL D+G++ ++GYPGGA L IYDAL     + H+LVRHEQAAVHMADG
Sbjct: 1   MELLSGADMLIRSLQDEGIEYIYGYPGGAALHIYDALFRQDKVKHILVRHEQAAVHMADG 60

Query: 61  LARATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLIGYDAFQECDMVG 120
            ARATG+ G VLVTSGPGATN ITGIATA+MDSIP+VVL GQVA++LIG DAFQE DM+G
Sbjct: 61  YARATGKPGTVLVTSGPGATNTITGIATAFMDSIPMVVLCGQVASTLIGEDAFQETDMMG 120

Query: 121 ISRPVVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDILNPANKLPYVWPESV 180
           +SRPVVKH+  V+  E+IP++++KA+++AA+GRPGPVVVD+PKD+  P  +  Y +P+ V
Sbjct: 121 VSRPVVKHNLSVRHPEEIPEIIRKAYYIAATGRPGPVVVDIPKDMTTPNERYEYAYPKKV 180

Query: 181 SMRSYNPTTTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVEALNLPVVCS 240
            +RSYNP   GH GQIK+A+  ++AAK+P++Y GGG +      QL E V  L  P+  +
Sbjct: 181 KLRSYNPAIRGHAGQIKKAVDMMLAAKRPIIYAGGGVVLGKASDQLTELVRLLGYPITNT 240

Query: 241 LMGLGAFPATHRQALGMLGMHGTYEANMTMHNADVIFAVGVRFDDRTTNNLAKYCPNATV 300
           LMG+G +PA+ +Q LG LGMHGTYEANM MH++D+I  VG RFDDR TN   K+CP A +
Sbjct: 241 LMGIGCYPASDKQHLGWLGMHGTYEANMAMHHSDLILCVGARFDDRVTNATEKFCPGARI 300

Query: 301 LHIDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQESAHQPLDEIRDWWQQIEQWRAR 360
           +HIDIDP SISKTV AD+PIVG    VL++ML L+ + +     D I  WW+QI++WRA 
Sbjct: 301 IHIDIDPASISKTVDADVPIVGPVDAVLKEMLSLVKEANEKPDADAIASWWKQIDEWRAF 360

Query: 361 QCLKYDTHSEKIKPQAVIETLWRLTKGDAYVTSDVGQHQMFAALYYPFDKPRRWINSGGL 420
             ++Y+T  + IKPQ VIE L RLT G+A+VTSDVGQHQMFAA YY FDKP RWINSGGL
Sbjct: 361 HGMRYETSPDVIKPQEVIEMLCRLTNGEAFVTSDVGQHQMFAAQYYKFDKPNRWINSGGL 420

Query: 421 GTMGFGLPAALGVKMALPEETVVCVTGDGSIQMNIQELSTALQYELPVLVVNLNNRYLGM 480
           GTMGFGLPAA+GVK+  P++ V+C+TG+GSIQMNIQELST  QY LPV ++NLNN+ LGM
Sbjct: 421 GTMGFGLPAAMGVKLTHPDDEVLCITGEGSIQMNIQELSTCKQYNLPVKIINLNNQALGM 480

Query: 481 VKQWQDMIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHELESKLSEALEQVRNNRL 540
           VKQWQDM Y  RH++SYM+SLPDF++LAEAYGH G++I    +LE+KL E L     + L
Sbjct: 481 VKQWQDMNYESRHAESYMESLPDFIKLAEAYGHKGVRIEKKEDLETKLKEVL--AMKDEL 538

Query: 541 VFVDVTVDGSEHVYPMQIRGGGMDEMWLSKTER 573
           VFVD+ VD  EHVYPMQ+  G M +MWLSKTER
Sbjct: 539 VFVDIYVDRFEHVYPMQVARGSMKDMWLSKTER 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: 1012
Number of extensions: 25
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 GFF543 HP15_531 (acetolactate synthase, large subunit, biosynthetic type)
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.508613.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                      -----------
   9.2e-262  855.3   0.4   1.1e-261  855.1   0.4    1.0  1  FitnessBrowser__Marino:GFF543  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Marino:GFF543  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  855.1   0.4  1.1e-261  1.1e-261       1     556 [.       4     567 ..       4     568 .. 0.97

  Alignments for each domain:
  == domain 1  score: 855.1 bits;  conditional E-value: 1.1e-261
                      TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGPGatnlv 79 
                                    l+ga++l++sl++eg+e+++GyPGGa l+iydal+ +++++hilvrheqaa+h+adGyara+Gk+G vl+tsGPGatn++
  FitnessBrowser__Marino:GFF543   4 LSGADMLIRSLQDEGIEYIYGYPGGAALHIYDALFrQDKVKHILVRHEQAAVHMADGYARATGKPGTVLVTSGPGATNTI 83 
                                    68*********************************99******************************************* PP

                      TIGR00118  80 tgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGrPGPvlvdlPk 159
                                    tgiata++ds+P+vvl Gqva++liG+dafqe d++G+++pv+kh++ v+++e++pei+++a++ia+tGrPGPv+vd+Pk
  FitnessBrowser__Marino:GFF543  84 TGIATAFMDSIPMVVLCGQVASTLIGEDAFQETDMMGVSRPVVKHNLSVRHPEEIPEIIRKAYYIAATGRPGPVVVDIPK 163
                                    ******************************************************************************** PP

                      TIGR00118 160 dvteaeieleve..ekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeaseelkelaerlkipvtttllG 237
                                    d+t+++ ++e+   +kv+l++y+p ++gh  qikka++++ +ak+P++++GgGv+ ++as++l+el+  l  p+t tl+G
  FitnessBrowser__Marino:GFF543 164 DMTTPNERYEYAypKKVKLRSYNPAIRGHAGQIKKAVDMMLAAKRPIIYAGGGVVLGKASDQLTELVRLLGYPITNTLMG 243
                                    ***99988877666****************************************************************** PP

                      TIGR00118 238 lGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihididPaeigknvkvdipivGd 317
                                    +G++p+ +++ lg lGmhGt+ean+a++++dl+++vGarfddrvt+  +kf+p a+iihididPa+i+k+v +d+pivG 
  FitnessBrowser__Marino:GFF543 244 IGCYPASDKQHLGWLGMHGTYEANMAMHHSDLILCVGARFDDRVTNATEKFCPGARIIHIDIDPASISKTVDADVPIVGP 323
                                    ******************************************************************************** PP

                      TIGR00118 318 akkvleellkklkee....ekkeke.WlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaa 392
                                    +  vl+e+l+ +ke     + + +  W+++i+ew++ + ++++++ + ikPq+vi+ l++l+++ea+vt+dvGqhqm+aa
  FitnessBrowser__Marino:GFF543 324 VDAVLKEMLSLVKEAnekpDADAIAsWWKQIDEWRAFHGMRYETSPDVIKPQEVIEMLCRLTNGEAFVTSDVGQHQMFAA 403
                                    *********99998865543333447****************************************************** PP

                      TIGR00118 393 qfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkq 472
                                    q+yk++kp+++i+sgGlGtmGfGlPaa+G+k+++p+++v+++tG+gs+qmn+qelst+++y++pvki++lnn+ lGmvkq
  FitnessBrowser__Marino:GFF543 404 QYYKFDKPNRWINSGGLGTMGFGLPAAMGVKLTHPDDEVLCITGEGSIQMNIQELSTCKQYNLPVKIINLNNQALGMVKQ 483
                                    ******************************************************************************** PP

                      TIGR00118 473 WqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevlPmvapGagld 551
                                    Wq++ ye r++e++++s lpdf+klaeayG+kg+riek+e+le klke+l++k e+v++d+ vd+ e+v+Pm++  ++++
  FitnessBrowser__Marino:GFF543 484 WQDMNYESRHAESYMES-LPDFIKLAEAYGHKGVRIEKKEDLETKLKEVLAMKdELVFVDIYVDRFEHVYPMQVARGSMK 562
                                    ****************5.********************************98879*******************9999** PP

                      TIGR00118 552 elvee 556
                                    +++ +
  FitnessBrowser__Marino:GFF543 563 DMWLS 567
                                    99975 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: 00:00:00.01
# Mc/sec: 22.95
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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