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 isozyme 2 large subunit; AHAS-II; ALS-II; Acetohydroxy-acid synthase II large subunit; EC 2.2.1.6 (characterized)
to candidate GFF1038 HP15_1017 acetolactate synthase, large subunit, biosynthetic type

Query= SwissProt::P0DP90
         (548 letters)



>FitnessBrowser__Marino:GFF1038
          Length = 566

 Score =  580 bits (1496), Expect = e-170
 Identities = 297/555 (53%), Positives = 385/555 (69%), Gaps = 11/555 (1%)

Query: 1   MNGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDG-GVEHLLCRHEQGAAMAAIGYAR 59
           MNGAQ ++ A     ++TVFGYPGG IMP+YDAL D  GVEH+LCRHEQG A+AA GYAR
Sbjct: 1   MNGAQHILEAFHRHNISTVFGYPGGCIMPLYDALVDDVGVEHVLCRHEQGCALAADGYAR 60

Query: 60  ATGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSL 119
           A+GK GVCIATSGPGATNLITG+A+A  DSIP++ ITGQV +  IGTDAFQE DVLG++L
Sbjct: 61  ASGKLGVCIATSGPGATNLITGVANAHRDSIPMLVITGQVPSGLIGTDAFQETDVLGMTL 120

Query: 120 ACTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVENEV 179
              KHS+L+   + LP IM EA ++A SGRPGPV +DIPKD+ L+     P+      E 
Sbjct: 121 GIVKHSYLINDADSLPIIMEEAIELAQSGRPGPVWIDIPKDLLLSDVADAPFPQAQPYEP 180

Query: 180 TFPHAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGAVEA 239
             P  ++++A  ML  A+KP+LY GGG+ +  A    R F  ++ +PA  TLKG+G    
Sbjct: 181 ASP--DLKEALAMLRAARKPLLYSGGGISLGHAEENFRAFAESSALPAVVTLKGIGNPGK 238

Query: 240 DYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPHASVIHMDIDPAE 299
             PY LGMLGMHG++AAN AV ECDLL+ +GAR DDR TGKL+ FAP+A +IH+D D AE
Sbjct: 239 HNPYNLGMLGMHGSRAANKAVDECDLLLVIGARLDDRATGKLDGFAPNARMIHIDADAAE 298

Query: 300 MNKLRQAHVALQGDLNALLPALQ-----QPLNQYDWQQHCAQLRDE---HSWRYDHPGDA 351
           +NKLR A +A++GDLN +L +L       PL   +WQ+ C         H+   + P   
Sbjct: 299 INKLRDADLAIRGDLNHILKSLAGELHADPLAISEWQKQCRSWYTTGGFHAADNEEPLAP 358

Query: 352 IYAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGLPAAV 411
           I  P  ++QLS   P D V+  DVGQHQMW AQH     P + +TS GLGTMGFGLPAA+
Sbjct: 359 ITGPAFIRQLSRIAPDDTVIACDVGQHQMWVAQHYDFDHPRHHLTSGGLGTMGFGLPAAI 418

Query: 412 GAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQE 471
           GAQ A  N TV+ ++GDGSFMMN QEL T++R  LP+K++++DNQ LGMVRQ Q+LF+  
Sbjct: 419 GAQFADRNSTVINVTGDGSFMMNAQELATIRRYNLPVKLIVMDNQCLGMVRQQQELFYNN 478

Query: 472 RYSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSIDELENVW 531
           R S+  L DNPDF+ +A AF I   +I R DQ+   ++T+L  +GP LLHV+I   ENVW
Sbjct: 479 RESQINLDDNPDFVAMARAFDIPALYIERTDQIRRGIETILAYNGPMLLHVAISREENVW 538

Query: 532 PLVPPGASNSEMLEK 546
           P+V PGASN++M+++
Sbjct: 539 PIVKPGASNTDMIDE 553


Lambda     K      H
   0.320    0.135    0.410 

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: 878
Number of extensions: 33
Number of successful extensions: 4
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: 548
Length of database: 566
Length adjustment: 36
Effective length of query: 512
Effective length of database: 530
Effective search space:   271360
Effective search space used:   271360
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 GFF1038 HP15_1017 (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.25182.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.8e-205  669.5   0.0   2.1e-205  669.3   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF1038  HP15_1017 acetolactate synthase,


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF1038  HP15_1017 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  669.3   0.0  2.1e-205  2.1e-205       1     556 [.       1     553 [.       1     554 [. 0.97

  Alignments for each domain:
  == domain 1  score: 669.3 bits;  conditional E-value: 2.1e-205
                           TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGPG 74 
                                         ++ga+ ++e+++++++ tvfGyPGG ++p+ydal  d ++eh+l rheq+ a aadGyarasGk Gv++atsGPG
  lcl|FitnessBrowser__Marino:GFF1038   1 MNGAQHILEAFHRHNISTVFGYPGGCIMPLYDALVdDVGVEHVLCRHEQGCALAADGYARASGKLGVCIATSGPG 75 
                                         78********************************9788************************************* PP

                           TIGR00118  75 atnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGr 149
                                         atnl+tg+a+a+ ds+P++v+tGqv++ liG+dafqe d+lG+tl ++khs+l+++a+ lp i++ea e+a++Gr
  lcl|FitnessBrowser__Marino:GFF1038  76 ATNLITGVANAHRDSIPMLVITGQVPSGLIGTDAFQETDVLGMTLGIVKHSYLINDADSLPIIMEEAIELAQSGR 150
                                         *************************************************************************** PP

                           TIGR00118 150 PGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeaseelkela 224
                                         PGPv +d+Pkd+  +++         +p  +p   +    +k+al ++++a+kP+l+ GgG+  ++a+e+++ +a
  lcl|FitnessBrowser__Marino:GFF1038 151 PGPVWIDIPKDLLLSDVAD-----APFPQAQPYEPA-SPDLKEALAMLRAARKPLLYSGGGISLGHAEENFRAFA 219
                                         ************9988754.....456777776544.5579********************************** PP

                           TIGR00118 225 erlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihidi 299
                                         e   +p + tl G+G   +++p  lgmlGmhG+++an av+e+dll+ +Gar+ddr tg+l+ fap+a++ihid 
  lcl|FitnessBrowser__Marino:GFF1038 220 ESSALPAVVTLKGIGNPGKHNPYNLGMLGMHGSRAANKAVDECDLLLVIGARLDDRATGKLDGFAPNARMIHIDA 294
                                         *************************************************************************** PP

                           TIGR00118 300 dPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekieewkkeyilkldeeeesikPq...kvikels 371
                                         d aei+k + +d++i Gd +++l+ l  +l++     +eW ++ ++w ++  ++   +ee+++P    ++i++ls
  lcl|FitnessBrowser__Marino:GFF1038 295 DAAEINKLRDADLAIRGDLNHILKSLAGELHADPLAISEWQKQCRSWYTTGGFHAADNEEPLAPItgpAFIRQLS 369
                                         *********************************999999************999999999988852227****** PP

                           TIGR00118 372 kllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqe 446
                                         ++++d+++++ dvGqhqmw+aq+y++++pr+++tsgGlGtmGfGlPaa+Ga+ a  ++tv++vtGdgsf+mn qe
  lcl|FitnessBrowser__Marino:GFF1038 370 RIAPDDTVIACDVGQHQMWVAQHYDFDHPRHHLTSGGLGTMGFGLPAAIGAQFADRNSTVINVTGDGSFMMNAQE 444
                                         *************************************************************************** PP

                           TIGR00118 447 lstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkea 521
                                         l+ti++y++pvk+++++n++lGmv+q qelfy++r s+ +l  ++pdfv++a+a+ + ++ ie+ +++   ++ +
  lcl|FitnessBrowser__Marino:GFF1038 445 LATIRRYNLPVKLIVMDNQCLGMVRQQQELFYNNRESQINLD-DNPDFVAMARAFDIPALYIERTDQIRRGIETI 518
                                         ******************************************.6******************************* PP

                           TIGR00118 522 leskepvlldvevdkeeevlPmvapGagldelvee 556
                                         l+ ++p+ll v + +ee+v+P+v pGa+++++++e
  lcl|FitnessBrowser__Marino:GFF1038 519 LAYNGPMLLHVAISREENVWPIVKPGASNTDMIDE 553
                                         ********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (566 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: 12.43
//
[ok]

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