Alignments for a candidate for ilvI in Dechloromonas agitata is5

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Dechloromonas agitata is5

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 WP_027458176.1 K420_RS0111370 acetolactate synthase catalytic subunit

Query= SwissProt::P0DP90
         (548 letters)



>NCBI__GCF_000519045.1:WP_027458176.1
          Length = 556

 Score =  508 bits (1307), Expect = e-148
 Identities = 267/552 (48%), Positives = 358/552 (64%), Gaps = 10/552 (1%)

Query: 1   MNGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGG-VEHLLCRHEQGAAMAAIGYAR 59
           + GAQ  V  L  QG++TV G PGGAI+P+YDAL     + H+L RHEQGA   A G AR
Sbjct: 5   LTGAQITVRLLERQGIHTVAGIPGGAILPIYDALGQSTQIHHVLARHEQGAGFMAQGMAR 64

Query: 60  ATGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSL 119
           +TG+  VC+A+SGPGATNL+T +ADA LDSIP+VAITGQV    IGTDAFQEVD  GLS+
Sbjct: 65  STGRPAVCLASSGPGATNLLTAIADAKLDSIPLVAITGQVPKAMIGTDAFQEVDTYGLSI 124

Query: 120 ACTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVENEV 179
             TKH+FLV S EEL  ++  AF +A SGRPGPVLVDIPKD+Q+ + ++  W    E++ 
Sbjct: 125 PITKHNFLVSSAEELLEVIPRAFAIAASGRPGPVLVDIPKDVQMQAIEIAAWPAPGEHQP 184

Query: 180 TFPHAE---VEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGA 236
             P A+   + +A  M+  A++P+LY+GGGV  A+A     E      +P   TL  LGA
Sbjct: 185 A-PVADGWALSEAAGMINAARRPILYLGGGVVHAEAAAEAVELAEKADLPTVMTLMALGA 243

Query: 237 VEADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPHASVIHMDID 296
           +  D+P  LGMLGMH  +  N A+ ECDLLIA+GARFDDR TGK+  F P A +IH+DID
Sbjct: 244 MPVDHPLSLGMLGMHAARYTNLALDECDLLIAIGARFDDRATGKVAAFCPQAKIIHIDID 303

Query: 297 PAEMNKLRQAHVALQGDLNA----LLPALQQPLNQYDWQQHCAQLRDEHSWRYDHPGDAI 352
           PAE++K++ AHV +  D+      LLPA+     + +W+Q  A L+ EH  +     D +
Sbjct: 304 PAELDKIKTAHVGITADIREALIRLLPAVAAS-ERTEWRQRVAALKAEHPLQMPGCDDPL 362

Query: 353 YAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGLPAAVG 412
               L++ ++     + V+ TDVGQHQMW AQ     RP  ++TS GLGTMGFG+PAA+G
Sbjct: 363 SHFGLIRTVAACLDNEAVIATDVGQHQMWVAQAYPLRRPRQWLTSGGLGTMGFGVPAAIG 422

Query: 413 AQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQER 472
           A +A P  TVVC +GDGS +MN+QEL T   + + LKI+L++N  LG+V Q Q LF+ ER
Sbjct: 423 AALAEPQRTVVCFTGDGSILMNIQELVTAAEENVNLKIILMNNATLGLVHQQQTLFYGER 482

Query: 473 YSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSIDELENVWP 532
              +     PDF+ +A  FGI    + +     AAL   +N  GP L+H SID  + V+P
Sbjct: 483 LFASQFKATPDFVKVAQGFGIAAVDLDQAANPCAALMEAINRPGPCLIHASIDAEQKVYP 542

Query: 533 LVPPGASNSEML 544
           +VPPGA+N +M+
Sbjct: 543 MVPPGAANRDMI 554


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: 821
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: 556
Length adjustment: 36
Effective length of query: 512
Effective length of database: 520
Effective search space:   266240
Effective search space used:   266240
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 WP_027458176.1 K420_RS0111370 (acetolactate synthase catalytic subunit)
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.12208.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.4e-212  690.6   0.5   8.4e-212  690.4   0.5    1.0  1  lcl|NCBI__GCF_000519045.1:WP_027458176.1  K420_RS0111370 acetolactate synt


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000519045.1:WP_027458176.1  K420_RS0111370 acetolactate synthase catalytic subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  690.4   0.5  8.4e-212  8.4e-212       1     555 [.       5     555 ..       5     556 .] 0.98

  Alignments for each domain:
  == domain 1  score: 690.4 bits;  conditional E-value: 8.4e-212
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 
                                               l+ga+i v+ l+++g++tv G+PGGa+lpiydal  + +++h+l+rheq+a  +a+G+ar++G++ v+l
  lcl|NCBI__GCF_000519045.1:WP_027458176.1   5 LTGAQITVRLLERQGIHTVAGIPGGAILPIYDALGqSTQIHHVLARHEQGAGFMAQGMARSTGRPAVCL 73 
                                               68********************************97889****************************** PP

                                 TIGR00118  69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137
                                               a sGPGatnl+t+ia+a lds+Plv++tGqv++++iG+dafqe+d  G+++p+tkh+flv++ae+l e+
  lcl|NCBI__GCF_000519045.1:WP_027458176.1  74 ASSGPGATNLLTAIADAKLDSIPLVAITGQVPKAMIGTDAFQEVDTYGLSIPITKHNFLVSSAEELLEV 142
                                               ********************************************************************* PP

                                 TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpg.ykptvkghklqikkaleliekakkPvl 205
                                               + +af ia++GrPGPvlvd+Pkdv+ ++ie+        pg ++p   ++   + +a+ +i++a++P+l
  lcl|NCBI__GCF_000519045.1:WP_027458176.1 143 IPRAFAIAASGRPGPVLVDIPKDVQMQAIEIAAW---PAPGeHQPAPVADGWALSEAAGMINAARRPIL 208
                                               ****************************999876...4454267888999999**************** PP

                                 TIGR00118 206 lvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavG 274
                                               + GgGv++aea +e +elae++++p ++tl+ lGa+p dhpl+lgmlGmh ++++nla++e+dllia+G
  lcl|NCBI__GCF_000519045.1:WP_027458176.1 209 YLGGGVVHAEAAAEAVELAEKADLPTVMTLMALGAMPVDHPLSLGMLGMHAARYTNLALDECDLLIAIG 277
                                               ********************************************************************* PP

                                 TIGR00118 275 arfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWleki 343
                                               arfddr tg++a f+p+akiihididPae++k+ ++++ i  d ++ l +ll ++ + e++e  W +++
  lcl|NCBI__GCF_000519045.1:WP_027458176.1 278 ARFDDRATGKVAAFCPQAKIIHIDIDPAELDKIKTAHVGITADIREALIRLLPAVAASERTE--WRQRV 344
                                               *********************************************************99999..***** PP

                                 TIGR00118 344 eewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtm 412
                                               + +k+e++l++   ++++    +i+++   l++ea+++tdvGqhqmw+aq y+ ++pr+++tsgGlGtm
  lcl|NCBI__GCF_000519045.1:WP_027458176.1 345 AALKAEHPLQMPGCDDPLSHFGLIRTVAACLDNEAVIATDVGQHQMWVAQAYPLRRPRQWLTSGGLGTM 413
                                               ********************************************************************* PP

                                 TIGR00118 413 GfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeer 481
                                               GfG+Paa+Ga +a+p+ tvv+ tGdgs+ mn+qel t++e ++++ki+++nn++lG+v+q q lfy er
  lcl|NCBI__GCF_000519045.1:WP_027458176.1 414 GFGVPAAIGAALAEPQRTVVCFTGDGSILMNIQELVTAAEENVNLKIILMNNATLGLVHQQQTLFYGER 482
                                               ********************************************************************* PP

                                 TIGR00118 482 ysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagl 550
                                                 ++++++ +pdfvk+a+++G+ ++ + + ++  ++l ea++  +p l+  ++d e++v+Pmv+pGa++
  lcl|NCBI__GCF_000519045.1:WP_027458176.1 483 LFASQFKA-TPDFVKVAQGFGIAAVDLDQAANPCAALMEAINRPGPCLIHASIDAEQKVYPMVPPGAAN 550
                                               *******5.************************************************************ PP

                                 TIGR00118 551 delve 555
                                                ++++
  lcl|NCBI__GCF_000519045.1:WP_027458176.1 551 RDMIG 555
                                               **996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (556 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: 10.75
//
[ok]

This GapMind analysis is from Apr 10 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:

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