Alignments for a candidate for ilvI in Stenotrophomonas chelatiphaga DSM 21508

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Stenotrophomonas chelatiphaga DSM 21508

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_057509298.1 ABB28_RS14475 acetolactate synthase 2 catalytic subunit

Query= SwissProt::P0DP90
         (548 letters)



>NCBI__GCF_001431535.1:WP_057509298.1
          Length = 578

 Score =  647 bits (1669), Expect = 0.0
 Identities = 327/553 (59%), Positives = 403/553 (72%), Gaps = 11/553 (1%)

Query: 2   NGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARAT 61
           NGA+W+  AL A+GV T+FGYPGG IMP YDAL D  ++H+L RHEQGAA+AA G+ARA+
Sbjct: 12  NGARWLTQALEAEGVQTLFGYPGGTIMPFYDALVDSRLKHVLVRHEQGAALAANGFARAS 71

Query: 62  GKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSLAC 121
           G+ GVCIATSGPGA+NL+TG+ADA+LDS+P+V ITGQV+ P +GTDAFQE+DV GL+L  
Sbjct: 72  GRVGVCIATSGPGASNLVTGIADAMLDSVPMVCITGQVATPLLGTDAFQELDVFGLTLPI 131

Query: 122 TKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVENEVTF 181
            KHS+LV+S+++LPR++AEAF +A  GRPGPVL+D+PKD+Q+A     P    V   V  
Sbjct: 132 VKHSWLVRSVDDLPRVVAEAFRIAREGRPGPVLIDLPKDVQVADASHLP--AHVPATVEA 189

Query: 182 PHAEVEQARQ----MLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGAV 237
           P A  EQA       +A A+KP++Y GGG+ +  AV ALR+F AA+ +PA  TL+GLGA+
Sbjct: 190 PPAPAEQAIADAIAAIAGAEKPVIYAGGGIALGDAVDALRDFAAASGIPAVLTLRGLGAL 249

Query: 238 EADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPHASVIHMDIDP 297
            A +P  LGMLGMHGT+AAN AVQE DLL+ +GARFDDR TGKL  FAP A V+H+D D 
Sbjct: 250 PAGHPQSLGMLGMHGTRAANMAVQEADLLLVLGARFDDRATGKLTEFAPFARVVHIDADA 309

Query: 298 AEMNKLRQAHVALQGDLNALLPALQQ-----PLNQYDWQQHCAQLRDEHSWRYDHPGDAI 352
            E++KLR A VA+ G++   + AL       P  Q  W+  CAQ R++   RYD PG  I
Sbjct: 310 YEISKLRTADVAVPGNVAQAIRALHAAFPAPPATQAAWRNRCAQHREKFIARYDAPGKHI 369

Query: 353 YAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGLPAAVG 412
           YAP LLK+LS+  PAD V+  DVGQHQMW AQH     P N +TS  LGTMGFGLPAA+G
Sbjct: 370 YAPALLKRLSELAPADAVIACDVGQHQMWVAQHCRFNHPRNHLTSGALGTMGFGLPAAMG 429

Query: 413 AQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQER 472
           AQ A P+ TVV +SGDGSFMMNVQEL T+ R +LP+KIVLLDN  LGMVRQWQ+LFF ER
Sbjct: 430 AQFACPDRTVVLVSGDGSFMMNVQELTTIARCRLPVKIVLLDNSSLGMVRQWQELFFAER 489

Query: 473 YSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSIDELENVWP 532
           YSE  L+DNPDF+ LA  FGI    I  +D VE  L  +L   GP LLHV+ID   NVWP
Sbjct: 490 YSEIDLSDNPDFVALAKVFGIAATRIDARDDVEGGLAALLAEPGPALLHVAIDARANVWP 549

Query: 533 LVPPGASNSEMLE 545
           LVPP  +NS MLE
Sbjct: 550 LVPPNTANSTMLE 562


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: 958
Number of extensions: 38
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: 548
Length of database: 578
Length adjustment: 36
Effective length of query: 512
Effective length of database: 542
Effective search space:   277504
Effective search space used:   277504
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_057509298.1 ABB28_RS14475 (acetolactate synthase 2 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.30430.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.3e-212  692.2   0.0   2.7e-212  692.1   0.0    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057509298.1  ABB28_RS14475 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057509298.1  ABB28_RS14475 acetolactate synthase 2 catalytic subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  692.1   0.0  2.7e-212  2.7e-212       3     556 ..      13     563 ..      11     564 .. 0.97

  Alignments for each domain:
  == domain 1  score: 692.1 bits;  conditional E-value: 2.7e-212
                                 TIGR00118   3 gaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvlats 71 
                                               ga+ l ++l++egv+t+fGyPGG+++p+ydal ds l+h+lvrheq+aa aa+G+arasG+vGv++ats
  lcl|NCBI__GCF_001431535.1:WP_057509298.1  13 GARWLTQALEAEGVQTLFGYPGGTIMPFYDALVDSRLKHVLVRHEQGAALAANGFARASGRVGVCIATS 81 
                                               8999***************************************************************** PP

                                 TIGR00118  72 GPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilke 140
                                               GPGa nlvtgia+a+ldsvP+v +tGqvat l+G+dafqe+d++G+tlp++khs+lv++++dlp+++ e
  lcl|NCBI__GCF_001431535.1:WP_057509298.1  82 GPGASNLVTGIADAMLDSVPMVCITGQVATPLLGTDAFQELDVFGLTLPIVKHSWLVRSVDDLPRVVAE 150
                                               ********************************************************************* PP

                                 TIGR00118 141 afeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGg 209
                                               af ia  GrPGPvl+dlPkdv+ a+ +     +v     +p   + ++ i+ a+ +i+ a+kPv+++Gg
  lcl|NCBI__GCF_001431535.1:WP_057509298.1 151 AFRIAREGRPGPVLIDLPKDVQVADASHLPA-HVPATVEAPP-APAEQAIADAIAAIAGAEKPVIYAGG 217
                                               **********************998876544.5555555554.455667******************** PP

                                 TIGR00118 210 GviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfd 278
                                               G+  ++a + l+++a +  ip + tl GlGa+p+ hp++lgmlGmhGt++an+av+eadll+ +Garfd
  lcl|NCBI__GCF_001431535.1:WP_057509298.1 218 GIALGDAVDALRDFAAASGIPAVLTLRGLGALPAGHPQSLGMLGMHGTRAANMAVQEADLLLVLGARFD 286
                                               ********************************************************************* PP

                                 TIGR00118 279 drvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekieewk 347
                                               dr tg+l++fap a+++hid d  ei+k +++d+++ G++ + ++ l ++  +   ++  W ++ ++++
  lcl|NCBI__GCF_001431535.1:WP_057509298.1 287 DRATGKLTEFAPFARVVHIDADAYEISKLRTADVAVPGNVAQAIRALHAAFPAPPATQAAWRNRCAQHR 355
                                               *************************************************99999999999********* PP

                                 TIGR00118 348 keyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGl 416
                                               ++ i ++d   ++i   +++k+ls+l++ +a+++ dvGqhqmw+aq+ ++++pr+++tsg lGtmGfGl
  lcl|NCBI__GCF_001431535.1:WP_057509298.1 356 EKFIARYDAPGKHIYAPALLKRLSELAPADAVIACDVGQHQMWVAQHCRFNHPRNHLTSGALGTMGFGL 424
                                               ********************************************************************* PP

                                 TIGR00118 417 PaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeeryset 485
                                               Paa+Ga+ a p+ tvv v+Gdgsf+mn+qel+ti++  +pvkiv+l+n+ lGmv+qWqelf+ eryse 
  lcl|NCBI__GCF_001431535.1:WP_057509298.1 425 PAAMGAQFACPDRTVVLVSGDGSFMMNVQELTTIARCRLPVKIVLLDNSSLGMVRQWQELFFAERYSEI 493
                                               ********************************************************************* PP

                                 TIGR00118 486 klaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldelv 554
                                                l+ ++pdfv+la+ +G+ ++ri  ++++e  l+ +l++ +p+ll v +d +++v+P+v+p ++++ ++
  lcl|NCBI__GCF_001431535.1:WP_057509298.1 494 DLS-DNPDFVALAKVFGIAATRIDARDDVEGGLAALLAEPGPALLHVAIDARANVWPLVPPNTANSTML 561
                                               **9.6***********************************************************99998 PP

                                 TIGR00118 555 ee 556
                                               e+
  lcl|NCBI__GCF_001431535.1:WP_057509298.1 562 ES 563
                                               75 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (578 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 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 7.81
//
[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