Alignments for a candidate for ilvI in Desulfallas geothermicus DSM 3669

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Desulfallas geothermicus DSM 3669

Align acetohydroxy-acid synthase large subunit (EC 2.2.1.6) (characterized)
to candidate WP_092483006.1 BM299_RS08285 biosynthetic-type acetolactate synthase large subunit

Query= metacyc::MONOMER-11900
         (599 letters)



>NCBI__GCF_900115975.1:WP_092483006.1
          Length = 552

 Score =  572 bits (1474), Expect = e-167
 Identities = 289/570 (50%), Positives = 390/570 (68%), Gaps = 25/570 (4%)

Query: 3   GAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARASG 62
           GAE ++++L AE V+ +FGYPGG +LP YDAL+ +DL H+LTRHEQ AAHAADGYARASG
Sbjct: 5   GAEILVQSLLAEGVDTIFGYPGGMVLPIYDALYDADLRHILTRHEQGAAHAADGYARASG 64

Query: 63  KVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMPIV 122
           K GVC+ TSGPGATNLVTG+A A+ DS PMVA+TGQV T L+G D+FQE D  G+ +PI 
Sbjct: 65  KPGVCLATSGPGATNLVTGIANAYMDSIPMVAITGQVVTSLLGKDSFQEADITGITLPIT 124

Query: 123 KHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLIGY 182
           KHN+ ++    + +  R AF IA+TGRPGPV ID+P+DV     D   +  P   +L GY
Sbjct: 125 KHNYLVKDVQDLAQTLREAFYIARTGRPGPVLIDIPRDVSGGTAD---YADPGPARLPGY 181

Query: 183 NPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMGKG 242
           +  T   P Q+ +A++ I  ++RP+I AGGGV+  GA+EELL+L E+L  PV TTLMG G
Sbjct: 182 SVNTKPDPEQVARAVRAIEESERPVIYAGGGVINGGAHEELLRLAEILLAPVATTLMGLG 241

Query: 243 CISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKIIHIDI 302
               NHPL++GM+GMHG+K ANY +SE D+LI +G RF DR+T  +++FA  A IIHIDI
Sbjct: 242 GFPGNHPLSVGMLGMHGSKYANYAVSECDLLIGVGVRFDDRVTSKLEAFAPGATIIHIDI 301

Query: 303 DPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVNSLKKS 362
           DPAEIGKNV VD+P+VGD +  L+++I+ L     +   E+  ++ I  W        K 
Sbjct: 302 DPAEIGKNVGVDIPVVGDVRNSLQKIIECL-----QPRLESRWRDKIQNW--------KK 348

Query: 363 SIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTI-ITTDVGQNQMWMAHYFKTQTPRSF 421
             P+   ++  +KPQ+++KE+       N+ +  + + TDVGQ+QMW AHY+    PR+F
Sbjct: 349 EYPIEFVENGRLKPQEVIKEM------YNVTRGEVRVVTDVGQHQMWAAHYYTYHRPRTF 402

Query: 422 LSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVICIFD 481
           ++SGGLGTMGFGFP+A+G +VA PD  V+CITGDG F MN QEL T+  YN+PV I I +
Sbjct: 403 ITSGGLGTMGFGFPAALGVQVACPDETVLCITGDGSFQMNSQELATVVHYNLPVKIGIIN 462

Query: 482 NRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKEAINC 541
           N  LGMV QWQ LFY +R   V   G PDF+KLAESYG    R+   +E+ EA++EA+  
Sbjct: 463 NGYLGMVRQWQELFYNRRYSYVEITG-PDFVKLAESYGAVGIRVSKKSEVREAMEEAMRV 521

Query: 542 DEPYLLDFAID-PSSALSMVPPGAKLTNII 570
             P ++DF I+   + L  VPPG  +  ++
Sbjct: 522 PGPVVIDFPIEREENVLPFVPPGEPINKML 551


Lambda     K      H
   0.319    0.137    0.405 

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: 949
Number of extensions: 37
Number of successful extensions: 6
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: 599
Length of database: 552
Length adjustment: 36
Effective length of query: 563
Effective length of database: 516
Effective search space:   290508
Effective search space used:   290508
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 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate WP_092483006.1 BM299_RS08285 (biosynthetic-type acetolactate synthase large 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.28807.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.8e-262  857.0   0.0   3.3e-262  856.8   0.0    1.0  1  lcl|NCBI__GCF_900115975.1:WP_092483006.1  BM299_RS08285 biosynthetic-type 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900115975.1:WP_092483006.1  BM299_RS08285 biosynthetic-type acetolactate synthase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  856.8   0.0  3.3e-262  3.3e-262       2     554 ..       4     551 ..       3     552 .] 0.98

  Alignments for each domain:
  == domain 1  score: 856.8 bits;  conditional E-value: 3.3e-262
                                 TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvlat 70 
                                               +gaeilv+sl +egv+t+fGyPGG vlpiydalyd +l+hil+rheq+aahaadGyarasGk+Gv+lat
  lcl|NCBI__GCF_900115975.1:WP_092483006.1   4 TGAEILVQSLLAEGVDTIFGYPGGMVLPIYDALYDADLRHILTRHEQGAAHAADGYARASGKPGVCLAT 72 
                                               79******************************************************************* PP

                                 TIGR00118  71 sGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilk 139
                                               sGPGatnlvtgia+ay+ds+P+v++tGqv tsl+G+d+fqe+di+Gitlp+tkh++lvk+++dl+++l+
  lcl|NCBI__GCF_900115975.1:WP_092483006.1  73 SGPGATNLVTGIANAYMDSIPMVAITGQVVTSLLGKDSFQEADITGITLPITKHNYLVKDVQDLAQTLR 141
                                               ********************************************************************* PP

                                 TIGR00118 140 eafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvG 208
                                               eaf+ia tGrPGPvl+d+P+dv+  + ++  +    lpgy  ++k+++ q+++a+ +ie++++Pv+++G
  lcl|NCBI__GCF_900115975.1:WP_092483006.1 142 EAFYIARTGRPGPVLIDIPRDVSGGTADYADPGPARLPGYSVNTKPDPEQVARAVRAIEESERPVIYAG 210
                                               ********************************************************************* PP

                                 TIGR00118 209 gGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarf 277
                                               gGvi ++a+eel +lae l +pv+ttl+GlG+fp +hpl++gmlGmhG+k+an+avse+dlli+vG+rf
  lcl|NCBI__GCF_900115975.1:WP_092483006.1 211 GGVINGGAHEELLRLAEILLAPVATTLMGLGGFPGNHPLSVGMLGMHGSKYANYAVSECDLLIGVGVRF 279
                                               ********************************************************************* PP

                                 TIGR00118 278 ddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekieew 346
                                               ddrvt++l+ fap a+iihididPaeigknv vdip+vGd+++ l+++++ l+ + +  ++W +ki++w
  lcl|NCBI__GCF_900115975.1:WP_092483006.1 280 DDRVTSKLEAFAPGATIIHIDIDPAEIGKNVGVDIPVVGDVRNSLQKIIECLQPRLE--SRWRDKIQNW 346
                                               **************************************************9987655..55******** PP

                                 TIGR00118 347 kkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfG 415
                                               kkey++++  e++ +kPq+vike+++++++e+ v tdvGqhqmwaa++y++++pr+fitsgGlGtmGfG
  lcl|NCBI__GCF_900115975.1:WP_092483006.1 347 KKEYPIEFV-ENGRLKPQEVIKEMYNVTRGEVRVVTDVGQHQMWAAHYYTYHRPRTFITSGGLGTMGFG 414
                                               *****8874.5678******************************************************* PP

                                 TIGR00118 416 lPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeeryse 484
                                               +PaalG++va p+etv+++tGdgsfqmn qel+t+v+y++pvki i+nn +lGmv+qWqelfy++rys 
  lcl|NCBI__GCF_900115975.1:WP_092483006.1 415 FPAALGVQVACPDETVLCITGDGSFQMNSQELATVVHYNLPVKIGIINNGYLGMVRQWQELFYNRRYSY 483
                                               ********************************************************************* PP

                                 TIGR00118 485 tklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldel 553
                                               ++++   pdfvklae+yG++gir++k++e+ e+++ea+++ +pv++d+ +++ee+vlP v+pG  ++++
  lcl|NCBI__GCF_900115975.1:WP_092483006.1 484 VEITG--PDFVKLAESYGAVGIRVSKKSEVREAMEEAMRVPGPVVIDFPIEREENVLPFVPPGEPINKM 550
                                               ***96..**********************************************************9999 PP

                                 TIGR00118 554 v 554
                                               +
  lcl|NCBI__GCF_900115975.1:WP_092483006.1 551 L 551
                                               7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (552 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 0.02s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 7.07
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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Protein sequences (fasta format)
Organisms (tab-delimited)
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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