Alignments for a candidate for ilvI in Desulfatibacillum aliphaticivorans DSM 15576

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Desulfatibacillum aliphaticivorans DSM 15576

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_028314078.1 G491_RS0107065 acetolactate synthase, large subunit, biosynthetic type

Query= metacyc::MONOMER-18810
         (585 letters)



>NCBI__GCF_000429905.1:WP_028314078.1
          Length = 562

 Score =  599 bits (1545), Expect = e-176
 Identities = 306/564 (54%), Positives = 395/564 (70%), Gaps = 5/564 (0%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           ++ GAEIL+  L  EGV+ ++GYPGG ++ +YDE+ K +   H LVRHEQ AVHAADGYA
Sbjct: 2   KLSGAEILLKMLESEGVDSIFGYPGGVLIGLYDEMAK-SNIRHYLVRHEQGAVHAADGYA 60

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           R +GKVGV LVTSGPG TN VTGIA+AY DSIPMVV+TG VPT+ IG DAFQE D VGIT
Sbjct: 61  RISGKVGVCLVTSGPGATNTVTGIASAYCDSIPMVVLTGQVPTNLIGNDAFQEVDIVGIT 120

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKS-IDMR 196
           RP  KHN+LVKDV +LA TI++AF IA +GRPGPV++D+PKDV      ++ PK  + MR
Sbjct: 121 RPCTKHNYLVKDVNELADTIREAFHIARSGRPGPVLIDLPKDVLAGTANFKQPKGPVTMR 180

Query: 197 SYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMG 256
           SYNP    ++ Q+ K +  L  A++P I  GGG++ +NAS  L   A     PVT TLMG
Sbjct: 181 SYNPTVTPNTKQLTKVIKELMKAKKPLIMAGGGIISSNASQALTDFARKLQIPVTTTLMG 240

Query: 257 LGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIH 316
           LGAFPG+    +GM+GMHGTY ANM+  +CDVL+ +G RFDDRV G    F SQA KIIH
Sbjct: 241 LGAFPGSDDLSLGMIGMHGTYRANMSTGDCDVLLGVGVRFDDRVTGKTDTFASQA-KIIH 299

Query: 317 IDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDC 376
           +DIDP+SI K V V IP+VG+ K  L +L   +   ++    E  A W + I +W++   
Sbjct: 300 VDIDPTSIRKNVPVSIPVVGDCKATLDKLNELLTGENLTEIPEKRAPWLKCIAEWKAAQR 359

Query: 377 LKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGT 436
           L YD++ ++IKPQYVVE++ ++T+G A I ++VGQ+QMWAAQFY FD+P R++ SGGLG 
Sbjct: 360 LAYDQT-DVIKPQYVVERLCKITEGKAIISTEVGQNQMWAAQFYDFDQPNRFVTSGGLGV 418

Query: 437 MGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVR 496
           MG GLP A+G + A P   VV + G+GSIQM IQEL T +Q+  PVK+  LNNGYLGMVR
Sbjct: 419 MGFGLPAAIGAQVAAPNDLVVDVAGDGSIQMNIQELGTAMQHKLPVKVVILNNGYLGMVR 478

Query: 497 QWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFLD 556
           QWQE+ +  RY  + MD  PDFVKLAEAYG  G+R  K  +V+  L++     +  V +D
Sbjct: 479 QWQELFFGKRYCATQMDVQPDFVKLAEAYGATGLRATKPEEVDEVLKKGL-AAEGPVIMD 537

Query: 557 FQTDPTENVWPMVQAGKGISEMLL 580
           F  +  E V+PMV AG  I+EMLL
Sbjct: 538 FVVEREECVYPMVPAGAPITEMLL 561


Lambda     K      H
   0.319    0.135    0.407 

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: 913
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: 585
Length of database: 562
Length adjustment: 36
Effective length of query: 549
Effective length of database: 526
Effective search space:   288774
Effective search space used:   288774
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_028314078.1 G491_RS0107065 (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.19757.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.7e-255  832.7   0.7   7.6e-255  832.5   0.7    1.0  1  lcl|NCBI__GCF_000429905.1:WP_028314078.1  G491_RS0107065 acetolactate synt


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000429905.1:WP_028314078.1  G491_RS0107065 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  832.5   0.7  7.6e-255  7.6e-255       1     554 [.       3     560 ..       3     562 .] 0.98

  Alignments for each domain:
  == domain 1  score: 832.5 bits;  conditional E-value: 7.6e-255
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               l+gaeil+++l++egv+ +fGyPGG ++ +yd++ +s+++h lvrheq+a+haadGyar sGkvGv+l+
  lcl|NCBI__GCF_000429905.1:WP_028314078.1   3 LSGAEILLKMLESEGVDSIFGYPGGVLIGLYDEMAKSNIRHYLVRHEQGAVHAADGYARISGKVGVCLV 71 
                                               68******************************************************************* PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPGatn+vtgia+ay ds+P+vvltGqv+t+liG+dafqe+di+Git+p+tkh++lvk++++l+ ++
  lcl|NCBI__GCF_000429905.1:WP_028314078.1  72 TSGPGATNTVTGIASAYCDSIPMVVLTGQVPTNLIGNDAFQEVDIVGITRPCTKHNYLVKDVNELADTI 140
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleve.ekvelpgykptvkghklqikkaleliekakkPvll 206
                                               +eaf+ia +GrPGPvl+dlPkdv + + +++++   v++++y+ptv+++++q+ k+++ ++kakkP+++
  lcl|NCBI__GCF_000429905.1:WP_028314078.1 141 REAFHIARSGRPGPVLIDLPKDVLAGTANFKQPkGPVTMRSYNPTVTPNTKQLTKVIKELMKAKKPLIM 209
                                               **************************9999988689********************************* PP

                                 TIGR00118 207 vGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGa 275
                                               +GgG+i ++as+ l+++a +l+ipvtttl+GlGafp  + l+lgm+GmhGt+ an++  ++d+l++vG+
  lcl|NCBI__GCF_000429905.1:WP_028314078.1 210 AGGGIISSNASQALTDFARKLQIPVTTTLMGLGAFPGSDDLSLGMIGMHGTYRANMSTGDCDVLLGVGV 278
                                               ********************************************************************* PP

                                 TIGR00118 276 rfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee...ekkeke..W 339
                                               rfddrvtg+ ++fa++akiih+didP++i knv v ip+vGd+k  l++l + l+ e   e  ek+  W
  lcl|NCBI__GCF_000429905.1:WP_028314078.1 279 RFDDRVTGKTDTFASQAKIIHVDIDPTSIRKNVPVSIPVVGDCKATLDKLNELLTGEnltEIPEKRapW 347
                                               ************************************************99999887766644444446* PP

                                 TIGR00118 340 lekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgG 408
                                               l+ i+ewk+ + l++d++ + ikPq+v+++l+k+++++ai++t+vGq+qmwaaqfy++++p++f+tsgG
  lcl|NCBI__GCF_000429905.1:WP_028314078.1 348 LKCIAEWKAAQRLAYDQT-DVIKPQYVVERLCKITEGKAIISTEVGQNQMWAAQFYDFDQPNRFVTSGG 415
                                               ************999976.68************************************************ PP

                                 TIGR00118 409 lGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelf 477
                                               lG mGfGlPaa+Ga+va p++ vv+v+Gdgs+qmn+qel t+++ ++pvk+vilnn +lGmv+qWqelf
  lcl|NCBI__GCF_000429905.1:WP_028314078.1 416 LGVMGFGLPAAIGAQVAAPNDLVVDVAGDGSIQMNIQELGTAMQHKLPVKVVILNNGYLGMVRQWQELF 484
                                               ********************************************************************* PP

                                 TIGR00118 478 yeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvap 546
                                               + +ry +t++   +pdfvklaeayG++g+r +kpee++e lk+ l+ ++pv++d++v++ee v+Pmv+ 
  lcl|NCBI__GCF_000429905.1:WP_028314078.1 485 FGKRYCATQMDV-QPDFVKLAEAYGATGLRATKPEEVDEVLKKGLAAEGPVIMDFVVEREECVYPMVPA 552
                                               ***********6.******************************************************** PP

                                 TIGR00118 547 Gagldelv 554
                                               Ga ++e++
  lcl|NCBI__GCF_000429905.1:WP_028314078.1 553 GAPITEML 560
                                               ******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (562 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: 10.48
//
[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