Alignments for a candidate for ilvI in Desulfotomaculum ruminis DSM 2154

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Desulfotomaculum ruminis DSM 2154

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_013840429.1 DESRU_RS01860 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_000215085.1:WP_013840429.1
          Length = 553

 Score =  580 bits (1496), Expect = e-170
 Identities = 292/562 (51%), Positives = 388/562 (69%), Gaps = 11/562 (1%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           +M GA+IL+ +L E GVE ++GYPGG  L IYD L+  +  +HILVRHEQ A HAADGYA
Sbjct: 2   KMSGAQILIDSLKEAGVETIFGYPGGQALPIYDALY-DSDLQHILVRHEQGAAHAADGYA 60

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           RA+GKVGV L TSGPG TN VTGIA AY+DS+PMV ITG VPT  +G+D+FQE D  GIT
Sbjct: 61  RASGKVGVCLATSGPGATNLVTGIANAYMDSVPMVAITGQVPTFLLGRDSFQEVDITGIT 120

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
            PI KHN++VKD++D+   +K+AF++A+TGRPGPV++DIPKD+S     YE    +++  
Sbjct: 121 LPITKHNYIVKDIKDMGRIVKEAFYVASTGRPGPVLIDIPKDISSGEMDYERNGCLNLPG 180

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257
           YNP  +     + +A+  +  +  P IY GGGV+ + A  EL++L+     PVT TLMGL
Sbjct: 181 YNPPREAREDLVNQALRAIAESRCPVIYAGGGVISSGAHQELKKLSETLLAPVTVTLMGL 240

Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHI 317
           G FPG     +GMLGMHG+  AN A+  CD+LIA+G RFDDRV G    F S A KIIHI
Sbjct: 241 GGFPGDHPLSLGMLGMHGSKYANYAVCECDLLIAVGVRFDDRVTGKIESFASNA-KIIHI 299

Query: 318 DIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDCL 377
           DIDP+ + K V+VDIP+ G+VK VL +L+ +++A            W E+I  W+     
Sbjct: 300 DIDPAEMGKNVQVDIPVTGDVKLVLNQLLERLEA-------RIPTAWQEKIAAWKKEYPF 352

Query: 378 KYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGTM 437
            YDR+ E +KPQ ++ +I   T G A I ++VGQHQMWAAQ+Y + +PR +I+SGGLGTM
Sbjct: 353 DYDRTGETLKPQQIIREIDRQTSGQARITTEVGQHQMWAAQYYTYTKPRSFISSGGLGTM 412

Query: 438 GVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVRQ 497
           G G P A+G++ A PE+ V  I G+GSIQM IQEL+T + Y+ PV +  +NNGYLGMVRQ
Sbjct: 413 GYGFPAAIGVQVACPEETVFDIAGDGSIQMNIQELATAVNYELPVNVAIMNNGYLGMVRQ 472

Query: 498 WQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFLDF 557
           WQE+ Y+ RYS S M + PDFVKLAE+YG  G R+ +  +V P L+ A + + + V +DF
Sbjct: 473 WQEMLYNRRYSQSEMKS-PDFVKLAESYGAEGYRITRKEEVTPVLQAAIQSR-KPVLMDF 530

Query: 558 QTDPTENVWPMVQAGKGISEML 579
             +P ENV P V  GKG++EML
Sbjct: 531 VVEPEENVLPFVPPGKGLNEML 552


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: 906
Number of extensions: 31
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: 553
Length adjustment: 36
Effective length of query: 549
Effective length of database: 517
Effective search space:   283833
Effective search space used:   283833
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_013840429.1 DESRU_RS01860 (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.9465.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.5e-268  877.0   0.0   2.8e-268  876.8   0.0    1.0  1  lcl|NCBI__GCF_000215085.1:WP_013840429.1  DESRU_RS01860 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000215085.1:WP_013840429.1  DESRU_RS01860 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  876.8   0.0  2.8e-268  2.8e-268       1     554 [.       3     552 ..       3     553 .] 0.99

  Alignments for each domain:
  == domain 1  score: 876.8 bits;  conditional E-value: 2.8e-268
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               ++ga+il++slk+ gvet+fGyPGG+ lpiydalyds+l+hilvrheq+aahaadGyarasGkvGv+la
  lcl|NCBI__GCF_000215085.1:WP_013840429.1   3 MSGAQILIDSLKEAGVETIFGYPGGQALPIYDALYDSDLQHILVRHEQGAAHAADGYARASGKVGVCLA 71 
                                               79******************************************************************* PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPGatnlvtgia+ay+dsvP+v++tGqv+t l+G d+fqe+di+Gitlp+tkh+++vk+ +d+ +i+
  lcl|NCBI__GCF_000215085.1:WP_013840429.1  72 TSGPGATNLVTGIANAYMDSVPMVAITGQVPTFLLGRDSFQEVDITGITLPITKHNYIVKDIKDMGRIV 140
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207
                                               keaf++astGrPGPvl+d+Pkd+++ e+++e +  ++lpgy+p  ++++  +++al +i++++ Pv+++
  lcl|NCBI__GCF_000215085.1:WP_013840429.1 141 KEAFYVASTGRPGPVLIDIPKDISSGEMDYERNGCLNLPGYNPPREAREDLVNQALRAIAESRCPVIYA 209
                                               ********************************************************************* PP

                                 TIGR00118 208 GgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGar 276
                                               GgGvi ++a++elk+l+e+l +pvt tl+GlG+fp dhpl+lgmlGmhG+k+an+av e+dlliavG+r
  lcl|NCBI__GCF_000215085.1:WP_013840429.1 210 GGGVISSGAHQELKKLSETLLAPVTVTLMGLGGFPGDHPLSLGMLGMHGSKYANYAVCECDLLIAVGVR 278
                                               ********************************************************************* PP

                                 TIGR00118 277 fddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekiee 345
                                               fddrvtg++++fa++akiihididPae+gknv+vdip+ Gd+k vl++ll++l+++  +   W eki+ 
  lcl|NCBI__GCF_000215085.1:WP_013840429.1 279 FDDRVTGKIESFASNAKIIHIDIDPAEMGKNVQVDIPVTGDVKLVLNQLLERLEARIPTA--WQEKIAA 345
                                               *****************************************************9988877..******* PP

                                 TIGR00118 346 wkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGf 414
                                               wkkey++ +d++ e++kPq++i+e+ ++++++a +tt+vGqhqmwaaq+y+++kpr+fi+sgGlGtmG+
  lcl|NCBI__GCF_000215085.1:WP_013840429.1 346 WKKEYPFDYDRTGETLKPQQIIREIDRQTSGQARITTEVGQHQMWAAQYYTYTKPRSFISSGGLGTMGY 414
                                               ********************************************************************* PP

                                 TIGR00118 415 GlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerys 483
                                               G+Paa+G++va peetv +++Gdgs+qmn+qel+t+v+y++pv + i+nn +lGmv+qWqe++y++rys
  lcl|NCBI__GCF_000215085.1:WP_013840429.1 415 GFPAAIGVQVACPEETVFDIAGDGSIQMNIQELATAVNYELPVNVAIMNNGYLGMVRQWQEMLYNRRYS 483
                                               ********************************************************************* PP

                                 TIGR00118 484 etklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGaglde 552
                                               +++++s  pdfvklae+yG++g ri+++ee+   l+ a++s++pvl+d++v+ ee+vlP v+pG+gl+e
  lcl|NCBI__GCF_000215085.1:WP_013840429.1 484 QSEMKS--PDFVKLAESYGAEGYRITRKEEVTPVLQAAIQSRKPVLMDFVVEPEENVLPFVPPGKGLNE 550
                                               *****6..************************************************************* PP

                                 TIGR00118 553 lv 554
                                               ++
  lcl|NCBI__GCF_000215085.1:WP_013840429.1 551 ML 552
                                               97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (553 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 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 7.27
//
[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