Alignments for a candidate for ilvI in Malonomonas rubra DSM 5091

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Malonomonas rubra DSM 5091

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_072904936.1 BUB13_RS01275 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_900142125.1:WP_072904936.1
          Length = 565

 Score =  629 bits (1621), Expect = 0.0
 Identities = 312/567 (55%), Positives = 409/567 (72%), Gaps = 5/567 (0%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           E+ G++IL+ +L +EGV+ V+GYPGGAV+ IYD+L   +  EH+L RHEQAAVHAADGYA
Sbjct: 2   ELTGSQILLESLQKEGVDTVFGYPGGAVINIYDDLF-DSPIEHVLTRHEQAAVHAADGYA 60

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           R TGKVGV + TSGPG TN VTGIATAY+DSIPMVVITG VPT  IG DAFQE D  GIT
Sbjct: 61  RCTGKVGVVIATSGPGATNTVTGIATAYMDSIPMVVITGQVPTPLIGNDAFQEADMCGIT 120

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
           RP  KHNFLV+D++DLA TIK+AF+IA TGRPGPV++D+PKD+     K++YP  + +R 
Sbjct: 121 RPCTKHNFLVQDIKDLARTIKEAFYIARTGRPGPVLIDLPKDIQVTKYKFKYPDKVSLRG 180

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257
           Y P   G+  QI KA  +L  A+RP  Y GGG+ L+ A++EL +L  +T  PVT TLM +
Sbjct: 181 YKPTYTGNKRQISKAAKMLLDAKRPVFYVGGGINLSAANEELVKLTEMTQTPVTTTLMAM 240

Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHI 317
             FP      +GMLGMHGT+ ANMA+  CD+L+AIGARFDDRV G    F  +A K+IHI
Sbjct: 241 SGFPQDHALALGMLGMHGTFYANMAVTECDLLVAIGARFDDRVTGRIDAFAKKA-KVIHI 299

Query: 318 DIDPSSISKRVKVDIPIVGNVKDVLQELIAQI--KASDIKPKREALAKWWEQIEQWRSVD 375
           DIDP+SI K V VD+PIVG++KDVL +L A +  K  +++       +W E +++W+   
Sbjct: 300 DIDPTSIKKNVAVDLPIVGDLKDVLSQLGAALAEKPDELQKLVSKTTEWRETVDEWKQKH 359

Query: 376 CLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLG 435
            + Y  S   IKPQ+V+EK+ ELT+ DA I ++VGQHQMW AQF++F +PR ++ SGGLG
Sbjct: 360 PMAYKHSESTIKPQFVIEKVRELTEDDAIITTEVGQHQMWTAQFFQFRQPRTFLTSGGLG 419

Query: 436 TMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMV 495
           TMG GLP A+G + A+PE++VV I+G+GS QM  QEL+T +QY  PVKI  LNN YLGMV
Sbjct: 420 TMGYGLPAALGAQVAYPERQVVDISGDGSFQMNSQELATLVQYKLPVKIVILNNNYLGMV 479

Query: 496 RQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFL 555
           RQWQ++ +D RYS + M+   DF+KLAEAYG  G++ +K  DVE  +++A  +    V +
Sbjct: 480 RQWQQMFFDKRYSQTVMELPIDFIKLAEAYGAAGLQCDKVGDVEATIKKALEIPG-PVLM 538

Query: 556 DFQTDPTENVWPMVQAGKGISEMLLGA 582
           +F+    ENV PMV AGKGI EM+L +
Sbjct: 539 EFKISREENVLPMVPAGKGIHEMVLAS 565


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: 873
Number of extensions: 23
Number of successful extensions: 5
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: 565
Length adjustment: 36
Effective length of query: 549
Effective length of database: 529
Effective search space:   290421
Effective search space used:   290421
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_072904936.1 BUB13_RS01275 (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.4395.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     1e-266  871.7   1.9   1.2e-266  871.5   1.9    1.0  1  lcl|NCBI__GCF_900142125.1:WP_072904936.1  BUB13_RS01275 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900142125.1:WP_072904936.1  BUB13_RS01275 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  871.5   1.9  1.2e-266  1.2e-266       1     555 [.       3     563 ..       3     565 .] 0.99

  Alignments for each domain:
  == domain 1  score: 871.5 bits;  conditional E-value: 1.2e-266
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               l+g++il+esl+kegv+tvfGyPGGav++iyd l+ds +eh+l+rheqaa+haadGyar++GkvGvv+a
  lcl|NCBI__GCF_900142125.1:WP_072904936.1   3 LTGSQILLESLQKEGVDTVFGYPGGAVINIYDDLFDSPIEHVLTRHEQAAVHAADGYARCTGKVGVVIA 71 
                                               689****************************************************************** PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPGatn+vtgiatay+ds+P+vv+tGqv+t liG+dafqe+d+ Git+p+tkh+flv++ +dl++++
  lcl|NCBI__GCF_900142125.1:WP_072904936.1  72 TSGPGATNTVTGIATAYMDSIPMVVITGQVPTPLIGNDAFQEADMCGITRPCTKHNFLVQDIKDLARTI 140
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207
                                               keaf+ia tGrPGPvl+dlPkd++ ++ ++++++kv+l+gykpt +g+k+qi ka++++  ak+Pv +v
  lcl|NCBI__GCF_900142125.1:WP_072904936.1 141 KEAFYIARTGRPGPVLIDLPKDIQVTKYKFKYPDKVSLRGYKPTYTGNKRQISKAAKMLLDAKRPVFYV 209
                                               ********************************************************************* PP

                                 TIGR00118 208 GgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGar 276
                                               GgG+  + a+eel++l+e+++ pvtttl+ + +fp+dh lalgmlGmhGt +an+av+e+dll+a+Gar
  lcl|NCBI__GCF_900142125.1:WP_072904936.1 210 GGGINLSAANEELVKLTEMTQTPVTTTLMAMSGFPQDHALALGMLGMHGTFYANMAVTECDLLVAIGAR 278
                                               ********************************************************************* PP

                                 TIGR00118 277 fddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee.......ekkeke 338
                                               fddrvtg ++ fa++ak+ihididP++i knv+vd+pivGd k vl++l ++l e+        +k++e
  lcl|NCBI__GCF_900142125.1:WP_072904936.1 279 FDDRVTGRIDAFAKKAKVIHIDIDPTSIKKNVAVDLPIVGDLKDVLSQLGAALAEKpdelqklVSKTTE 347
                                               *************************************************99999888877766566778 PP

                                 TIGR00118 339 WlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsg 407
                                               W e ++ewk++++++++++e++ikPq vi+++ +l++d+ai+tt+vGqhqmw+aqf+++++pr+f+tsg
  lcl|NCBI__GCF_900142125.1:WP_072904936.1 348 WRETVDEWKQKHPMAYKHSESTIKPQFVIEKVRELTEDDAIITTEVGQHQMWTAQFFQFRQPRTFLTSG 416
                                               ********************************************************************* PP

                                 TIGR00118 408 GlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqel 476
                                               GlGtmG+GlPaalGa+va pe +vv+++Gdgsfqmn qel+t+v+y++pvkivilnn++lGmv+qWq++
  lcl|NCBI__GCF_900142125.1:WP_072904936.1 417 GLGTMGYGLPAALGAQVAYPERQVVDISGDGSFQMNSQELATLVQYKLPVKIVILNNNYLGMVRQWQQM 485
                                               ********************************************************************* PP

                                 TIGR00118 477 fyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmva 545
                                               f+++rys+t ++    df+klaeayG+ g++  k  ++e+ +k+ale  +pvl+++++ +ee+vlPmv+
  lcl|NCBI__GCF_900142125.1:WP_072904936.1 486 FFDKRYSQTVMEL-PIDFIKLAEAYGAAGLQCDKVGDVEATIKKALEIPGPVLMEFKISREENVLPMVP 553
                                               ************6.88***************************************************** PP

                                 TIGR00118 546 pGagldelve 555
                                                G+g++e+v 
  lcl|NCBI__GCF_900142125.1:WP_072904936.1 554 AGKGIHEMVL 563
                                               ********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (565 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: 00:00:00.03
# Mc/sec: 8.43
//
[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