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_072909015.1 BUB13_RS12045 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_900142125.1:WP_072909015.1
          Length = 556

 Score =  487 bits (1253), Expect = e-142
 Identities = 266/563 (47%), Positives = 350/563 (62%), Gaps = 10/563 (1%)

Query: 21  GAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYARAT 80
           GA+IL+  L +EGV  ++GYPGG  L ++DEL      +HILVRHEQ A HAADGYAR T
Sbjct: 4   GAQILLECLKKEGVSTIFGYPGGRSLLVHDELMDDPDIKHILVRHEQGAAHAADGYARTT 63

Query: 81  GKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGITRPI 140
           G+VGV L TSGPG TN VTGIATAY+DS+PMV +T  VPT AIG DAFQE D VGITRPI
Sbjct: 64  GQVGVCLSTSGPGATNLVTGIATAYMDSVPMVALTCQVPTAAIGNDAFQEADMVGITRPI 123

Query: 141 VKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRSYNP 200
            KHN++V D+ DLA  I +AF+IA T RPGPV+VD+P DV     K    +    R Y  
Sbjct: 124 TKHNYVVTDINDLAKIIHEAFYIARTRRPGPVLVDLPSDVIGAKIKPVESEPAKRRGYQE 183

Query: 201 VNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGLGAF 260
               +  QI+KA A++  A+RP IY GGG+ L+N++D+LR LA     PVT+TLMG+G  
Sbjct: 184 KPSLNLKQIQKAAAMINKAKRPLIYAGGGITLSNSTDKLRALAEKGNLPVTHTLMGVGIM 243

Query: 261 PGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHIDID 320
              S   +GMLGM+G + ANMA+  CD LIAIGARFDDRV GN   F  +A KIIH DID
Sbjct: 244 DPDSPLSIGMLGMYGAWYANMAVSECDCLIAIGARFDDRVTGNVESFAPKA-KIIHFDID 302

Query: 321 PSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDCLKYD 380
           P+SI K V+  +PIV +  + L+ L   I+  D        + W+E I  ++    L   
Sbjct: 303 PTSIRKVVQGGLPIVCDAAEALEPLTELIEPKD-------RSSWFEDIASYKEKAPLPRP 355

Query: 381 RSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGTMGVG 440
               I+ P  V+E I  +      + SDVG  QMW A +  F  PR++I SGGLGTMG  
Sbjct: 356 ERDHIV-PHEVMEAIHAIAGDQPVVASDVGLSQMWTANYLPFAGPRQYITSGGLGTMGYA 414

Query: 441 LPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVRQWQE 500
           LP AMG     PE+ V  I G+G+ QM  QEL+TC QY+ PVK   LNNG LGMVRQ+Q 
Sbjct: 415 LPAAMGAAMGCPERAVFAINGDGAFQMNCQELATCAQYNIPVKCIILNNGKLGMVRQFQR 474

Query: 501 IEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFLDFQTD 560
           +  D+RY+ + +    DF K++E +G   + V++  D++  L++A  +    V ++    
Sbjct: 475 LLLDSRYASTDLGNHVDFCKVSEGFGVKALYVKRQEDLQSVLQQAMDIPG-PVVVEVPIH 533

Query: 561 PTENVWPMVQAGKGISEMLLGAE 583
           P    +PMV  G   ++M+  A+
Sbjct: 534 PDTYSFPMVLPGSDATQMVFDAD 556


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: 862
Number of extensions: 30
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: 585
Length of database: 556
Length adjustment: 36
Effective length of query: 549
Effective length of database: 520
Effective search space:   285480
Effective search space used:   285480
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_072909015.1 BUB13_RS12045 (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.14678.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.3e-225  736.0   0.0   1.6e-225  735.7   0.0    1.0  1  lcl|NCBI__GCF_900142125.1:WP_072909015.1  BUB13_RS12045 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900142125.1:WP_072909015.1  BUB13_RS12045 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  735.7   0.0  1.6e-225  1.6e-225       2     554 ..       3     552 ..       2     555 .. 0.98

  Alignments for each domain:
  == domain 1  score: 735.7 bits;  conditional E-value: 1.6e-225
                                 TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               +ga+il+e lkkegv t+fGyPGG  l ++d+l  d +++hilvrheq+aahaadGyar++G+vGv+l+
  lcl|NCBI__GCF_900142125.1:WP_072909015.1   3 TGAQILLECLKKEGVSTIFGYPGGRSLLVHDELMdDPDIKHILVRHEQGAAHAADGYARTTGQVGVCLS 71 
                                               79********************************788******************************** PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPGatnlvtgiatay+dsvP+v+lt qv+t++iG+dafqe+d++Git+p+tkh+++v++ +dl++i+
  lcl|NCBI__GCF_900142125.1:WP_072909015.1  72 TSGPGATNLVTGIATAYMDSVPMVALTCQVPTAAIGNDAFQEADMVGITRPITKHNYVVTDINDLAKII 140
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207
                                               +eaf+ia t rPGPvlvdlP dv  a+i+   +e  + +gy+ + + + +qi+ka+ +i+kak+P++++
  lcl|NCBI__GCF_900142125.1:WP_072909015.1 141 HEAFYIARTRRPGPVLVDLPSDVIGAKIKPVESEPAKRRGYQEKPSLNLKQIQKAAAMINKAKRPLIYA 209
                                               ******************************999************************************ PP

                                 TIGR00118 208 GgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGar 276
                                               GgG+  ++++++l+ lae+ ++pvt+tl+G+G ++ d pl++gmlGm+G+ +an+avse+d+lia+Gar
  lcl|NCBI__GCF_900142125.1:WP_072909015.1 210 GGGITLSNSTDKLRALAEKGNLPVTHTLMGVGIMDPDSPLSIGMLGMYGAWYANMAVSECDCLIAIGAR 278
                                               ********************************************************************* PP

                                 TIGR00118 277 fddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekiee 345
                                               fddrvtgn+++fap+akiih+didP++i k+v+  +piv da + le l + ++ +++++  W+e i++
  lcl|NCBI__GCF_900142125.1:WP_072909015.1 279 FDDRVTGNVESFAPKAKIIHFDIDPTSIRKVVQGGLPIVCDAAEALEPLTELIEPKDRSS--WFEDIAS 345
                                               ******************************************************999998..******* PP

                                 TIGR00118 346 wkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGf 414
                                               +k++ +l    e ++i P +v+++++ ++ d+ +v++dvG  qmw+a+++++  pr++itsgGlGtmG+
  lcl|NCBI__GCF_900142125.1:WP_072909015.1 346 YKEKAPLPRP-ERDHIVPHEVMEAIHAIAGDQPVVASDVGLSQMWTANYLPFAGPRQYITSGGLGTMGY 413
                                               *****97655.56789***************************************************** PP

                                 TIGR00118 415 GlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerys 483
                                                lPaa+Ga ++ pe +v a++Gdg+fqmn+qel+t+++y+ipvk +ilnn  lGmv+q+q+l+ + ry+
  lcl|NCBI__GCF_900142125.1:WP_072909015.1 414 ALPAAMGAAMGCPERAVFAINGDGAFQMNCQELATCAQYNIPVKCIILNNGKLGMVRQFQRLLLDSRYA 482
                                               ********************************************************************* PP

                                 TIGR00118 484 etklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGaglde 552
                                               +t l++ + df k++e++Gvk++ ++++e+l++ l++a+   +pv+++v ++ ++  +Pmv pG+  ++
  lcl|NCBI__GCF_900142125.1:WP_072909015.1 483 STDLGN-HVDFCKVSEGFGVKALYVKRQEDLQSVLQQAMDIPGPVVVEVPIHPDTYSFPMVLPGSDATQ 550
                                               *****6.9************************************************************9 PP

                                 TIGR00118 553 lv 554
                                               +v
  lcl|NCBI__GCF_900142125.1:WP_072909015.1 551 MV 552
                                               98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (556 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: 10.84
//
[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