Alignments for a candidate for ilvI in Hydrogenovibrio kuenenii DSM 12350

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Hydrogenovibrio kuenenii DSM 12350

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_024851531.1 N745_RS0107615 acetolactate synthase 3 large subunit

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



>NCBI__GCF_000526715.1:WP_024851531.1
          Length = 568

 Score =  764 bits (1972), Expect = 0.0
 Identities = 374/567 (65%), Positives = 444/567 (78%), Gaps = 5/567 (0%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTK-FEHILVRHEQAAVHAADGY 76
           E+ GA+ILVH L +EGVE +WGYPGGA L IYD L    K  +H+LVRHEQAAVHAADGY
Sbjct: 2   ELTGAQILVHYLEDEGVELIWGYPGGAALPIYDALDTDAKKLKHVLVRHEQAAVHAADGY 61

Query: 77  ARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGI 136
           AR+TGK GV LVTSGPG TN VTGIATA++DSIPMVVITG VPT  IG DAFQE DTVGI
Sbjct: 62  ARSTGKPGVTLVTSGPGATNTVTGIATAFMDSIPMVVITGQVPTALIGLDAFQEIDTVGI 121

Query: 137 TRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMR 196
           TRPIVKHNFLVKDV DLA T+KKAF+IA TGRPGPVVVDIPKDV      YEYP+ + +R
Sbjct: 122 TRPIVKHNFLVKDVNDLAMTLKKAFYIATTGRPGPVVVDIPKDVQNAKSTYEYPQEVSLR 181

Query: 197 SYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMG 256
           SY PV KGHSGQI+KA+ ++  AERP +YTGGGVVL NAS EL  LA     PVTNTLMG
Sbjct: 182 SYVPVTKGHSGQIKKAIEMMAAAERPILYTGGGVVLGNASQELTDLARKLNFPVTNTLMG 241

Query: 257 LGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIH 316
           LGA+P    QFVGMLGMHGTYEAN+AM N D++IAIG+RFDDRV GN   F   A K+IH
Sbjct: 242 LGAYPANDSQFVGMLGMHGTYEANLAMHNSDLIIAIGSRFDDRVTGNLEKFCPDA-KVIH 300

Query: 317 IDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDI-KPKREALAKWWEQIEQWRSVD 375
           IDIDP+SISK V VDIPIVG VK VL E++  +  ++I +   EA+A WW QI +WR+ D
Sbjct: 301 IDIDPASISKNVAVDIPIVGPVKQVLSEMLNLLSKNNIGEANAEAIAAWWAQINEWRATD 360

Query: 376 CLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLG 435
           CL+Y+++   IKPQ  ++ +WE+T GDA++ SDVGQHQM+AAQ+Y+F++PRRWINSGGLG
Sbjct: 361 CLRYEQTGNKIKPQAAMQAVWEVTNGDAYVTSDVGQHQMFAAQYYRFNKPRRWINSGGLG 420

Query: 436 TMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMV 495
           TMG GLP AMG++ A+P+  VV +TGEGS+QM IQELSTCLQY  P+KI  LNNG+LGMV
Sbjct: 421 TMGFGLPAAMGVQAAYPDATVVCVTGEGSVQMNIQELSTCLQYGLPIKIICLNNGFLGMV 480

Query: 496 RQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAF--RLKDRTV 553
           RQWQE  YD RYS SYMD+LPDFVKL+EAYGH G+R++    +   L E F  + KD+ V
Sbjct: 481 RQWQEFFYDRRYSMSYMDSLPDFVKLSEAYGHAGVRIDNPETMRSQLEEVFSDKYKDKLV 540

Query: 554 FLDFQTDPTENVWPMVQAGKGISEMLL 580
           F+D  TD  ENV+PMV AG G+ EM+L
Sbjct: 541 FVDIITDQQENVYPMVPAGAGLDEMIL 567


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: 1011
Number of extensions: 37
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: 568
Length adjustment: 36
Effective length of query: 549
Effective length of database: 532
Effective search space:   292068
Effective search space used:   292068
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_024851531.1 N745_RS0107615 (acetolactate synthase 3 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.1942.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.2e-269  879.9   1.7   3.7e-269  879.8   1.7    1.0  1  lcl|NCBI__GCF_000526715.1:WP_024851531.1  N745_RS0107615 acetolactate synt


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000526715.1:WP_024851531.1  N745_RS0107615 acetolactate synthase 3 large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  879.8   1.7  3.7e-269  3.7e-269       1     555 [.       3     567 ..       3     568 .] 0.98

  Alignments for each domain:
  == domain 1  score: 879.8 bits;  conditional E-value: 3.7e-269
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly..dselehilvrheqaaahaadGyarasGkvGvv 67 
                                               l+ga+ilv+ l++egve ++GyPGGa lpiydal   +++l+h+lvrheqaa+haadGyar++Gk+Gv+
  lcl|NCBI__GCF_000526715.1:WP_024851531.1   3 LTGAQILVHYLEDEGVELIWGYPGGAALPIYDALDtdAKKLKHVLVRHEQAAVHAADGYARSTGKPGVT 71 
                                               68********************************987889***************************** PP

                                 TIGR00118  68 latsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpe 136
                                               l+tsGPGatn+vtgiata++ds+P+vv+tGqv+t+liG dafqeid +Git+p++kh+flvk+++dl+ 
  lcl|NCBI__GCF_000526715.1:WP_024851531.1  72 LVTSGPGATNTVTGIATAFMDSIPMVVITGQVPTALIGLDAFQEIDTVGITRPIVKHNFLVKDVNDLAM 140
                                               ********************************************************************* PP

                                 TIGR00118 137 ilkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvl 205
                                               +lk+af+ia+tGrPGPv+vd+Pkdv++a+ ++e++++v+l++y p +kgh  qikka+e++++a++P+l
  lcl|NCBI__GCF_000526715.1:WP_024851531.1 141 TLKKAFYIATTGRPGPVVVDIPKDVQNAKSTYEYPQEVSLRSYVPVTKGHSGQIKKAIEMMAAAERPIL 209
                                               ********************************************************************* PP

                                 TIGR00118 206 lvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavG 274
                                               + GgGv+ ++as+el++la +l+ pvt tl+GlGa+p+++ +++gmlGmhGt+eanla++++dl+ia+G
  lcl|NCBI__GCF_000526715.1:WP_024851531.1 210 YTGGGVVLGNASQELTDLARKLNFPVTNTLMGLGAYPANDSQFVGMLGMHGTYEANLAMHNSDLIIAIG 278
                                               ********************************************************************* PP

                                 TIGR00118 275 arfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee.....ekkeke 338
                                                rfddrvtgnl+kf+p+ak+ihididPa+i+knv+vdipivG +k+vl+e+l+ l+++     + + + 
  lcl|NCBI__GCF_000526715.1:WP_024851531.1 279 SRFDDRVTGNLEKFCPDAKVIHIDIDPASISKNVAVDIPIVGPVKQVLSEMLNLLSKNnigeaNAEAIA 347
                                               ******************************************************999888865444444 PP

                                 TIGR00118 339 .WlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfits 406
                                                W+++i+ew+++ +l+++++ ++ikPq+ +++++++++++a+vt+dvGqhqm+aaq+y+++kpr++i+s
  lcl|NCBI__GCF_000526715.1:WP_024851531.1 348 aWWAQINEWRATDCLRYEQTGNKIKPQAAMQAVWEVTNGDAYVTSDVGQHQMFAAQYYRFNKPRRWINS 416
                                               7******************************************************************** PP

                                 TIGR00118 407 gGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqe 475
                                               gGlGtmGfGlPaa+G++ a p++tvv+vtG+gs+qmn+qelst+ +y++p+ki++lnn +lGmv+qWqe
  lcl|NCBI__GCF_000526715.1:WP_024851531.1 417 GGLGTMGFGLPAAMGVQAAYPDATVVCVTGEGSVQMNIQELSTCLQYGLPIKIICLNNGFLGMVRQWQE 485
                                               ********************************************************************* PP

                                 TIGR00118 476 lfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk...epvlldvevdkeeevl 541
                                               +fy++rys +++ s lpdfvkl+eayG+ g+ri +pe + ++l+e+++ k   ++v++d+  d++e+v+
  lcl|NCBI__GCF_000526715.1:WP_024851531.1 486 FFYDRRYSMSYMDS-LPDFVKLSEAYGHAGVRIDNPETMRSQLEEVFSDKykdKLVFVDIITDQQENVY 553
                                               *************5.********************************9877779*************** PP

                                 TIGR00118 542 PmvapGagldelve 555
                                               Pmv+ Gaglde++ 
  lcl|NCBI__GCF_000526715.1:WP_024851531.1 554 PMVPAGAGLDEMIL 567
                                               ************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (568 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 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 9.08
//
[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)
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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