Alignments for a candidate for ilvI in Thermovibrio ammonificans HB-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Thermovibrio ammonificans HB-1

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_013537219.1 THEAM_RS02375 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_000185805.1:WP_013537219.1
          Length = 579

 Score =  625 bits (1612), Expect = 0.0
 Identities = 317/568 (55%), Positives = 399/568 (70%), Gaps = 7/568 (1%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           ++ GAEIL+ AL  EGVE ++GYPGGAVL IYD L   +  +H L RHEQ A HAADGYA
Sbjct: 2   KLSGAEILLRALELEGVEKIFGYPGGAVLDIYDRL-PFSPIKHYLTRHEQGAAHAADGYA 60

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           R TGKVGV   TSGPG TN VTG+ATA +DS+P+V  TGNVPT+ IG DAFQE DTVGIT
Sbjct: 61  RVTGKVGVCFATSGPGATNLVTGLATAQIDSVPVVAFTGNVPTYMIGNDAFQEVDTVGIT 120

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKY---EYPKSID 194
           RPI KHNFLVKDV++LA T+KKAF+IA TGRPG V+VD+PKDV+R    +   EY   + 
Sbjct: 121 RPITKHNFLVKDVKELADTVKKAFYIARTGRPGVVLVDLPKDVTRELADFFEEEYKSPVQ 180

Query: 195 MRSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTL 254
           +RSY PV KGH GQI++A   +  AERP +Y GGG V + A+D + +LA +   P+  TL
Sbjct: 181 IRSYKPVLKGHPGQIKRAAKAIASAERPVLYIGGGTVSSGAADLVVKLAEVANIPMVATL 240

Query: 255 MGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKI 314
           MGL A PG    F+GMLGMHGTY ANMA+Q CD+LIA+GARFDDRV G  + F   A K+
Sbjct: 241 MGLTAVPGDHPFFLGMLGMHGTYAANMAVQECDLLIAVGARFDDRVTGKLSEFAPNA-KV 299

Query: 315 IHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKR--EALAKWWEQIEQWR 372
           IHIDID + I K   VDIPIVG+ K VL+EL+ +++    K +       KW  ++  W 
Sbjct: 300 IHIDIDSAEIGKNRAVDIPIVGDAKLVLEELLPEVEKQVAKNREFYGVREKWIVKVRSWA 359

Query: 373 SVDCLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSG 432
               L Y+ S  +IKPQ+V+EKIWE+TKG+A I +DVGQHQMW AQFYKF  PR+ + SG
Sbjct: 360 ERYPLWYEPSDRVIKPQFVIEKIWEVTKGEAIITTDVGQHQMWTAQFYKFRFPRQLVTSG 419

Query: 433 GLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYL 492
           GLGTMG GLP A+G K   P+K V  I+G+GS QM +QE+ T + Y+ P+K+  +NN +L
Sbjct: 420 GLGTMGFGLPAAVGAKVGRPDKTVFCISGDGSFQMNMQEVVTAVHYNIPIKVAIINNSFL 479

Query: 493 GMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRT 552
           GMVRQWQ I YD  YS  ++D  PDFV+L EA G VG+R E+  +VE  L+EA  + DR 
Sbjct: 480 GMVRQWQGIFYDRNYSQVHLDVQPDFVRLVEAMGAVGLRAERPQEVEEVLKEAMAINDRP 539

Query: 553 VFLDFQTDPTENVWPMVQAGKGISEMLL 580
           V +DF  D  E+V+PMV  G  + EM+L
Sbjct: 540 VVIDFIVDREEDVFPMVPPGGALHEMIL 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: 983
Number of extensions: 35
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: 579
Length adjustment: 36
Effective length of query: 549
Effective length of database: 543
Effective search space:   298107
Effective search space used:   298107
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_013537219.1 THEAM_RS02375 (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.24378.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-257  841.5   0.3   1.7e-257  841.3   0.3    1.0  1  lcl|NCBI__GCF_000185805.1:WP_013537219.1  THEAM_RS02375 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000185805.1:WP_013537219.1  THEAM_RS02375 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  841.3   0.3  1.7e-257  1.7e-257       1     555 [.       3     567 ..       3     569 .. 0.97

  Alignments for each domain:
  == domain 1  score: 841.3 bits;  conditional E-value: 1.7e-257
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               l+gaeil+++l+ egve++fGyPGGavl+iyd+l  s ++h l+rheq+aahaadGyar++GkvGv++a
  lcl|NCBI__GCF_000185805.1:WP_013537219.1   3 LSGAEILLRALELEGVEKIFGYPGGAVLDIYDRLPFSPIKHYLTRHEQGAAHAADGYARVTGKVGVCFA 71 
                                               68******************************************************************* PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPGatnlvtg+ata +dsvP+v++tG v+t +iG+dafqe+d +Git+p+tkh+flvk++++l+ ++
  lcl|NCBI__GCF_000185805.1:WP_013537219.1  72 TSGPGATNLVTGLATAQIDSVPVVAFTGNVPTYMIGNDAFQEVDTVGITRPITKHNFLVKDVKELADTV 140
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaei...eleveekvelpgykptvkghklqikkaleliekakkPv 204
                                               k+af+ia tGrPG vlvdlPkdvt++     e e+++ v++++ykp +kgh+ qik+a+++i++a++Pv
  lcl|NCBI__GCF_000185805.1:WP_013537219.1 141 KKAFYIARTGRPGVVLVDLPKDVTRELAdffEEEYKSPVQIRSYKPVLKGHPGQIKRAAKAIASAERPV 209
                                               ***********************998651115566799******************************* PP

                                 TIGR00118 205 llvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliav 273
                                               l++GgG + ++a + +++lae ++ip+++tl+Gl a+p dhp +lgmlGmhGt++an+av+e+dlliav
  lcl|NCBI__GCF_000185805.1:WP_013537219.1 210 LYIGGGTVSSGAADLVVKLAEVANIPMVATLMGLTAVPGDHPFFLGMLGMHGTYAANMAVQECDLLIAV 278
                                               ********************************************************************* PP

                                 TIGR00118 274 GarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee.......ekk 335
                                               Garfddrvtg+l++fap+ak+ihidid aeigkn++vdipivGdak vleell +++++          
  lcl|NCBI__GCF_000185805.1:WP_013537219.1 279 GARFDDRVTGKLSEFAPNAKVIHIDIDSAEIGKNRAVDIPIVGDAKLVLEELLPEVEKQvaknrefYGV 347
                                               *****************************************************9999997754433122 PP

                                 TIGR00118 336 ekeWlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfi 404
                                                ++W+ k+++w ++y+l+++ ++  ikPq vi+++++++k+eai+ttdvGqhqmw+aqfyk++ pr+ +
  lcl|NCBI__GCF_000185805.1:WP_013537219.1 348 REKWIVKVRSWAERYPLWYEPSDRVIKPQFVIEKIWEVTKGEAIITTDVGQHQMWTAQFYKFRFPRQLV 416
                                               346****************************************************************** PP

                                 TIGR00118 405 tsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqW 473
                                               tsgGlGtmGfGlPaa+Gakv+ p++tv +++Gdgsfqmn+qe+ t+v+y+ip+k+ i+nn++lGmv+qW
  lcl|NCBI__GCF_000185805.1:WP_013537219.1 417 TSGGLGTMGFGLPAAVGAKVGRPDKTVFCISGDGSFQMNMQEVVTAVHYNIPIKVAIINNSFLGMVRQW 485
                                               ********************************************************************* PP

                                 TIGR00118 474 qelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevl 541
                                               q +fy++ ys+++l   +pdfv+l ea+G++g+r e+p+e+ee lkea++ + +pv++d+ vd+ee+v+
  lcl|NCBI__GCF_000185805.1:WP_013537219.1 486 QGIFYDRNYSQVHLDV-QPDFVRLVEAMGAVGLRAERPQEVEEVLKEAMAINdRPVVIDFIVDREEDVF 553
                                               ***************6.********************************99879*************** PP

                                 TIGR00118 542 PmvapGagldelve 555
                                               Pmv+pG++l+e++ 
  lcl|NCBI__GCF_000185805.1:WP_013537219.1 554 PMVPPGGALHEMIL 567
                                               ************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (579 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: 9.88
//
[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