Alignments for a candidate for ilvI in Sulfurivirga caldicuralii DSM 17737

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Sulfurivirga caldicuralii DSM 17737

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_074201498.1 BUQ81_RS06015 acetolactate synthase 3 large subunit

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



>NCBI__GCF_900141795.1:WP_074201498.1
          Length = 568

 Score =  760 bits (1963), Expect = 0.0
 Identities = 374/567 (65%), Positives = 449/567 (79%), Gaps = 5/567 (0%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTK-FEHILVRHEQAAVHAADGY 76
           E+ GA+I++  L +EGVE++WGYPGGAVL IYD L    K  +H LVRHEQAAVHAADGY
Sbjct: 2   ELTGAQIVIKFLEDEGVEHIWGYPGGAVLPIYDALDTDAKNLQHFLVRHEQAAVHAADGY 61

Query: 77  ARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGI 136
           AR+TGK GVALVTSGPG TNAVTGIATAY+DSIP+VV+TG VPT  IG DAFQE DTVG+
Sbjct: 62  ARSTGKPGVALVTSGPGATNAVTGIATAYMDSIPLVVLTGQVPTSMIGLDAFQEVDTVGV 121

Query: 137 TRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMR 196
           TRPIVKHNFLVKDV DLA T+KKAF+IA TGRPGPVVVDIPKDV      Y YP+ + MR
Sbjct: 122 TRPIVKHNFLVKDVNDLAMTLKKAFYIATTGRPGPVVVDIPKDVQTAKSDYTYPQEVKMR 181

Query: 197 SYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMG 256
           SY PV KGHSGQI++AV ++  AERP  Y GGGVVL +AS++L  LA   G+PVT TLM 
Sbjct: 182 SYQPVTKGHSGQIKRAVEMMLSAERPIFYVGGGVVLDDASEQLVTLAKKLGYPVTTTLMA 241

Query: 257 LGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIH 316
           LGA+P    Q++GMLGMHGTYEAN+AM + D LIAIGARFDDRV GN   F   A KIIH
Sbjct: 242 LGAYPADDPQWLGMLGMHGTYEANLAMHHADTLIAIGARFDDRVTGNIEKFCPNA-KIIH 300

Query: 317 IDIDPSSISKRVKVDIPIVGNVKDVLQEL---IAQIKASDIKPKREALAKWWEQIEQWRS 373
           +DIDP+SISK V+VDIPIVG+V+ VL+++   + +      KP +E L +WWEQI +W+ 
Sbjct: 301 VDIDPASISKNVQVDIPIVGSVRSVLEDMNHVLDRQLEKGAKPDQEKLDEWWEQIREWQQ 360

Query: 374 VDCLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGG 433
           V+CLKY  +   IKPQ  VE ++ +T+GDAF+ SDVGQHQM+AAQ+Y+F++PRRWINSGG
Sbjct: 361 VECLKYSTAGSKIKPQAAVEAVYRITQGDAFVTSDVGQHQMYAAQYYRFNKPRRWINSGG 420

Query: 434 LGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLG 493
           LGTMG GLP AMG++ A P+  VV ITGEGSIQM IQELSTCLQY  P+KI +LNNG+LG
Sbjct: 421 LGTMGFGLPAAMGVQLAHPDATVVCITGEGSIQMNIQELSTCLQYGWPIKIVNLNNGFLG 480

Query: 494 MVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTV 553
           MVRQWQE+ Y+ RYS SYMD+LPDFVKLAEAYGHVG+R+EK  ++E  L+EAF LKDR V
Sbjct: 481 MVRQWQELFYERRYSMSYMDSLPDFVKLAEAYGHVGLRIEKPDELEAKLQEAFALKDRLV 540

Query: 554 FLDFQTDPTENVWPMVQAGKGISEMLL 580
           F+D Q +  ENV+PM+ AG G  EM+L
Sbjct: 541 FIDIQVEAQENVYPMIPAGAGQDEMIL 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: 959
Number of extensions: 36
Number of successful extensions: 4
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_074201498.1 BUQ81_RS06015 (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.26695.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.1e-271  886.2   1.8   4.6e-271  886.0   1.8    1.0  1  lcl|NCBI__GCF_900141795.1:WP_074201498.1  BUQ81_RS06015 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900141795.1:WP_074201498.1  BUQ81_RS06015 acetolactate synthase 3 large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  886.0   1.8  4.6e-271  4.6e-271       1     555 [.       3     567 ..       3     568 .] 0.98

  Alignments for each domain:
  == domain 1  score: 886.0 bits;  conditional E-value: 4.6e-271
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly..dselehilvrheqaaahaadGyarasGkvGvv 67 
                                               l+ga+i+++ l++egve+++GyPGGavlpiydal   +++l+h lvrheqaa+haadGyar++Gk+Gv+
  lcl|NCBI__GCF_900141795.1:WP_074201498.1   3 LTGAQIVIKFLEDEGVEHIWGYPGGAVLPIYDALDtdAKNLQHFLVRHEQAAVHAADGYARSTGKPGVA 71 
                                               68********************************987889***************************** PP

                                 TIGR00118  68 latsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpe 136
                                               l+tsGPGatn+vtgiatay+ds+PlvvltGqv+ts+iG dafqe+d +G+t+p++kh+flvk+++dl+ 
  lcl|NCBI__GCF_900141795.1:WP_074201498.1  72 LVTSGPGATNAVTGIATAYMDSIPLVVLTGQVPTSMIGLDAFQEVDTVGVTRPIVKHNFLVKDVNDLAM 140
                                               ********************************************************************* PP

                                 TIGR00118 137 ilkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvl 205
                                               +lk+af+ia+tGrPGPv+vd+Pkdv++a+ +++++++v++++y+p +kgh  qik+a+e++ +a++P+ 
  lcl|NCBI__GCF_900141795.1:WP_074201498.1 141 TLKKAFYIATTGRPGPVVVDIPKDVQTAKSDYTYPQEVKMRSYQPVTKGHSGQIKRAVEMMLSAERPIF 209
                                               ********************************************************************* PP

                                 TIGR00118 206 lvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavG 274
                                               +vGgGv+  +ase+l+ la++l  pvtttl+ lGa+p+d+p+ lgmlGmhGt+eanla+++ad lia+G
  lcl|NCBI__GCF_900141795.1:WP_074201498.1 210 YVGGGVVLDDASEQLVTLAKKLGYPVTTTLMALGAYPADDPQWLGMLGMHGTYEANLAMHHADTLIAIG 278
                                               ********************************************************************* PP

                                 TIGR00118 275 arfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee........ekk 335
                                               arfddrvtgn++kf+p+akiih+didPa+i+knv+vdipivG +++vle++ + l ++        ++k
  lcl|NCBI__GCF_900141795.1:WP_074201498.1 279 ARFDDRVTGNIEKFCPNAKIIHVDIDPASISKNVQVDIPIVGSVRSVLEDMNHVLDRQlekgakpdQEK 347
                                               ***************************************************988877777788774333 PP

                                 TIGR00118 336 ekeWlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfi 404
                                                 eW+e+i+ew++  +lk+++  ++ikPq+ +++++++++++a+vt+dvGqhqm+aaq+y+++kpr++i
  lcl|NCBI__GCF_900141795.1:WP_074201498.1 348 LDEWWEQIREWQQVECLKYSTAGSKIKPQAAVEAVYRITQGDAFVTSDVGQHQMYAAQYYRFNKPRRWI 416
                                               345****************************************************************** PP

                                 TIGR00118 405 tsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqW 473
                                               +sgGlGtmGfGlPaa+G+++a+p++tvv++tG+gs+qmn+qelst+ +y+ p+kiv+lnn +lGmv+qW
  lcl|NCBI__GCF_900141795.1:WP_074201498.1 417 NSGGLGTMGFGLPAAMGVQLAHPDATVVCITGEGSIQMNIQELSTCLQYGWPIKIVNLNNGFLGMVRQW 485
                                               ********************************************************************* PP

                                 TIGR00118 474 qelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevl 541
                                               qelfye+rys +++ s lpdfvklaeayG++g+riekp+ele+kl+ea++ k ++v++d++v+ +e+v+
  lcl|NCBI__GCF_900141795.1:WP_074201498.1 486 QELFYERRYSMSYMDS-LPDFVKLAEAYGHVGLRIEKPDELEAKLQEAFALKdRLVFIDIQVEAQENVY 553
                                               ***************5.*******************************9987699************** PP

                                 TIGR00118 542 PmvapGagldelve 555
                                               Pm++ Gag de++ 
  lcl|NCBI__GCF_900141795.1:WP_074201498.1 554 PMIPAGAGQDEMIL 567
                                               ************85 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 0.02s 00:00:00.05 Elapsed: 00:00:00.03
# Mc/sec: 8.51
//
[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