Alignments for a candidate for ilvI in Thermodesulforhabdus norvegica DSM 9990

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Thermodesulforhabdus norvegica DSM 9990

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_093393436.1 BM091_RS03295 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_900114975.1:WP_093393436.1
          Length = 570

 Score =  632 bits (1630), Expect = 0.0
 Identities = 320/571 (56%), Positives = 410/571 (71%), Gaps = 11/571 (1%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           ++ GA+I    L  EGVE ++GYPGGAVL IY E+ K     HILVRHEQ A H ADGYA
Sbjct: 2   KLTGAQIFFECLKREGVEVIFGYPGGAVLDIYHEMPKHN-IRHILVRHEQGAAHMADGYA 60

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           RA+GKVGV LVTSGPG TN VTGIATAY+DSIP+VV TG VPT  IG DAFQE D VGIT
Sbjct: 61  RASGKVGVCLVTSGPGATNTVTGIATAYMDSIPIVVFTGQVPTALIGNDAFQEVDIVGIT 120

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
           RP  KHN+LVKDVRDL   IK+AF++A +GRPGPV+VD+PKDV + +    YP+++++R 
Sbjct: 121 RPCTKHNYLVKDVRDLPRIIKEAFYLARSGRPGPVLVDLPKDVIQASTNLSYPETVNLRG 180

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257
           Y P  + H GQ++KA   ++ A+RP IY GGGV+ ++A +EL + A +   PVT TLMGL
Sbjct: 181 YKPTVEPHRGQLKKAAQAIRKAQRPVIYAGGGVIHSSARNELTKFAEMLQIPVTTTLMGL 240

Query: 258 GAFPGTSKQ--------FVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTS 309
           GAFP  +++        ++GMLGMHGT+ ANMA+ +CD+L AIGARFDDRV G    F  
Sbjct: 241 GAFPAVTEKGTFNLHPLWLGMLGMHGTFRANMAVTHCDLLFAIGARFDDRVTGKVEGFAP 300

Query: 310 QARKIIHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIE 369
           +A KIIHID+DP+SISK V+VDIPIVG+ K  L+ LI   +   ++   E  A W +QIE
Sbjct: 301 KA-KIIHIDVDPTSISKNVRVDIPIVGDCKRALRYLIEMFQEEPLENVEERRAPWLKQIE 359

Query: 370 QWRSVDCLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWI 429
           +W+    L Y +    IKPQ+V+EKI+EL++GDA I ++VGQ+QMW AQ+Y F EPR  I
Sbjct: 360 EWKKTYPLAYKQQEGRIKPQFVIEKIYELSRGDAIIATEVGQNQMWTAQYYHFTEPRTLI 419

Query: 430 NSGGLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNN 489
            SGGLGTMG G P A+G + A P+K V+ I G+GSIQM IQEL T +  + PVK+  LNN
Sbjct: 420 TSGGLGTMGYGFPAAIGAQVARPDKLVIDIAGDGSIQMNIQELITAVCNELPVKVAILNN 479

Query: 490 GYLGMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLK 549
           GYLGMVRQWQE+ Y+  Y  + ++  PDFVKLAEAYG VG+R  K  +VEP +++AF + 
Sbjct: 480 GYLGMVRQWQELFYEKNYCATCLEGGPDFVKLAEAYGAVGLRATKPEEVEPVIKKAFEI- 538

Query: 550 DRTVFLDFQTDPTENVWPMVQAGKGISEMLL 580
            + V +DF  +P E V+PMV AGK I+EMLL
Sbjct: 539 PKPVLMDFVVEPEEGVYPMVPAGKTITEMLL 569


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: 964
Number of extensions: 32
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: 570
Length adjustment: 36
Effective length of query: 549
Effective length of database: 534
Effective search space:   293166
Effective search space used:   293166
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_093393436.1 BM091_RS03295 (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.29750.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.3e-267  873.9   0.0   2.6e-267  873.7   0.0    1.0  1  lcl|NCBI__GCF_900114975.1:WP_093393436.1  BM091_RS03295 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900114975.1:WP_093393436.1  BM091_RS03295 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  873.7   0.0  2.6e-267  2.6e-267       1     554 [.       3     568 ..       3     570 .] 0.97

  Alignments for each domain:
  == domain 1  score: 873.7 bits;  conditional E-value: 2.6e-267
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               l+ga+i+ e lk+egve++fGyPGGavl+iy ++ + +++hilvrheq+aah+adGyarasGkvGv+l+
  lcl|NCBI__GCF_900114975.1:WP_093393436.1   3 LTGAQIFFECLKREGVEVIFGYPGGAVLDIYHEMPKHNIRHILVRHEQGAAHMADGYARASGKVGVCLV 71 
                                               68******************************************************************* PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPGatn+vtgiatay+ds+P+vv+tGqv+t+liG+dafqe+di+Git+p+tkh++lvk+++dlp+i+
  lcl|NCBI__GCF_900114975.1:WP_093393436.1  72 TSGPGATNTVTGIATAYMDSIPIVVFTGQVPTALIGNDAFQEVDIVGITRPCTKHNYLVKDVRDLPRII 140
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207
                                               keaf++a +GrPGPvlvdlPkdv +a+++l+++e+v+l+gykptv++h+ q+kka+++i+ka++Pv+++
  lcl|NCBI__GCF_900114975.1:WP_093393436.1 141 KEAFYLARSGRPGPVLVDLPKDVIQASTNLSYPETVNLRGYKPTVEPHRGQLKKAAQAIRKAQRPVIYA 209
                                               ********************************************************************* PP

                                 TIGR00118 208 GgGviiaeaseelkelaerlkipvtttllGlGafped........hplalgmlGmhGtkeanlavsead 268
                                               GgGvi++ a +el+++ae+l+ipvtttl+GlGafp+         hpl lgmlGmhGt  an+av+++d
  lcl|NCBI__GCF_900114975.1:WP_093393436.1 210 GGGVIHSSARNELTKFAEMLQIPVTTTLMGLGAFPAVtekgtfnlHPLWLGMLGMHGTFRANMAVTHCD 278
                                               **********************************96323344445999********************* PP

                                 TIGR00118 269 lliavGarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee..... 332
                                               ll+a+Garfddrvtg+++ fap+akiihid+dP++i+knv+vdipivGd+k+ l+ l++  +ee     
  lcl|NCBI__GCF_900114975.1:WP_093393436.1 279 LLFAIGARFDDRVTGKVEGFAPKAKIIHIDVDPTSISKNVRVDIPIVGDCKRALRYLIEMFQEEplenv 347
                                               ***********************************************************9999988643 PP

                                 TIGR00118 333 ekkeke..WlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkk 399
                                               e++  +  Wl++ieewkk+y+l+++++e+ ikPq vi+++++l +++ai++t+vGq+qmw+aq+y++++
  lcl|NCBI__GCF_900114975.1:WP_093393436.1 348 EER--RapWLKQIEEWKKTYPLAYKQQEGRIKPQFVIEKIYELSRGDAIIATEVGQNQMWTAQYYHFTE 414
                                               333..356************************************************************* PP

                                 TIGR00118 400 prkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellG 468
                                               pr+ itsgGlGtmG+G+Paa+Ga+va p++ v++++Gdgs+qmn+qel t+v  ++pvk+ ilnn +lG
  lcl|NCBI__GCF_900114975.1:WP_093393436.1 415 PRTLITSGGLGTMGYGFPAAIGAQVARPDKLVIDIAGDGSIQMNIQELITAVCNELPVKVAILNNGYLG 483
                                               ********************************************************************* PP

                                 TIGR00118 469 mvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdke 537
                                               mv+qWqelfye+ y +t+l+ + pdfvklaeayG++g+r +kpee+e  +k+a+e  +pvl+d++v+ e
  lcl|NCBI__GCF_900114975.1:WP_093393436.1 484 MVRQWQELFYEKNYCATCLE-GGPDFVKLAEAYGAVGLRATKPEEVEPVIKKAFEIPKPVLMDFVVEPE 551
                                               ********************.6*********************************************** PP

                                 TIGR00118 538 eevlPmvapGagldelv 554
                                               e v+Pmv+ G++++e++
  lcl|NCBI__GCF_900114975.1:WP_093393436.1 552 EGVYPMVPAGKTITEML 568
                                               ***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (570 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: 11.41
//
[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