Alignments for a candidate for ilvI in Chlorobaculum parvum NCIB 8327

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Chlorobaculum parvum NCIB 8327

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_012501887.1 CPAR_RS03240 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_000020505.1:WP_012501887.1
          Length = 573

 Score =  580 bits (1494), Expect = e-170
 Identities = 290/562 (51%), Positives = 388/562 (69%), Gaps = 9/562 (1%)

Query: 21  GAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYARAT 80
           G+EI   +L  E V+Y++GYPGGA+L +Y+ LH     +HILVRHEQ A H A+GYARAT
Sbjct: 10  GSEIFFESLRRENVDYIFGYPGGALLKVYETLHDVEDIKHILVRHEQGATHMAEGYARAT 69

Query: 81  GKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGITRPI 140
           G+ GV LVTSGPG TN VTGIA AY+DS PMVV TG VP+  IG DAFQE D VGITRPI
Sbjct: 70  GRPGVVLVTSGPGATNTVTGIANAYMDSSPMVVFTGQVPSSLIGNDAFQEADIVGITRPI 129

Query: 141 VKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRSYNP 200
            KHNFLVKDV++LA+TI+KAFF+A  GRPGPV+VD+PKDV    C +E+P+S+++R + P
Sbjct: 130 TKHNFLVKDVKELASTIRKAFFLATHGRPGPVLVDMPKDVLNAICTFEWPESVEIRGFKP 189

Query: 201 VNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGLGAF 260
             K H+ Q++KA  ++  A+RP  Y GGG++ A AS+ELR+LA     PVT TL GLGAF
Sbjct: 190 TIKCHTNQVQKAAKMIAKAKRPLFYVGGGIITAEASEELRKLAIEQQIPVTMTLNGLGAF 249

Query: 261 PGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHIDID 320
           PG     +GMLGMHGTY AN A+ +CD+LIA+GARFDDRV G    F +QA  IIH DID
Sbjct: 250 PGDHPLSMGMLGMHGTYWANQAVNSCDLLIAVGARFDDRVTGKIDTFATQAH-IIHNDID 308

Query: 321 PSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPK-REALAKWWEQIEQWRSVDCLKY 379
           P+++ K +KVD+P+VG+ KD L  L+      +  PK +E  ++W +QIE WR    + Y
Sbjct: 309 PTNVDKNIKVDLPVVGDSKDFLASLL------EAMPKGKEDRSEWLDQIEGWRKQCPMDY 362

Query: 380 DRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGTMGV 439
               + +K ++V++++ + T G A I +DVGQHQMW AQ+YKF EPR  I SGGLGTMG 
Sbjct: 363 TIEPDSLKTEFVIDEVSKKTNGHAVIITDVGQHQMWTAQYYKFTEPRSIITSGGLGTMGY 422

Query: 440 GLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVRQWQ 499
           GLP  +G      ++ V+  TG+G + M IQEL T +    PVK+  +NN YLGMVRQWQ
Sbjct: 423 GLPACIGAAFGVTDRPVILFTGDGGLMMNIQELVTAVHNKLPVKLFLINNSYLGMVRQWQ 482

Query: 500 EIEYDNRYSHSYM-DALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFLDFQ 558
           E+ +  +Y+ + + ++ PDFVK+AEA+G   +R +     + A+ EA    D  + ++F+
Sbjct: 483 ELFHQEKYTFTDLEESNPDFVKVAEAFGCKALRADNPESAKKAIDEALAYNDGPILVEFK 542

Query: 559 TDPTENVWPMVQAGKGISEMLL 580
               + V+PMV AG  IS+MLL
Sbjct: 543 VIRKDMVFPMVPAGASISDMLL 564


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: 919
Number of extensions: 39
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: 573
Length adjustment: 36
Effective length of query: 549
Effective length of database: 537
Effective search space:   294813
Effective search space used:   294813
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_012501887.1 CPAR_RS03240 (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.20255.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-247  808.5   0.1   1.6e-247  808.3   0.1    1.0  1  lcl|NCBI__GCF_000020505.1:WP_012501887.1  CPAR_RS03240 acetolactate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020505.1:WP_012501887.1  CPAR_RS03240 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  808.3   0.1  1.6e-247  1.6e-247       2     555 ..       9     564 ..       8     566 .. 0.99

  Alignments for each domain:
  == domain 1  score: 808.3 bits;  conditional E-value: 1.6e-247
                                 TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               +g+ei+ esl++e+v+++fGyPGGa+l++y++l+  ++++hilvrheq+a+h+a+Gyara+G++Gvvl+
  lcl|NCBI__GCF_000020505.1:WP_012501887.1   9 NGSEIFFESLRRENVDYIFGYPGGALLKVYETLHdVEDIKHILVRHEQGATHMAEGYARATGRPGVVLV 77 
                                               799*******************************889******************************** PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPGatn+vtgia+ay+ds+P+vv+tGqv++sliG+dafqe+di+Git+p+tkh+flvk++++l++++
  lcl|NCBI__GCF_000020505.1:WP_012501887.1  78 TSGPGATNTVTGIANAYMDSSPMVVFTGQVPSSLIGNDAFQEADIVGITRPITKHNFLVKDVKELASTI 146
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207
                                               ++af +a+ GrPGPvlvd+Pkdv +a +++e +e+ve++g+kpt+k h++q++ka+++i+kak+P+ +v
  lcl|NCBI__GCF_000020505.1:WP_012501887.1 147 RKAFFLATHGRPGPVLVDMPKDVLNAICTFEWPESVEIRGFKPTIKCHTNQVQKAAKMIAKAKRPLFYV 215
                                               ********************************************************************* PP

                                 TIGR00118 208 GgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGar 276
                                               GgG+i+aeaseel++la +++ipvt+tl GlGafp dhpl++gmlGmhGt+ an av+ +dlliavGar
  lcl|NCBI__GCF_000020505.1:WP_012501887.1 216 GGGIITAEASEELRKLAIEQQIPVTMTLNGLGAFPGDHPLSMGMLGMHGTYWANQAVNSCDLLIAVGAR 284
                                               ********************************************************************* PP

                                 TIGR00118 277 fddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekiee 345
                                               fddrvtg++++fa++a+iih didP++++kn+kvd+p+vGd+k  l+ ll+++ + +++ +eWl++ie 
  lcl|NCBI__GCF_000020505.1:WP_012501887.1 285 FDDRVTGKIDTFATQAHIIHNDIDPTNVDKNIKVDLPVVGDSKDFLASLLEAMPKGKEDRSEWLDQIEG 353
                                               ******************************************************99999999******* PP

                                 TIGR00118 346 wkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGf 414
                                               w+k++++ +  e +s+k   vi+e+sk ++++a++ tdvGqhqmw+aq+yk+++pr+ itsgGlGtmG+
  lcl|NCBI__GCF_000020505.1:WP_012501887.1 354 WRKQCPMDYTIEPDSLKTEFVIDEVSKKTNGHAVIITDVGQHQMWTAQYYKFTEPRSIITSGGLGTMGY 422
                                               ********************************************************************* PP

                                 TIGR00118 415 GlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerys 483
                                               GlPa +Ga  ++ +  v+  tGdg+++mn+qel t+v+ ++pvk+ ++nn++lGmv+qWqelf++e+y+
  lcl|NCBI__GCF_000020505.1:WP_012501887.1 423 GLPACIGAAFGVTDRPVILFTGDGGLMMNIQELVTAVHNKLPVKLFLINNSYLGMVRQWQELFHQEKYT 491
                                               ********************************************************************* PP

                                 TIGR00118 484 etklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevlPmvapGagld 551
                                                t l++++pdfvk+aea+G k++r  +pe ++++++eal+ + +p+l++++v +++ v+Pmv+ Ga+++
  lcl|NCBI__GCF_000020505.1:WP_012501887.1 492 FTDLEESNPDFVKVAEAFGCKALRADNPESAKKAIDEALAYNdGPILVEFKVIRKDMVFPMVPAGASIS 560
                                               ***************************************98879************************* PP

                                 TIGR00118 552 elve 555
                                               +++ 
  lcl|NCBI__GCF_000020505.1:WP_012501887.1 561 DMLL 564
                                               9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (573 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: 11.62
//
[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