Alignments for a candidate for ilvI in Paraburkholderia phymatum STM815

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Paraburkholderia phymatum STM815

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_012406585.1 BPHY_RS37050 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_000020045.1:WP_012406585.1
          Length = 591

 Score =  760 bits (1963), Expect = 0.0
 Identities = 364/565 (64%), Positives = 441/565 (78%), Gaps = 2/565 (0%)

Query: 21  GAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYARAT 80
           GA+I++  L  EGV+ VWGYPGGAVL +YD L +     H+LVRHEQAAVHAADG+ARAT
Sbjct: 27  GAQIVLSVLRAEGVDTVWGYPGGAVLPLYDALQETVDITHLLVRHEQAAVHAADGFARAT 86

Query: 81  GKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGITRPI 140
           GKVGVALVTSGPGVTN VTGIATAY DSIPMVVI+GNVPTH+IG DAFQECD VGITR I
Sbjct: 87  GKVGVALVTSGPGVTNTVTGIATAYFDSIPMVVISGNVPTHSIGTDAFQECDAVGITRSI 146

Query: 141 VKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRSYNP 200
           VKHNFLV D+  LA T+K AF+IA TGRPGPV+VDIPKDV +        +S+ +RSY P
Sbjct: 147 VKHNFLVLDISQLAKTLKSAFYIARTGRPGPVLVDIPKDVLQAKTPLSIAESVALRSYRP 206

Query: 201 VNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGLGAF 260
             + H GQ+R+A   L  + RP I  GGG V + AS+E+ +L      PVTNTLM LGAF
Sbjct: 207 RTEPHVGQVRRAAEALARSRRPCILVGGGAVASAASEEIAELVRRLDAPVTNTLMALGAF 266

Query: 261 PGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHIDID 320
           P + ++ +GM G+HGTYEAN+AMQ+CDVLIA+GARFDDRVIGN   F S  R IIH+DID
Sbjct: 267 PASDRRCLGMPGLHGTYEANLAMQHCDVLIALGARFDDRVIGNTGEFQSDRRTIIHVDID 326

Query: 321 PSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDCLKYD 380
           P++I KRV+VDIPIVG+VK   + ++ Q++A  I         WW++I  WR   CL Y+
Sbjct: 327 PATIDKRVQVDIPIVGDVKTAARAILEQLRAQRINDGNR--NDWWKEIGNWREKRCLAYE 384

Query: 381 RSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGTMGVG 440
             +++IKPQ+V++++WE T GDA+ICSDVGQHQMWAAQ Y FD+PRRWINSGGLGTMGVG
Sbjct: 385 PDADVIKPQFVIQQLWEATGGDAYICSDVGQHQMWAAQLYGFDKPRRWINSGGLGTMGVG 444

Query: 441 LPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVRQWQE 500
           LPYAMG+K+A P+ +VV +TG+GSIQMCIQELSTC QYD  VKI SLNNGYLGMVRQ Q 
Sbjct: 445 LPYAMGVKRALPDADVVAVTGDGSIQMCIQELSTCRQYDLGVKIVSLNNGYLGMVRQLQH 504

Query: 501 IEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFLDFQTD 560
           + Y +RYSHSYMDALPDFV LA AYGHVG R+E+  DVEP LREA  +K RTVF+DF  D
Sbjct: 505 VNYRDRYSHSYMDALPDFVALARAYGHVGFRIERPCDVEPVLREALAMKQRTVFMDFAID 564

Query: 561 PTENVWPMVQAGKGISEMLLGAEDL 585
           P+ENVWPMV+AG G+++ML+ + D+
Sbjct: 565 PSENVWPMVRAGAGLTDMLMNSRDV 589


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: 26
Number of successful extensions: 2
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: 591
Length adjustment: 37
Effective length of query: 548
Effective length of database: 554
Effective search space:   303592
Effective search space used:   303592
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_012406585.1 BPHY_RS37050 (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.8730.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.3e-240  785.5   0.0   1.6e-240  785.3   0.0    1.0  1  lcl|NCBI__GCF_000020045.1:WP_012406585.1  BPHY_RS37050 acetolactate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020045.1:WP_012406585.1  BPHY_RS37050 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  785.3   0.0  1.6e-240  1.6e-240       2     555 ..      26     584 ..      25     586 .. 0.98

  Alignments for each domain:
  == domain 1  score: 785.3 bits;  conditional E-value: 1.6e-240
                                 TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               +ga+i+++ l++egv+tv+GyPGGavlp+ydal  + +++h+lvrheqaa+haadG+ara+GkvGv+l+
  lcl|NCBI__GCF_000020045.1:WP_012406585.1  26 SGAQIVLSVLRAEGVDTVWGYPGGAVLPLYDALQeTVDITHLLVRHEQAAVHAADGFARATGKVGVALV 94 
                                               79********************************889******************************** PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPG tn+vtgiatay ds+P+vv++G v+t+ iG+dafqe+d +Git++++kh+flv + ++l+++l
  lcl|NCBI__GCF_000020045.1:WP_012406585.1  95 TSGPGVTNTVTGIATAYFDSIPMVVISGNVPTHSIGTDAFQECDAVGITRSIVKHNFLVLDISQLAKTL 163
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207
                                               k af+ia tGrPGPvlvd+Pkdv +a++ l++ e+v l++y+p++++h  q+++a+e+++++++P +lv
  lcl|NCBI__GCF_000020045.1:WP_012406585.1 164 KSAFYIARTGRPGPVLVDIPKDVLQAKTPLSIAESVALRSYRPRTEPHVGQVRRAAEALARSRRPCILV 232
                                               ********************************************************************* PP

                                 TIGR00118 208 GgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGar 276
                                               GgG++++ asee+ el+ rl++pvt tl+ lGafp+ +++ lgm G+hGt+eanla++++d+lia+Gar
  lcl|NCBI__GCF_000020045.1:WP_012406585.1 233 GGGAVASAASEEIAELVRRLDAPVTNTLMALGAFPASDRRCLGMPGLHGTYEANLAMQHCDVLIALGAR 301
                                               ********************************************************************* PP

                                 TIGR00118 277 fddrvtgnlakfapeak.iihididPaeigknvkvdipivGdakkvleellkklkee..ekkeke.Wle 341
                                               fddrv gn  +f ++ + iih+didPa i+k v+vdipivGd+k+  + +l++l+++  ++ +++ W++
  lcl|NCBI__GCF_000020045.1:WP_012406585.1 302 FDDRVIGNTGEFQSDRRtIIHVDIDPATIDKRVQVDIPIVGDVKTAARAILEQLRAQriNDGNRNdWWK 370
                                               ************9876559*********************************99999653333335*** PP

                                 TIGR00118 342 kieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlG 410
                                               +i +w+++ +l+++ + + ikPq vi++l++ + ++a++ +dvGqhqmwaaq y ++kpr++i+sgGlG
  lcl|NCBI__GCF_000020045.1:WP_012406585.1 371 EIGNWREKRCLAYEPDADVIKPQFVIQQLWEATGGDAYICSDVGQHQMWAAQLYGFDKPRRWINSGGLG 439
                                               ********************************************************************* PP

                                 TIGR00118 411 tmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfye 479
                                               tmG GlP a+G+k a p+++vvavtGdgs+qm +qelst+++yd+ vkiv lnn +lGmv+q q++ y+
  lcl|NCBI__GCF_000020045.1:WP_012406585.1 440 TMGVGLPYAMGVKRALPDADVVAVTGDGSIQMCIQELSTCRQYDLGVKIVSLNNGYLGMVRQLQHVNYR 508
                                               ********************************************************************* PP

                                 TIGR00118 480 erysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevlPmvapG 547
                                               +rys++++ + lpdfv+la+ayG++g rie+p ++e  l+eal++k + v++d+ +d +e+v+Pmv  G
  lcl|NCBI__GCF_000020045.1:WP_012406585.1 509 DRYSHSYMDA-LPDFVALARAYGHVGFRIERPCDVEPVLREALAMKqRTVFMDFAIDPSENVWPMVRAG 576
                                               *********5.********************************988689******************** PP

                                 TIGR00118 548 agldelve 555
                                               agl++++ 
  lcl|NCBI__GCF_000020045.1:WP_012406585.1 577 AGLTDMLM 584
                                               *****985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (591 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: 11.89
//
[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