Alignments for a candidate for ilvI in Paraburkholderia sp. CCGE1002

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Paraburkholderia sp. CCGE1002

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_013088923.1 BC1002_RS04655 acetolactate synthase 3 large subunit

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



>NCBI__GCF_000092885.1:WP_013088923.1
          Length = 587

 Score =  949 bits (2452), Expect = 0.0
 Identities = 456/585 (77%), Positives = 519/585 (88%)

Query: 1   MPSAEFSHADSNSSAAPEMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEH 60
           MPSAEFS +D+      + IGA +L+ ALA+E VE++WGYPGG+VLYIYDEL+KQ KF+H
Sbjct: 3   MPSAEFSTSDTTPPHEADSIGATVLMKALADEDVEFIWGYPGGSVLYIYDELYKQDKFQH 62

Query: 61  ILVRHEQAAVHAADGYARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPT 120
           +LVRHEQAAVHAAD YAR+TGKVGV LVTSGPGVTNAVTGIATAY+DSIPMVVI+G VPT
Sbjct: 63  VLVRHEQAAVHAADAYARSTGKVGVCLVTSGPGVTNAVTGIATAYMDSIPMVVISGQVPT 122

Query: 121 HAIGQDAFQECDTVGITRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDV 180
            AIGQDAFQECDTVGITRP VKHNFLVKDVRDLAAT+KKAF+IA TGRPGPV++DIPKDV
Sbjct: 123 AAIGQDAFQECDTVGITRPCVKHNFLVKDVRDLAATVKKAFYIARTGRPGPVLIDIPKDV 182

Query: 181 SRNACKYEYPKSIDMRSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELR 240
           S+  C+YE  KS+ +RSYNPV KGHSGQIRKAV+LL  A+RPYIYTGGG+VLA+AS EL 
Sbjct: 183 SKAPCQYEPIKSVSLRSYNPVTKGHSGQIRKAVSLLLSAKRPYIYTGGGIVLADASRELN 242

Query: 241 QLAALTGHPVTNTLMGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRV 300
           Q A L G+PVTNTLMGLG +  + K+F+GMLGMHGTYEANMAMQ+CDVLIAIGARFDDRV
Sbjct: 243 QFADLLGYPVTNTLMGLGGYRSSDKKFLGMLGMHGTYEANMAMQHCDVLIAIGARFDDRV 302

Query: 301 IGNPAHFTSQARKIIHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREA 360
           IG+P HF S+ RKIIHIDIDPSSISKRVKVDIPIVG+VK+VL+ELI Q++ ++  P   A
Sbjct: 303 IGDPNHFASRPRKIIHIDIDPSSISKRVKVDIPIVGDVKEVLKELIEQLQTAEHGPDTAA 362

Query: 361 LAKWWEQIEQWRSVDCLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFY 420
           LA WW+ IE WR+ DCLK+DR S+IIKPQYVVEK WELT G+AF+CSDVGQHQMWAAQFY
Sbjct: 363 LADWWKDIEGWRAKDCLKFDRKSDIIKPQYVVEKAWELTDGNAFVCSDVGQHQMWAAQFY 422

Query: 421 KFDEPRRWINSGGLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDT 480
           KF++PR WINSGGLGTMG GLP AMG+K A P+ +V+ ITGEGSIQMCIQELSTC QYD 
Sbjct: 423 KFNKPRHWINSGGLGTMGFGLPAAMGVKMAHPDDDVLCITGEGSIQMCIQELSTCKQYDL 482

Query: 481 PVKICSLNNGYLGMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEP 540
           P+KI SLNN YLGMVRQWQ+IEY  RYSHSYMDALPDFVKLAEAYGHVGMR+E+T+DVEP
Sbjct: 483 PIKIISLNNRYLGMVRQWQQIEYSKRYSHSYMDALPDFVKLAEAYGHVGMRIERTADVEP 542

Query: 541 ALREAFRLKDRTVFLDFQTDPTENVWPMVQAGKGISEMLLGAEDL 585
           AL+EA RLKDRTVFLDFQTDPTENVWPMVQAGKGI+EML+G+EDL
Sbjct: 543 ALKEALRLKDRTVFLDFQTDPTENVWPMVQAGKGITEMLMGSEDL 587


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: 1061
Number of extensions: 28
Number of successful extensions: 1
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: 587
Length adjustment: 37
Effective length of query: 548
Effective length of database: 550
Effective search space:   301400
Effective search space used:   301400
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_013088923.1 BC1002_RS04655 (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.10701.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.4e-262  855.3   0.0   1.1e-261  855.1   0.0    1.0  1  lcl|NCBI__GCF_000092885.1:WP_013088923.1  BC1002_RS04655 acetolactate synt


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092885.1:WP_013088923.1  BC1002_RS04655 acetolactate synthase 3 large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  855.1   0.0  1.1e-261  1.1e-261       3     554 ..      23     581 ..      21     584 .. 0.98

  Alignments for each domain:
  == domain 1  score: 855.1 bits;  conditional E-value: 1.1e-261
                                 TIGR00118   3 gaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlat 70 
                                               ga++l+++l +e+ve ++GyPGG+vl iyd+ly +++++h+lvrheqaa+haad yar++GkvGv+l+t
  lcl|NCBI__GCF_000092885.1:WP_013088923.1  23 GATVLMKALADEDVEFIWGYPGGSVLYIYDELYkQDKFQHVLVRHEQAAVHAADAYARSTGKVGVCLVT 91 
                                               899******************************999********************************* PP

                                 TIGR00118  71 sGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilk 139
                                               sGPG tn+vtgiatay+ds+P+vv++Gqv+t++iG+dafqe+d +Git+p++kh+flvk+++dl++++k
  lcl|NCBI__GCF_000092885.1:WP_013088923.1  92 SGPGVTNAVTGIATAYMDSIPMVVISGQVPTAAIGQDAFQECDTVGITRPCVKHNFLVKDVRDLAATVK 160
                                               ********************************************************************* PP

                                 TIGR00118 140 eafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvG 208
                                               +af+ia tGrPGPvl+d+Pkdv++a +++e  ++v+l++y+p +kgh  qi+ka+ l+ +ak+P ++ G
  lcl|NCBI__GCF_000092885.1:WP_013088923.1 161 KAFYIARTGRPGPVLIDIPKDVSKAPCQYEPIKSVSLRSYNPVTKGHSGQIRKAVSLLLSAKRPYIYTG 229
                                               ********************************************************************* PP

                                 TIGR00118 209 gGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarf 277
                                               gG++ a+as+el+++a+ l  pvt tl+GlG++ + ++++lgmlGmhGt+ean+a++++d+lia+Garf
  lcl|NCBI__GCF_000092885.1:WP_013088923.1 230 GGIVLADASRELNQFADLLGYPVTNTLMGLGGYRSSDKKFLGMLGMHGTYEANMAMQHCDVLIAIGARF 298
                                               ********************************************************************* PP

                                 TIGR00118 278 ddrvtgnlakfapea.kiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke.Wl 340
                                               ddrv g+ ++fa++  kiihididP++i+k vkvdipivGd+k+vl+el+++l++     ++     W+
  lcl|NCBI__GCF_000092885.1:WP_013088923.1 299 DDRVIGDPNHFASRPrKIIHIDIDPSSISKRVKVDIPIVGDVKEVLKELIEQLQTAehgpDTAALAdWW 367
                                               ************98626***********************************999866653333335** PP

                                 TIGR00118 341 ekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGl 409
                                               + ie w+++ +lk+d++++ ikPq+v+++ ++l++++a+v +dvGqhqmwaaqfyk++kpr++i+sgGl
  lcl|NCBI__GCF_000092885.1:WP_013088923.1 368 KDIEGWRAKDCLKFDRKSDIIKPQYVVEKAWELTDGNAFVCSDVGQHQMWAAQFYKFNKPRHWINSGGL 436
                                               ********************************************************************* PP

                                 TIGR00118 410 GtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfy 478
                                               GtmGfGlPaa+G+k+a+p+++v+++tG+gs+qm +qelst+++yd+p+ki+ lnn++lGmv+qWq++ y
  lcl|NCBI__GCF_000092885.1:WP_013088923.1 437 GTMGFGLPAAMGVKMAHPDDDVLCITGEGSIQMCIQELSTCKQYDLPIKIISLNNRYLGMVRQWQQIEY 505
                                               ********************************************************************* PP

                                 TIGR00118 479 eerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevlPmvap 546
                                               ++rys++++ + lpdfvklaeayG++g+rie+ +++e +lkeal+ k + v+ld++ d +e+v+Pmv  
  lcl|NCBI__GCF_000092885.1:WP_013088923.1 506 SKRYSHSYMDA-LPDFVKLAEAYGHVGMRIERTADVEPALKEALRLKdRTVFLDFQTDPTENVWPMVQA 573
                                               **********5.********************************988689******************* PP

                                 TIGR00118 547 Gagldelv 554
                                               G+g++e++
  lcl|NCBI__GCF_000092885.1:WP_013088923.1 574 GKGITEML 581
                                               ******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (587 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: 00:00:00.03
# Mc/sec: 10.53
//
[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