Alignments for a candidate for ilvI in Cupriavidus basilensis 4G11

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Cupriavidus basilensis 4G11

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate RR42_RS05435 RR42_RS05435 acetolactate synthase 3 catalytic subunit

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



>FitnessBrowser__Cup4G11:RR42_RS05435
          Length = 586

 Score = 1132 bits (2929), Expect = 0.0
 Identities = 555/585 (94%), Positives = 575/585 (98%), Gaps = 1/585 (0%)

Query: 1   MPSAEFSHADSNSSAAPEMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEH 60
           MPSAEF HADSNSSAAPEMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDE +KQ K EH
Sbjct: 3   MPSAEF-HADSNSSAAPEMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDEFYKQKKIEH 61

Query: 61  ILVRHEQAAVHAADGYARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPT 120
           ILVRHEQAAVHAADGYARATGKVG ALVTSGPGVTNAVTGIATAYLDSIPMV+ITGNVPT
Sbjct: 62  ILVRHEQAAVHAADGYARATGKVGCALVTSGPGVTNAVTGIATAYLDSIPMVIITGNVPT 121

Query: 121 HAIGQDAFQECDTVGITRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDV 180
           HAIGQDAFQECDTVGITRPIVKHNFLVKDVRDLAATIKKAF+IAATGRPGPVVVDIPKDV
Sbjct: 122 HAIGQDAFQECDTVGITRPIVKHNFLVKDVRDLAATIKKAFYIAATGRPGPVVVDIPKDV 181

Query: 181 SRNACKYEYPKSIDMRSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELR 240
           SRN+CKYEYPKSIDMRSYNPVNKGHSGQIRKA+ALLQGAERP+IY GGGVVLANAS+ELR
Sbjct: 182 SRNSCKYEYPKSIDMRSYNPVNKGHSGQIRKALALLQGAERPFIYAGGGVVLANASEELR 241

Query: 241 QLAALTGHPVTNTLMGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRV 300
           QLAALTGHPVTNTLMGLG+FPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRV
Sbjct: 242 QLAALTGHPVTNTLMGLGSFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRV 301

Query: 301 IGNPAHFTSQARKIIHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREA 360
           IGNPAHFTSQ RKIIHIDIDPSSISKRVKVDIPIVG+VKDVLQELI+Q++ASD+KPKREA
Sbjct: 302 IGNPAHFTSQPRKIIHIDIDPSSISKRVKVDIPIVGHVKDVLQELISQLQASDVKPKREA 361

Query: 361 LAKWWEQIEQWRSVDCLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFY 420
           LAKWWEQIEQWRSVDCLKYDR+SEIIKPQYVVEKIWELT GDAF+CSDVGQHQMWAAQFY
Sbjct: 362 LAKWWEQIEQWRSVDCLKYDRNSEIIKPQYVVEKIWELTHGDAFVCSDVGQHQMWAAQFY 421

Query: 421 KFDEPRRWINSGGLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDT 480
           KF+EPRRWINSGGLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQM IQELSTCLQYDT
Sbjct: 422 KFNEPRRWINSGGLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMNIQELSTCLQYDT 481

Query: 481 PVKICSLNNGYLGMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEP 540
           PVKIC+LNN YLGMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGH+GMR+EKT+DVEP
Sbjct: 482 PVKICALNNRYLGMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHIGMRIEKTADVEP 541

Query: 541 ALREAFRLKDRTVFLDFQTDPTENVWPMVQAGKGISEMLLGAEDL 585
           ALREAFRLKDRTVFLDFQTDPTENVWPMVQAGKGISEMLLGAEDL
Sbjct: 542 ALREAFRLKDRTVFLDFQTDPTENVWPMVQAGKGISEMLLGAEDL 586


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: 1233
Number of extensions: 30
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: 586
Length adjustment: 37
Effective length of query: 548
Effective length of database: 549
Effective search space:   300852
Effective search space used:   300852
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 RR42_RS05435 RR42_RS05435 (acetolactate synthase 3 catalytic 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.1502.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.8e-261  852.5   0.3   7.8e-261  852.3   0.3    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS05435  RR42_RS05435 acetolactate syntha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS05435  RR42_RS05435 acetolactate synthase 3 catalytic subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  852.3   0.3  7.8e-261  7.8e-261       1     554 [.      20     580 ..      20     583 .. 0.98

  Alignments for each domain:
  == domain 1  score: 852.3 bits;  conditional E-value: 7.8e-261
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 
                                               + gaeilv++l +egve+v+GyPGGavl iyd++y ++++ehilvrheqaa+haadGyara+GkvG++l
  lcl|FitnessBrowser__Cup4G11:RR42_RS05435  20 MIGAEILVHALAEEGVEYVWGYPGGAVLYIYDEFYkQKKIEHILVRHEQAAVHAADGYARATGKVGCAL 88 
                                               679********************************9999****************************** PP

                                 TIGR00118  69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137
                                               +tsGPG tn+vtgiataylds+P+v++tG v+t++iG+dafqe+d +Git+p++kh+flvk+++dl+++
  lcl|FitnessBrowser__Cup4G11:RR42_RS05435  89 VTSGPGVTNAVTGIATAYLDSIPMVIITGNVPTHAIGQDAFQECDTVGITRPIVKHNFLVKDVRDLAAT 157
                                               ********************************************************************* PP

                                 TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvll 206
                                               +k+af+ia+tGrPGPv+vd+Pkdv+++++++e+++++++++y+p  kgh  qi+kal l++ a++P ++
  lcl|FitnessBrowser__Cup4G11:RR42_RS05435 158 IKKAFYIAATGRPGPVVVDIPKDVSRNSCKYEYPKSIDMRSYNPVNKGHSGQIRKALALLQGAERPFIY 226
                                               ********************************************************************* PP

                                 TIGR00118 207 vGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGa 275
                                               +GgGv+ a+aseel++la  +  pvt tl+GlG+fp + ++++gmlGmhGt+ean+a++++d+lia+Ga
  lcl|FitnessBrowser__Cup4G11:RR42_RS05435 227 AGGGVVLANASEELRQLAALTGHPVTNTLMGLGSFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGA 295
                                               ********************************************************************* PP

                                 TIGR00118 276 rfddrvtgnlakfapea.kiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke. 338
                                               rfddrv gn a+f+++  kiihididP++i+k vkvdipivG +k vl+el+++l++     +++    
  lcl|FitnessBrowser__Cup4G11:RR42_RS05435 296 RFDDRVIGNPAHFTSQPrKIIHIDIDPSSISKRVKVDIPIVGHVKDVLQELISQLQASdvkpKREALAk 364
                                               *************998626***********************************999877753333335 PP

                                 TIGR00118 339 WlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsg 407
                                               W+e+ie+w++  +lk+d+++e ikPq+v++++++l++++a+v +dvGqhqmwaaqfyk+++pr++i+sg
  lcl|FitnessBrowser__Cup4G11:RR42_RS05435 365 WWEQIEQWRSVDCLKYDRNSEIIKPQYVVEKIWELTHGDAFVCSDVGQHQMWAAQFYKFNEPRRWINSG 433
                                               ********************************************************************* PP

                                 TIGR00118 408 GlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqel 476
                                               GlGtmG GlP a+G+k a pe++vv++tG+gs+qmn+qelst+ +yd+pvki+ lnn++lGmv+qWqe+
  lcl|FitnessBrowser__Cup4G11:RR42_RS05435 434 GLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMNIQELSTCLQYDTPVKICALNNRYLGMVRQWQEI 502
                                               ********************************************************************* PP

                                 TIGR00118 477 fyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevlPmv 544
                                                y++rys++++ + lpdfvklaeayG+ g+riek +++e +l+ea++ k + v+ld++ d +e+v+Pmv
  lcl|FitnessBrowser__Cup4G11:RR42_RS05435 503 EYDNRYSHSYMDA-LPDFVKLAEAYGHIGMRIEKTADVEPALREAFRLKdRTVFLDFQTDPTENVWPMV 570
                                               ************5.********************************988689***************** PP

                                 TIGR00118 545 apGagldelv 554
                                                 G+g++e++
  lcl|FitnessBrowser__Cup4G11:RR42_RS05435 571 QAGKGISEML 580
                                               ********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (586 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: 12.81
//
[ok]

This GapMind analysis is from Apr 09 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