Alignments for a candidate for ilvI in Clostridium acetobutylicum ATCC 824

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Clostridium acetobutylicum ATCC 824

Align acetohydroxy-acid synthase large subunit (EC 2.2.1.6) (characterized)
to candidate NP_349766.1 CA_C3169 acetolactate synthase large subunit

Query= metacyc::MONOMER-11900
         (599 letters)



>NCBI__GCF_000008765.1:NP_349766.1
          Length = 554

 Score =  495 bits (1275), Expect = e-144
 Identities = 267/573 (46%), Positives = 369/573 (64%), Gaps = 29/573 (5%)

Query: 2   NGAEAMIKALEAEKVEILFGYPGGALLPFYDALHH-SDLIHLLTRHEQAAAHAADGYARA 60
           NG+  +++ L+ + V+ +FGYPGGA+L  +DAL+  S++  +LT HEQ A+HAADGYARA
Sbjct: 4   NGSRIILECLKEQGVDTIFGYPGGAVLNIFDALYSFSEIRCVLTSHEQGASHAADGYARA 63

Query: 61  SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMP 120
           +GKVGVC+ TSGPGATNLVTG+ATA+ DS PMVA+TGQV T LIG D+FQE+D   + MP
Sbjct: 64  TGKVGVCLATSGPGATNLVTGIATAYMDSVPMVAITGQVATSLIGKDSFQEVDITDITMP 123

Query: 121 IVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLI 180
           I KHNF ++K   + +  R AF IAQ+GRPGPV ID+PKDV   E + +    P K++  
Sbjct: 124 ITKHNFIVRKVEDLADTIRKAFYIAQSGRPGPVLIDIPKDVTGNECEYEPRK-PEKIEKS 182

Query: 181 GYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMG 240
                      +++ AI+L+  +KRP+I+ GGG  +S A++EL  L E L  PVC+T+MG
Sbjct: 183 SVRDA------EVEGAIELLLESKRPVIIVGGGCNISEASKELKILQEKLKCPVCSTMMG 236

Query: 241 KGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKIIHI 300
            G  S    +  GMVGMHGTK +N  + ESD++I+IGCRFSDR+T +  +FA NAKI+HI
Sbjct: 237 LGAFSGKDDMFTGMVGMHGTKASNKSICESDLVIAIGCRFSDRVTSNADTFAKNAKILHI 296

Query: 301 DIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIE-NVNSL 359
           DID AE+ KN+  D  I+GD + +LK+V ++L       ++E N      +W E  +  L
Sbjct: 297 DIDEAEVSKNIKADSFIIGDVEEVLKKVNEKL------TAREGN------EWTEYALGLL 344

Query: 360 KKSSIPVMDYDDI-PIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQTP 418
           KK    V+  +    + P  ++K+L  + D        IITT+VGQNQ+W    +    P
Sbjct: 345 KKDKSKVLRINKCDSVNPVYVIKKLYELTDG-----EAIITTEVGQNQIWATQGYIYTKP 399

Query: 419 RSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVIC 478
           RSF++SGGLGTMG+GF +AIGA V K D     I GDG F MN  EL T+  Y +PV I 
Sbjct: 400 RSFITSGGLGTMGYGFGAAIGASVGK-DKMTFDIAGDGSFRMNINELATVVRYKLPVKII 458

Query: 479 IFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKEA 538
           + +N  LGMV QWQNLFY KR  S       DF+K+AE YG    R+++   +  ALK+A
Sbjct: 459 VLNNNVLGMVRQWQNLFYKKRYSSTTLERDTDFVKIAEGYGALGLRVDTNAGVESALKKA 518

Query: 539 INCDEPYLLDFAI-DPSSALSMVPPGAKLTNII 570
           I+ D P ++DF + +   A  +VPPGA + N++
Sbjct: 519 IDYDGPVVIDFTVGEDEMATPIVPPGADIENMV 551


Lambda     K      H
   0.319    0.137    0.405 

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: 818
Number of extensions: 21
Number of successful extensions: 6
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: 599
Length of database: 554
Length adjustment: 36
Effective length of query: 563
Effective length of database: 518
Effective search space:   291634
Effective search space used:   291634
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 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate NP_349766.1 CA_C3169 (acetolactate synthase 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.17637.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
   1.1e-224  732.9   1.0   1.3e-224  732.7   1.0    1.0  1  lcl|NCBI__GCF_000008765.1:NP_349766.1  CA_C3169 acetolactate synthase l


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000008765.1:NP_349766.1  CA_C3169 acetolactate synthase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  732.7   1.0  1.3e-224  1.3e-224       2     555 ..       4     552 ..       3     554 .] 0.96

  Alignments for each domain:
  == domain 1  score: 732.7 bits;  conditional E-value: 1.3e-224
                              TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsG 72 
                                            +g++i++e lk++gv+t+fGyPGGavl+i+daly  se++ +l+ heq+a+haadGyara+GkvGv+latsG
  lcl|NCBI__GCF_000008765.1:NP_349766.1   4 NGSRIILECLKEQGVDTIFGYPGGAVLNIFDALYsFSEIRCVLTSHEQGASHAADGYARATGKVGVCLATSG 75 
                                            5899******************************88************************************ PP

                              TIGR00118  73 PGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafei 144
                                            PGatnlvtgiatay+dsvP+v++tGqvatsliG+d+fqe+di+ it+p+tkh+f+v+k+edl+ ++++af+i
  lcl|NCBI__GCF_000008765.1:NP_349766.1  76 PGATNLVTGIATAYMDSVPMVAITGQVATSLIGKDSFQEVDITDITMPITKHNFIVRKVEDLADTIRKAFYI 147
                                            ************************************************************************ PP

                              TIGR00118 145 astGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaea 216
                                            a++GrPGPvl+d+Pkdvt +e+e+e ++         + + + + ++ a+el+ ++k+Pv++vGgG  i+ea
  lcl|NCBI__GCF_000008765.1:NP_349766.1 148 AQSGRPGPVLIDIPKDVTGNECEYEPRKP----EKIEKSSVRDAEVEGAIELLLESKRPVIIVGGGCNISEA 215
                                            ************************99843....3344556677899************************** PP

                              TIGR00118 217 seelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakf 288
                                            s+elk l e+lk pv++t++GlGaf  ++  + gm+GmhGtk++n ++ e+dl+ia+G+rf+drvt+n ++f
  lcl|NCBI__GCF_000008765.1:NP_349766.1 216 SKELKILQEKLKCPVCSTMMGLGAFSGKDDMFTGMVGMHGTKASNKSICESDLVIAIGCRFSDRVTSNADTF 287
                                            ************************************************************************ PP

                              TIGR00118 289 apeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlek.ieewkkeyilkld.eee 358
                                            a++aki+hidid ae++kn+k+d  i+Gd+++vl+++ +kl+++e +e  W+e  +  +kk++   l  ++ 
  lcl|NCBI__GCF_000008765.1:NP_349766.1 288 AKNAKILHIDIDEAEVSKNIKADSFIIGDVEEVLKKVNEKLTAREGNE--WTEYaLGLLKKDKSKVLRiNKC 357
                                            ******************************************999888..9875256677777766651455 PP

                              TIGR00118 359 esikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeet 430
                                            +s++P +vik+l++l+++eai+tt+vGq+q+wa+q y ++kpr+fitsgGlGtmG+G+ aa+Ga v+k+ + 
  lcl|NCBI__GCF_000008765.1:NP_349766.1 358 DSVNPVYVIKKLYELTDGEAIITTEVGQNQIWATQGYIYTKPRSFITSGGLGTMGYGFGAAIGASVGKD-KM 428
                                            78****************************************************************975.66 PP

                              TIGR00118 431 vvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayG 502
                                              +++Gdgsf mn++el+t+v+y++pvki++lnn++lGmv+qWq+lfy++rys+t+l+   +dfvk+ae+yG
  lcl|NCBI__GCF_000008765.1:NP_349766.1 429 TFDIAGDGSFRMNINELATVVRYKLPVKIIVLNNNVLGMVRQWQNLFYKKRYSSTTLER-DTDFVKIAEGYG 499
                                            78********************************************************5.9*********** PP

                              TIGR00118 503 vkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldelve 555
                                            + g+r+ +++ +e++lk+a+  ++pv++d++v ++e + P+v+pGa ++++v 
  lcl|NCBI__GCF_000008765.1:NP_349766.1 500 ALGLRVDTNAGVESALKKAIDYDGPVVIDFTVGEDEMATPIVPPGADIENMVV 552
                                            **************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (554 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: 10.47
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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