Alignments for a candidate for ilvI in Heliobacterium modesticaldum Ice1; ATCC 51547

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Heliobacterium modesticaldum Ice1; ATCC 51547

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_041313651.1 HM1_RS08905 acetolactate synthase, large subunit, biosynthetic type

Query= BRENDA::P9WG41
         (618 letters)



>NCBI__GCF_000019165.1:WP_041313651.1
          Length = 565

 Score =  546 bits (1407), Expect = e-160
 Identities = 287/564 (50%), Positives = 380/564 (67%), Gaps = 6/564 (1%)

Query: 37  QLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVRHEQGAGHAASGYA 96
           ++TGAQA++ SLE+ GV++IFG PGG VLP+YD L+D K LRHVL RHEQGA HAA GYA
Sbjct: 2   KMTGAQAIVTSLEKEGVELIFGYPGGQVLPLYDALYDCK-LRHVLTRHEQGAAHAADGYA 60

Query: 97  HVTGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADISGIT 156
             TG+VGVC ATSGPGATNL+T +A A MDS+P+V ITGQV   +IG D+FQEADI+GIT
Sbjct: 61  RATGKVGVCFATSGPGATNLITGIATAYMDSVPMVCITGQVPLSVIGKDSFQEADITGIT 120

Query: 157 MPITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFSWPPRMELPG 216
            PITKHN+LV++  D+PRV+ EAF+IA +GRPG V++D+PK ++     F +P  + L G
Sbjct: 121 APITKHNYLVKNAKDLPRVIKEAFYIARTGRPGPVVIDVPKCLMTTTIDFEYPETVRLRG 180

Query: 217 YKPNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVTTLMAR 276
           YKP  +  + +V   A+ +A A+KP+ +VGGGVI  EA   LR + +   IP++ +LM  
Sbjct: 181 YKPQAEGKAAEVEAVAQALAEAKKPLFFVGGGVINAEAAPLLRRIVKTHRIPLIGSLMGL 240

Query: 277 GAFPDSHRQNLGMPGMHGTVAAVAALQRSDLLIALGTRFDDRVTGKLDSFAPEAKVIHAD 336
           GA P +    LGM GMHGTVAA  A+   DLL+ +G RFDDRVTG L  FA  A+V H D
Sbjct: 241 GAIPVTDPLFLGMVGMHGTVAANRAVMECDLLVGIGVRFDDRVTGLLTRFAANARVAHFD 300

Query: 337 IDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPGTIEMADWWAYLNGVRKTYPLSY 396
           ID AE+ KN  AD+ +VGD++  +  L + +      G     DW   +    +  PLSY
Sbjct: 301 IDRAEVNKNVVADLAVVGDLRWSLAALESAMADLAGEGGRRWEDWRLQVTRWSEEAPLSY 360

Query: 397 GPQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFIRYEKPRSWLNSGGLGTMG 456
             +SD  + P+ VIE++      +AV V  VGQHQMWAAQ+ R+++PRS++ SGGLGTMG
Sbjct: 361 -QKSDDVIKPQSVIEEIDRQTKSEAVIVTDVGQHQMWAAQYYRFQRPRSFITSGGLGTMG 419

Query: 457 FAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATCAVEGIPVKVALINNGNLGMVRQW 516
           + +PAA+GA++  P   V  I GDG F M  QELAT     +P+K+A++NN  LGMVRQW
Sbjct: 420 YGLPAAIGAQMGQPNKSVVLISGDGSFLMNCQELATAVEHRLPLKMAILNNNVLGMVRQW 479

Query: 517 QSLFYAERYSQTDLATHSHRIPDFVKLAEALGCVGLRCEREEDVVDVINQARAINDCPVV 576
           Q LF+ +RYS T  A       D+V+LAEA G  GLR ER E++ +VI +A A  + PVV
Sbjct: 480 QKLFFNQRYSYTRFANGG---TDYVRLAEAFGATGLRAERPEEMPEVIAKALA-TEGPVV 535

Query: 577 IDFIVGADAQVWPMVAAGTSNDEI 600
           +D  V AD  V PMV AG   D++
Sbjct: 536 MDIRVCADENVLPMVPAGAPLDQM 559


Lambda     K      H
   0.319    0.136    0.414 

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: 976
Number of extensions: 48
Number of successful extensions: 5
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: 618
Length of database: 565
Length adjustment: 37
Effective length of query: 581
Effective length of database: 528
Effective search space:   306768
Effective search space used:   306768
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_041313651.1 HM1_RS08905 (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.19020.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.7e-248  809.4   0.1   8.9e-248  809.2   0.1    1.0  1  lcl|NCBI__GCF_000019165.1:WP_041313651.1  HM1_RS08905 acetolactate synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000019165.1:WP_041313651.1  HM1_RS08905 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  809.2   0.1  8.9e-248  8.9e-248       1     555 [.       3     561 ..       3     563 .. 0.98

  Alignments for each domain:
  == domain 1  score: 809.2 bits;  conditional E-value: 8.9e-248
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               ++ga+++v sl+kegve +fGyPGG+vlp+ydalyd +l+h+l+rheq+aahaadGyara+GkvGv++a
  lcl|NCBI__GCF_000019165.1:WP_041313651.1   3 MTGAQAIVTSLEKEGVELIFGYPGGQVLPLYDALYDCKLRHVLTRHEQGAAHAADGYARATGKVGVCFA 71 
                                               79******************************************************************* PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPGatnl+tgiatay+dsvP+v +tGqv+ s+iG+d+fqe+di+Git p+tkh++lvk+a+dlp+++
  lcl|NCBI__GCF_000019165.1:WP_041313651.1  72 TSGPGATNLITGIATAYMDSVPMVCITGQVPLSVIGKDSFQEADITGITAPITKHNYLVKNAKDLPRVI 140
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207
                                               keaf+ia tGrPGPv++d+Pk +++++i++e++e+v l+gykp+ +g+ + ++++++++++akkP+ +v
  lcl|NCBI__GCF_000019165.1:WP_041313651.1 141 KEAFYIARTGRPGPVVIDVPKCLMTTTIDFEYPETVRLRGYKPQAEGKAAEVEAVAQALAEAKKPLFFV 209
                                               ********************************************************************* PP

                                 TIGR00118 208 GgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGar 276
                                               GgGvi aea   l++++++ +ip++ +l+GlGa+p ++pl+lgm+GmhGt +an av e+dll+++G+r
  lcl|NCBI__GCF_000019165.1:WP_041313651.1 210 GGGVINAEAAPLLRRIVKTHRIPLIGSLMGLGAIPVTDPLFLGMVGMHGTVAANRAVMECDLLVGIGVR 278
                                               ********************************************************************* PP

                                 TIGR00118 277 fddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkekeWle 341
                                               fddrvtg l++fa++a++ h+did ae++knv +d+++vGd +  l+ l +++ +      ++ ++W  
  lcl|NCBI__GCF_000019165.1:WP_041313651.1 279 FDDRVTGLLTRFAANARVAHFDIDRAEVNKNVVADLAVVGDLRWSLAALESAMADLagegGRRWEDWRL 347
                                               *********************************************999998888876655444456999 PP

                                 TIGR00118 342 kieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlG 410
                                               ++++w +e +l+++++++ ikPq+vi+e+ +++k ea++ tdvGqhqmwaaq+y++++pr+fitsgGlG
  lcl|NCBI__GCF_000019165.1:WP_041313651.1 348 QVTRWSEEAPLSYQKSDDVIKPQSVIEEIDRQTKSEAVIVTDVGQHQMWAAQYYRFQRPRSFITSGGLG 416
                                               ********************************************************************* PP

                                 TIGR00118 411 tmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfye 479
                                               tmG+GlPaa+Ga++++p+++vv ++Gdgsf mn+qel+t+ve  +p+k+ ilnn++lGmv+qWq+lf++
  lcl|NCBI__GCF_000019165.1:WP_041313651.1 417 TMGYGLPAAIGAQMGQPNKSVVLISGDGSFLMNCQELATAVEHRLPLKMAILNNNVLGMVRQWQKLFFN 485
                                               ********************************************************************* PP

                                 TIGR00118 480 erysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGa 548
                                               +rys t +a++ +d+v+laea+G++g+r e+pee+ e +++al++++pv++d++v  +e+vlPmv+ Ga
  lcl|NCBI__GCF_000019165.1:WP_041313651.1 486 QRYSYTRFANGGTDYVRLAEAFGATGLRAERPEEMPEVIAKALATEGPVVMDIRVCADENVLPMVPAGA 554
                                               ********************************************************************* PP

                                 TIGR00118 549 gldelve 555
                                                ld++++
  lcl|NCBI__GCF_000019165.1:WP_041313651.1 555 PLDQMIN 561
                                               *****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (565 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 0.02s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 7.73
//
[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