Alignments for a candidate for ilvI in Allochromatium vinosum DSM 180

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Allochromatium vinosum DSM 180

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_012971780.1 ALVIN_RS12990 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_000025485.1:WP_012971780.1
          Length = 577

 Score =  411 bits (1056), Expect = e-119
 Identities = 249/582 (42%), Positives = 340/582 (58%), Gaps = 37/582 (6%)

Query: 21  GAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKF-----EHILVRHEQAAVHAADG 75
           GA IL+  L + GVE ++G+ GGAV+ I+ E++K+ +        +L R E  A HAA+G
Sbjct: 8   GAAILLDVLNDLGVETIFGHTGGAVIPIHVEINKRLRAGTPVPRFVLCRQEGGAGHAAEG 67

Query: 76  YARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVG 135
           YARA+G+VGVAL TSGPG TN +T IA AY DS+P + ITG VP+ AIG DAFQE D VG
Sbjct: 68  YARASGRVGVALATSGPGATNLITPIADAYKDSLPTLFITGQVPSRAIGTDAFQEVDMVG 127

Query: 136 ITRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDM 195
           +TRPI KHN+LVKDV DL   +++A  +A  GRPGPVVVDI KDV   A +      +  
Sbjct: 128 LTRPISKHNYLVKDVADLEWVLREAHALAMHGRPGPVVVDICKDVQLTALETANVPRVRH 187

Query: 196 RSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLM 255
           R     +   +  I +A+A    AERP +  GGGV+ ANA+  L++ A     PVT T  
Sbjct: 188 RESVDFDAARADAILEALA---RAERPVVKAGGGVIHANAALALQRFAERFDVPVTTTFN 244

Query: 256 GLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKII 315
            LGA P      +GM GMHGT  AN A+++ D+++++G RFDDRV        ++ ++I 
Sbjct: 245 ALGALPFELAYNLGMPGMHGTVPANYALRDADLILSLGGRFDDRV---AVRGFAEGKRIA 301

Query: 316 HIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVD 375
           H+DIDPS I K +  D+ +V      L E +A   AS    +     +W   I +WR   
Sbjct: 302 HVDIDPSEIDKTIATDLNLVA----TLDEFLAHALASGRSARH---PEWMTLIGEWRQRM 354

Query: 376 CLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLG 435
              Y + SE IKPQ  +E I +LT G+A + + VGQHQMW+AQ+Y+F  PR+WI+SGGLG
Sbjct: 355 MPPYGQ-SEYIKPQAAIEVISDLTGGEATLVTGVGQHQMWSAQYYRFRRPRQWISSGGLG 413

Query: 436 TMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMV 495
           TMG GLP A+G     P   VV I G+GS QM IQEL T +    P+KI  LNN +LGMV
Sbjct: 414 TMGFGLPAAIGAWYGDPTHPVVLIDGDGSFQMNIQELGTVVANRIPLKIFVLNNSFLGMV 473

Query: 496 RQWQEIEYDNRYSHSYM----DALPDFVKLAE----------AYGHVGMRVEKTSDVEP- 540
           RQW+++  D  +  + +    D  PD + L +             HV  R++     +P 
Sbjct: 474 RQWEDMMDDGHHYETCLARTADCDPDCIDLDQGCRRQIPNLTGLKHVYPRLKTVRLRDPE 533

Query: 541 ALRE---AFRLKDRTVFLDFQTDPTENVWPMVQAGKGISEML 579
            LRE   A   +   V +D   D  ENV PM++ G  + +M+
Sbjct: 534 TLREDIAAVLAEPGPVLVDVWIDKAENVIPMIRPGHSLEQMI 575


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: 909
Number of extensions: 43
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: 585
Length of database: 577
Length adjustment: 36
Effective length of query: 549
Effective length of database: 541
Effective search space:   297009
Effective search space used:   297009
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_012971780.1 ALVIN_RS12990 (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.1396.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.7e-181  589.7   0.0     1e-180  587.8   0.0    1.7  1  lcl|NCBI__GCF_000025485.1:WP_012971780.1  ALVIN_RS12990 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025485.1:WP_012971780.1  ALVIN_RS12990 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  587.8   0.0    1e-180    1e-180       2     555 ..       7     576 ..       6     577 .] 0.91

  Alignments for each domain:
  == domain 1  score: 587.8 bits;  conditional E-value: 1e-180
                                 TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly......dselehilvrheqaaahaadGyarasGkv 64 
                                               +ga il++ l++ gvet+fG+ GGav+pi+ ++       +   +++l r e +a haa+GyarasG+v
  lcl|NCBI__GCF_000025485.1:WP_012971780.1   7 TGAAILLDVLNDLGVETIFGHTGGAVIPIHVEINkrlragTPVPRFVLCRQEGGAGHAAEGYARASGRV 75 
                                               79****************************999866643222348************************ PP

                                 TIGR00118  65 GvvlatsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaed 133
                                               Gv+latsGPGatnl+t+ia+ay ds+P + +tGqv++++iG+dafqe+d++G+t+p+ kh++lvk+++d
  lcl|NCBI__GCF_000025485.1:WP_012971780.1  76 GVALATSGPGATNLITPIADAYKDSLPTLFITGQVPSRAIGTDAFQEVDMVGLTRPISKHNYLVKDVAD 144
                                               ********************************************************************* PP

                                 TIGR00118 134 lpeilkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakk 202
                                               l  +l+ea  +a  GrPGPv+vd+ kdv+ +++e+    +v    ++  v  + ++  ++le++++a++
  lcl|NCBI__GCF_000025485.1:WP_012971780.1 145 LEWVLREAHALAMHGRPGPVVVDICKDVQLTALETANVPRVR---HRESVDFDAARADAILEALARAER 210
                                               ******************************999988776665...566788888999999********* PP

                                 TIGR00118 203 PvllvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlli 271
                                               Pv+ +GgGvi+a+a   l+++aer+++pvttt+  lGa+p +    lgm GmhGt  an+a+++adl++
  lcl|NCBI__GCF_000025485.1:WP_012971780.1 211 PVVKAGGGVIHANAALALQRFAERFDVPVTTTFNALGALPFELAYNLGMPGMHGTVPANYALRDADLIL 279
                                               ********************************************************************* PP

                                 TIGR00118 272 avGarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWl 340
                                               ++G rfddrv+  ++ fa+  +i h+didP+ei+k++++d+ +v    + l++ l+  ++ ++ e  W+
  lcl|NCBI__GCF_000025485.1:WP_012971780.1 280 SLGGRFDDRVA--VRGFAEGKRIAHVDIDPSEIDKTIATDLNLVATLDEFLAHALASGRSARHPE--WM 344
                                               *********96..99*****************************998888888777766655555..** PP

                                 TIGR00118 341 ekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGl 409
                                                 i ew++++++ +  ++e ikPq+ i+ +s l+ +ea + t+vGqhqmw+aq+y++++pr++i+sgGl
  lcl|NCBI__GCF_000025485.1:WP_012971780.1 345 TLIGEWRQRMMPPYG-QSEYIKPQAAIEVISDLTGGEATLVTGVGQHQMWSAQYYRFRRPRQWISSGGL 412
                                               **********98876.5678************************************************* PP

                                 TIGR00118 410 GtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfy 478
                                               GtmGfGlPaa+Ga  + p + vv ++Gdgsfqmn+qel t+v   ip+ki +lnn++lGmv+qW +++ 
  lcl|NCBI__GCF_000025485.1:WP_012971780.1 413 GTMGFGLPAAIGAWYGDPTHPVVLIDGDGSFQMNIQELGTVVANRIPLKIFVLNNSFLGMVRQWEDMMD 481
                                               ********************************************************************9 PP

                                 TIGR00118 479 eerysetklase...lpdfvklaea........yG.......vkgiriekpeeleeklkealeskepvl 529
                                               ++ + et+la      pd + l ++         G       +k++r+++pe l e ++ +l++ +pvl
  lcl|NCBI__GCF_000025485.1:WP_012971780.1 482 DGHHYETCLARTadcDPDCIDLDQGcrrqipnlTGlkhvyprLKTVRLRDPETLREDIAAVLAEPGPVL 550
                                               99999999875311245555543331111111123111111357899********************** PP

                                 TIGR00118 530 ldvevdkeeevlPmvapGagldelve 555
                                               +dv +dk e+v+Pm+ pG++l++++e
  lcl|NCBI__GCF_000025485.1:WP_012971780.1 551 VDVWIDKAENVIPMIRPGHSLEQMIE 576
                                               ************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (577 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: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.06
# Mc/sec: 4.99
//
[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