Alignments for a candidate for ilvI in Beijerinckia indica subsp. indica ATCC 9039

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Beijerinckia indica subsp. indica ATCC 9039

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_012385382.1 BIND_RS12235 acetolactate synthase 3 large subunit

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



>NCBI__GCF_000019845.1:WP_012385382.1
          Length = 586

 Score =  621 bits (1602), Expect = 0.0
 Identities = 314/566 (55%), Positives = 410/566 (72%), Gaps = 5/566 (0%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           +M GA+++V AL ++GV+ ++GYPGGAVL IYD L  Q   +H+LVRHEQ AVHAA+GYA
Sbjct: 4   KMTGAQMVVTALKDQGVDTIFGYPGGAVLPIYDALFHQNSVKHVLVRHEQGAVHAAEGYA 63

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           R++GK+GV LVTSGPG TNAVTG+  A LDSIP+V ITG VPTH IG DAFQECDTVGIT
Sbjct: 64  RSSGKIGVVLVTSGPGATNAVTGLTDALLDSIPLVCITGQVPTHLIGSDAFQECDTVGIT 123

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
           R   KHN+LV+ V DL   + +AF++A  GRPGPVV+DIPKDV      Y  P++I+ ++
Sbjct: 124 RHCTKHNYLVRQVEDLPRILHEAFYVAQHGRPGPVVIDIPKDVQFALGLYAGPENIEHKT 183

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLA--NASDELRQLAALTGHPVTNTLM 255
           Y P  KG  G+I +A++ +  A+RP  YTGGG++ +   AS  LR+L  LTG P+T+TLM
Sbjct: 184 YKPAFKGDLGRIDEALSWIAAAKRPIFYTGGGIINSGPEASALLRELVDLTGAPITSTLM 243

Query: 256 GLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKII 315
           GLGA+P +S +++GMLGMHGTYEAN AM +CD++IAIGARFDDR+ G    F+  +RK I
Sbjct: 244 GLGAYPASSPRWLGMLGMHGTYEANNAMHDCDLMIAIGARFDDRITGRIDAFSPGSRK-I 302

Query: 316 HIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVD 375
           HIDIDPSSI+K VKVD+ IVG+   VL++++A+ K   +      L KWW++I+ WR+  
Sbjct: 303 HIDIDPSSINKTVKVDLGIVGDCTAVLRDMVARWKERHLACDAAVLQKWWQEIDHWRARK 362

Query: 376 CLKYDRSSEIIKPQYVVEKIWELTKG-DAFICSDVGQHQMWAAQFYKFDEPRRWINSGGL 434
            L Y  S+++IKPQY +++++ELT+G D +I ++VGQHQMWAAQ Y FDEP RW+ SGGL
Sbjct: 363 SLAYRASNKVIKPQYAIQRLFELTRGRDTYISTEVGQHQMWAAQHYHFDEPNRWMTSGGL 422

Query: 435 GTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGM 494
           GTMG GLP A+G + A P   VV I GE SI M IQELST +Q+  PVKI  LNN Y+GM
Sbjct: 423 GTMGYGLPAAIGAQMAHPGSLVVDIAGEASILMNIQELSTAVQFRLPVKIFILNNQYMGM 482

Query: 495 VRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVF 554
           VRQWQE+ +  RYS SY +ALPDFVKLAEAYG  G+R    + ++ A+ E      + V 
Sbjct: 483 VRQWQELLHGGRYSESYSEALPDFVKLAEAYGCHGIRCADPNTLDAAILEMIE-TPKPVL 541

Query: 555 LDFQTDPTENVWPMVQAGKGISEMLL 580
            D   D  EN  PM+ +GK  +EM+L
Sbjct: 542 FDCIVDREENCLPMIPSGKAHNEMIL 567


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: 959
Number of extensions: 27
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: 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 WP_012385382.1 BIND_RS12235 (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.2140208.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.8e-244  797.6   0.0   3.2e-244  797.4   0.0    1.0  1  NCBI__GCF_000019845.1:WP_012385382.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000019845.1:WP_012385382.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  797.4   0.0  3.2e-244  3.2e-244       1     555 [.       5     567 ..       5     569 .. 0.98

  Alignments for each domain:
  == domain 1  score: 797.4 bits;  conditional E-value: 3.2e-244
                             TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsG 72 
                                           ++ga+++v +lk++gv+t+fGyPGGavlpiydal+ ++ ++h+lvrheq+a+haa+Gyar+sGk+Gvvl+tsG
  NCBI__GCF_000019845.1:WP_012385382.1   5 MTGAQMVVTALKDQGVDTIFGYPGGAVLPIYDALFhQNSVKHVLVRHEQGAVHAAEGYARSSGKIGVVLVTSG 77 
                                           79********************************98999********************************** PP

                             TIGR00118  73 PGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeia 145
                                           PGatn+vtg+++a lds+Plv +tGqv+t+liGsdafqe+d +Git+ +tkh++lv+++edlp+il+eaf++a
  NCBI__GCF_000019845.1:WP_012385382.1  78 PGATNAVTGLTDALLDSIPLVCITGQVPTHLIGSDAFQECDTVGITRHCTKHNYLVRQVEDLPRILHEAFYVA 150
                                           ************************************************************************* PP

                             TIGR00118 146 stGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviia..ea 216
                                           + GrPGPv++d+Pkdv+ a   +  +e++e ++ykp  kg+  +i +al  i++ak+P+ + GgG+i +  ea
  NCBI__GCF_000019845.1:WP_012385382.1 151 QHGRPGPVVIDIPKDVQFALGLYAGPENIEHKTYKPAFKGDLGRIDEALSWIAAAKRPIFYTGGGIINSgpEA 223
                                           *******************************************************************874469 PP

                             TIGR00118 217 seelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfa 289
                                           s+ l+el++ + +p+t+tl+GlGa+p+  p+ lgmlGmhGt+ean a++++dl+ia+Garfddr+tg ++ f+
  NCBI__GCF_000019845.1:WP_012385382.1 224 SALLRELVDLTGAPITSTLMGLGAYPASSPRWLGMLGMHGTYEANNAMHDCDLMIAIGARFDDRITGRIDAFS 296
                                           99*********************************************************************** PP

                             TIGR00118 290 peakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke.Wlekieewkkeyilkldee 357
                                           p ++ ihididP++i+k+vkvd+ ivGd++ vl++++++ ke+    +    + W+++i++w++++ l++  +
  NCBI__GCF_000019845.1:WP_012385382.1 297 PGSRKIHIDIDPSSINKTVKVDLGIVGDCTAVLRDMVARWKERhlacDAAVLQkWWQEIDHWRARKSLAYRAS 369
                                           ***************************************999977764444455******************* PP

                             TIGR00118 358 eesikPqkvikelskllkd.eaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpee 429
                                           ++ ikPq+ i++l +l+++ +++++t+vGqhqmwaaq+y++++p++++tsgGlGtmG+GlPaa+Ga++a+p +
  NCBI__GCF_000019845.1:WP_012385382.1 370 NKVIKPQYAIQRLFELTRGrDTYISTEVGQHQMWAAQHYHFDEPNRWMTSGGLGTMGYGLPAAIGAQMAHPGS 442
                                           *****************9989**************************************************** PP

                             TIGR00118 430 tvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayG 502
                                            vv+++G++s+ mn+qelst+v++ +pvki ilnn+++Gmv+qWqel++ +ryse++ ++ lpdfvklaeayG
  NCBI__GCF_000019845.1:WP_012385382.1 443 LVVDIAGEASILMNIQELSTAVQFRLPVKIFILNNQYMGMVRQWQELLHGGRYSESYSEA-LPDFVKLAEAYG 514
                                           **********************************************************95.************ PP

                             TIGR00118 503 vkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldelve 555
                                            +gir ++p+ l++++ e++e+ +pvl+d  vd+ee++lPm+++G++ +e++ 
  NCBI__GCF_000019845.1:WP_012385382.1 515 CHGIRCADPNTLDAAILEMIETPKPVLFDCIVDREENCLPMIPSGKAHNEMIL 567
                                           ***************************************************96 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 33.13
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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