Alignments for a candidate for ilvI in Sphingomonas koreensis DSMZ 15582

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Sphingomonas koreensis DSMZ 15582

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate Ga0059261_0068 Ga0059261_0068 acetolactate synthase, large subunit (EC 2.2.1.6)

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



>FitnessBrowser__Korea:Ga0059261_0068
          Length = 581

 Score =  608 bits (1567), Expect = e-178
 Identities = 316/571 (55%), Positives = 393/571 (68%), Gaps = 7/571 (1%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           E  GA+IL+ A  + GVE ++GYPGGAVL IYD + +QTK  HILVRHEQAA HAA+GYA
Sbjct: 3   EKSGADILIEAFNDLGVEVIFGYPGGAVLPIYDAIFQQTKIRHILVRHEQAATHAAEGYA 62

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           RATGK GV LVTSGPG TNAVTGI  A +DSIPMVVITG VP+H IG DAFQE DTVGIT
Sbjct: 63  RATGKPGVVLVTSGPGATNAVTGITDALMDSIPMVVITGQVPSHLIGSDAFQEADTVGIT 122

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
           R   KHN+LVKD   L + + +AF IA +GRPGPVV+DIPKDV     +Y  P  I  ++
Sbjct: 123 RHCTKHNYLVKDPAHLGSIVHEAFHIATSGRPGPVVIDIPKDVQIATARYSKPGPIQHKT 182

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLA--NASDELRQLAALTGHPVTNTLM 255
           Y P  K     I  AV +L  AERP  YTGGGV+ +   AS  LR+LA +TG PVT+TLM
Sbjct: 183 YRPQVKADKALIESAVEMLAAAERPVFYTGGGVINSGPQASQLLRELARITGAPVTSTLM 242

Query: 256 GLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKII 315
           GLGAFP +S Q++GMLGMHGTYEAN AM   D+++AIGARFDDRV G    F   ARK I
Sbjct: 243 GLGAFPASSDQWLGMLGMHGTYEANYAMNQADLIVAIGARFDDRVTGRLDAFAPHARK-I 301

Query: 316 HIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVD 375
           HIDID SS++K V+VD+PIV +V   L+++I   KA   +  R  L++WW +IE WR+V 
Sbjct: 302 HIDIDRSSMNKTVRVDLPIVADVGHALEDMIRIWKAR--QHPRPDLSEWWSRIEGWRAVK 359

Query: 376 CLKYDRSSEIIKPQYVVEKIWELTKGDA-FICSDVGQHQMWAAQFYKFDEPRRWINSGGL 434
           CL +   S  I PQ  +  +WE T+  A  I ++VGQHQMWAAQ + F+ P +W+ SGGL
Sbjct: 360 CLDFPEDSNEIMPQRAIRALWEATRDQAPIITTEVGQHQMWAAQHFHFESPNKWLTSGGL 419

Query: 435 GTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGM 494
           GTMG GLP A+G +   P+  V+ I GE SIQM IQEL+T  QY  PVKI  LNN Y+GM
Sbjct: 420 GTMGYGLPAAIGAQLGHPDALVIDIAGEASIQMNIQELATATQYRLPVKIFILNNEYMGM 479

Query: 495 VRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVF 554
           VRQWQE+ Y +RYS SY DALPDFVKL EAYG  G+R+E    ++  +  A    D  V 
Sbjct: 480 VRQWQELTYSSRYSESYSDALPDFVKLGEAYGWEGIRIEGKDQLDDGI-AAMLAHDGPVI 538

Query: 555 LDFQTDPTENVWPMVQAGKGISEMLLGAEDL 585
           +D +     N +PM+ +G   ++MLL + ++
Sbjct: 539 VDCRVAKLANCFPMIPSGAAHTDMLLQSAEV 569


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: 951
Number of extensions: 37
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: 581
Length adjustment: 36
Effective length of query: 549
Effective length of database: 545
Effective search space:   299205
Effective search space used:   299205
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 Ga0059261_0068 Ga0059261_0068 (acetolactate synthase, large subunit (EC 2.2.1.6))
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.4451.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-243  795.4   0.1   1.6e-243  795.1   0.1    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_0068  Ga0059261_0068 acetolactate synt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_0068  Ga0059261_0068 acetolactate synthase, large subunit (EC 2.2.1.6)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  795.1   0.1  1.6e-243  1.6e-243       2     555 ..       5     564 ..       4     566 .. 0.97

  Alignments for each domain:
  == domain 1  score: 795.1 bits;  conditional E-value: 1.6e-243
                                 TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               +ga+il+e++++ gve++fGyPGGavlpiyda++ + +++hilvrheqaa+haa+Gyara+Gk+Gvvl+
  lcl|FitnessBrowser__Korea:Ga0059261_0068   5 SGADILIEAFNDLGVEVIFGYPGGAVLPIYDAIFqQTKIRHILVRHEQAATHAAEGYARATGKPGVVLV 73 
                                               79********************************999******************************** PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPGatn+vtgi++a +ds+P+vv+tGqv+++liGsdafqe+d +Git+ +tkh++lvk+++ l +i+
  lcl|FitnessBrowser__Korea:Ga0059261_0068  74 TSGPGATNAVTGITDALMDSIPMVVITGQVPSHLIGSDAFQEADTVGITRHCTKHNYLVKDPAHLGSIV 142
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207
                                               +eaf+ia++GrPGPv++d+Pkdv+ a+ +++++  ++ ++y+p+vk++k+ i+ a+e++++a++Pv + 
  lcl|FitnessBrowser__Korea:Ga0059261_0068 143 HEAFHIATSGRPGPVVIDIPKDVQIATARYSKPGPIQHKTYRPQVKADKALIESAVEMLAAAERPVFYT 211
                                               ********************************************************************* PP

                                 TIGR00118 208 GgGviia..easeelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavG 274
                                               GgGvi +  +as+ l+ela  + +pvt+tl+GlGafp+   + lgmlGmhGt+ean+a+++adl++a+G
  lcl|FitnessBrowser__Korea:Ga0059261_0068 212 GGGVINSgpQASQLLRELARITGAPVTSTLMGLGAFPASSDQWLGMLGMHGTYEANYAMNQADLIVAIG 280
                                               *****87336999******************************************************** PP

                                 TIGR00118 275 arfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee..ekkeke.Wl 340
                                               arfddrvtg l+ fap+a+ ihidid ++++k+v+vd+piv d+ + le++++  k++   + +   W+
  lcl|FitnessBrowser__Korea:Ga0059261_0068 281 ARFDDRVTGRLDAFAPHARKIHIDIDRSSMNKTVRVDLPIVADVGHALEDMIRIWKARqhPRPDLSeWW 349
                                               ***************************************************9976665444555545** PP

                                 TIGR00118 341 ekieewkkeyilkldeeeesikPqkvikelskllkdea.ivttdvGqhqmwaaqfyktkkprkfitsgG 408
                                               ++ie w++ ++l + e++++i Pq+ i++l++ ++d+a i+tt+vGqhqmwaaq++++++p+k++tsgG
  lcl|FitnessBrowser__Korea:Ga0059261_0068 350 SRIEGWRAVKCLDFPEDSNEIMPQRAIRALWEATRDQApIITTEVGQHQMWAAQHFHFESPNKWLTSGG 418
                                               ***********************************976599**************************** PP

                                 TIGR00118 409 lGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelf 477
                                               lGtmG+GlPaa+Ga++++p++ v++++G++s+qmn+qel+t+++y +pvki ilnne++Gmv+qWqel 
  lcl|FitnessBrowser__Korea:Ga0059261_0068 419 LGTMGYGLPAAIGAQLGHPDALVIDIAGEASIQMNIQELATATQYRLPVKIFILNNEYMGMVRQWQELT 487
                                               ********************************************************************* PP

                                 TIGR00118 478 yeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvap 546
                                               y+ ryse++  + lpdfvkl eayG +girie +++l++ ++ +l++++pv++d +v+k ++++Pm+++
  lcl|FitnessBrowser__Korea:Ga0059261_0068 488 YSSRYSESYSDA-LPDFVKLGEAYGWEGIRIEGKDQLDDGIAAMLAHDGPVIVDCRVAKLANCFPMIPS 555
                                               **********95.******************************************************** PP

                                 TIGR00118 547 Gagldelve 555
                                               Ga+ ++++ 
  lcl|FitnessBrowser__Korea:Ga0059261_0068 556 GAAHTDMLL 564
                                               *****9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (581 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 8.06
//
[ok]

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

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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