Alignments for a candidate for ilvI in Pseudarthrobacter sulfonivorans Ar51

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Pseudarthrobacter sulfonivorans Ar51

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_058932074.1 AU252_RS19110 acetolactate synthase large subunit

Query= BRENDA::P9WG41
         (618 letters)



>NCBI__GCF_001484605.1:WP_058932074.1
          Length = 635

 Score =  819 bits (2115), Expect = 0.0
 Identities = 398/578 (68%), Positives = 470/578 (81%), Gaps = 4/578 (0%)

Query: 38  LTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVRHEQGAGHAASGYAH 97
           +TG+QA++RSLEELGVD IFG+PGGA+LP YDPL  S  + HVLVRHEQGAGHAA GYA 
Sbjct: 57  MTGSQAIVRSLEELGVDDIFGLPGGAILPTYDPLMASS-MNHVLVRHEQGAGHAAQGYAM 115

Query: 98  VTGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADISGITM 157
           VTGRVGVC+ATSGPGATNLVT + DA MDS+P+VAITGQV  G+IGTDAFQEADI GITM
Sbjct: 116 VTGRVGVCIATSGPGATNLVTAIMDAHMDSVPIVAITGQVSSGVIGTDAFQEADIVGITM 175

Query: 158 PITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFSWPPRMELPGY 217
           PITKH+FLV   +DIP V+AEAFH+A+SGRPG VLVD+ KD  QGQ TFSWPP+++LPGY
Sbjct: 176 PITKHSFLVTDPNDIPHVMAEAFHLASSGRPGPVLVDVAKDAQQGQMTFSWPPKIDLPGY 235

Query: 218 KPNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVTTLMARG 277
           +P T+ H++QVREAAKLIA+A KPVLYVGGGV++  A  +LRELAELTG PVVTTLMARG
Sbjct: 236 RPVTRGHNKQVREAAKLIASATKPVLYVGGGVVKAHAAAELRELAELTGAPVVTTLMARG 295

Query: 278 AFPDSHRQNLGMPGMHGTVAAVAALQRSDLLIALGTRFDDRVTGKLDSFAPEAKVIHADI 337
            FPDSH Q++GMPGMHGTV+AV ALQ+SDLLI LG RFDDRVTG L SFAP AKVIHADI
Sbjct: 296 VFPDSHPQHVGMPGMHGTVSAVTALQQSDLLITLGARFDDRVTGILKSFAPNAKVIHADI 355

Query: 338 DPAEIGKNRHADVPIVGDVKAVITELIAMLR-HHHIPGTIEMADWWAYLNGVRKTYPLSY 396
           DPAEI KNR ADVPIVG VK +I EL   +R      GT ++  WWA+LN +++TYPL +
Sbjct: 356 DPAEISKNRTADVPIVGSVKEIIPELTEAVRSQFESAGTPDLTTWWAFLNNLKETYPLGW 415

Query: 397 GPQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFIRYEKPRSWLNSGGLGTMG 456
               DG  +P+ VIE++G + GP+ ++VAGVGQHQMWAAQFI+YE+P +WLNSGG GTMG
Sbjct: 416 TEPEDGLSAPQRVIERIGALTGPEGIYVAGVGQHQMWAAQFIKYERPHAWLNSGGAGTMG 475

Query: 457 FAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATCAVEGIPVKVALINNGNLGMVRQW 516
           +A+PAAMGAK+  P   VWAIDGDGCFQMTNQELATCA+  IP+KVA+INN +LGMVRQW
Sbjct: 476 YAVPAAMGAKVGEPDRVVWAIDGDGCFQMTNQELATCAINKIPIKVAIINNSSLGMVRQW 535

Query: 517 QSLFYAERYSQTDLAT--HSHRIPDFVKLAEALGCVGLRCEREEDVVDVINQARAINDCP 574
           Q+LFY  RYS TDL T   + RIPDFVKL EA GC   RCER+ED+   I +A  IND P
Sbjct: 536 QTLFYEGRYSNTDLNTGHETVRIPDFVKLGEAYGCASFRCERDEDIDATIQKALEINDRP 595

Query: 575 VVIDFIVGADAQVWPMVAAGTSNDEIQAARGIRPLFDD 612
           VVIDF+V  D+ VWPMV AG SND+IQ AR + P +++
Sbjct: 596 VVIDFVVSPDSMVWPMVPAGVSNDQIQVARNMTPEWEE 633


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: 1262
Number of extensions: 55
Number of successful extensions: 4
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: 635
Length adjustment: 38
Effective length of query: 580
Effective length of database: 597
Effective search space:   346260
Effective search space used:   346260
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: 54 (25.4 bits)

Align candidate WP_058932074.1 AU252_RS19110 (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.7888.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.3e-229  746.6   1.0   9.7e-229  746.3   1.0    1.0  1  lcl|NCBI__GCF_001484605.1:WP_058932074.1  AU252_RS19110 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001484605.1:WP_058932074.1  AU252_RS19110 acetolactate synthase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  746.3   1.0  9.7e-229  9.7e-229       1     553 [.      57     621 ..      57     625 .. 0.97

  Alignments for each domain:
  == domain 1  score: 746.3 bits;  conditional E-value: 9.7e-229
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               ++g++++v+sl++ gv+ +fG PGGa+lp yd l +s ++h+lvrheq+a haa+Gya ++G+vGv++a
  lcl|NCBI__GCF_001484605.1:WP_058932074.1  57 MTGSQAIVRSLEELGVDDIFGLPGGAILPTYDPLMASSMNHVLVRHEQGAGHAAQGYAMVTGRVGVCIA 125
                                               79******************************************************************* PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPGatnlvt+i +a++dsvP+v++tGqv++ +iG+dafqe+di+Git+p+tkhsflv++++d+p+++
  lcl|NCBI__GCF_001484605.1:WP_058932074.1 126 TSGPGATNLVTAIMDAHMDSVPIVAITGQVSSGVIGTDAFQEADIVGITMPITKHSFLVTDPNDIPHVM 194
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207
                                                eaf++as+GrPGPvlvd+ kd ++ +++++ + k++lpgy+p ++gh++q+++a++li++a kPvl+v
  lcl|NCBI__GCF_001484605.1:WP_058932074.1 195 AEAFHLASSGRPGPVLVDVAKDAQQGQMTFSWPPKIDLPGYRPVTRGHNKQVREAAKLIASATKPVLYV 263
                                               ********************************************************************* PP

                                 TIGR00118 208 GgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGar 276
                                               GgGv++a+a +el+elae + +pv+ttl+  G fp+ hp+ +gm GmhGt  a +a++++dlli++Gar
  lcl|NCBI__GCF_001484605.1:WP_058932074.1 264 GGGVVKAHAAAELRELAELTGAPVVTTLMARGVFPDSHPQHVGMPGMHGTVSAVTALQQSDLLITLGAR 332
                                               ********************************************************************* PP

                                 TIGR00118 277 fddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee.....ekkeke.W 339
                                               fddrvtg l++fap+ak+ih didPaei+kn+++d+pivG +k+++ el ++++++     +  +   W
  lcl|NCBI__GCF_001484605.1:WP_058932074.1 333 FDDRVTGILKSFAPNAKVIHADIDPAEISKNRTADVPIVGSVKEIIPELTEAVRSQfesagTP-DLTtW 400
                                               ****************************************************99998766433.4445* PP

                                 TIGR00118 340 lekieewkkeyilkldeeees.ikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsg 407
                                               ++ ++++k++y+l   e e+   +Pq+vi+++  l+  e i+ ++vGqhqmwaaqf k+++p+ +++sg
  lcl|NCBI__GCF_001484605.1:WP_058932074.1 401 WAFLNNLKETYPLGWTEPEDGlSAPQRVIERIGALTGPEGIYVAGVGQHQMWAAQFIKYERPHAWLNSG 469
                                               *************96666665279********************************************* PP

                                 TIGR00118 408 GlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqel 476
                                               G+GtmG+ +Paa+Gakv++p+  v a++Gdg fqm+ qel+t++  +ip+k+ i+nn+ lGmv+qWq l
  lcl|NCBI__GCF_001484605.1:WP_058932074.1 470 GAGTMGYAVPAAMGAKVGEPDRVVWAIDGDGCFQMTNQELATCAINKIPIKVAIINNSSLGMVRQWQTL 538
                                               ********************************************************************* PP

                                 TIGR00118 477 fyeerysetklas.....elpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeee 539
                                               fye+rys+t l++       pdfvkl eayG  + r e++e++++ +++ale + +pv++d++v  ++ 
  lcl|NCBI__GCF_001484605.1:WP_058932074.1 539 FYEGRYSNTDLNTghetvRIPDFVKLGEAYGCASFRCERDEDIDATIQKALEINdRPVVIDFVVSPDSM 607
                                               *********99862222247********************************9879************* PP

                                 TIGR00118 540 vlPmvapGagldel 553
                                               v+Pmv+ G ++d++
  lcl|NCBI__GCF_001484605.1:WP_058932074.1 608 VWPMVPAGVSNDQI 621
                                               **********9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (635 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 0.00s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 10.92
//
[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