Alignments for a candidate for ilvI in Xenophilus azovorans DSM 13620

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Xenophilus azovorans DSM 13620

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_038215894.1 Q392_RS26710 acetolactate synthase 3 catalytic subunit

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



>NCBI__GCF_000745855.1:WP_038215894.1
          Length = 591

 Score =  902 bits (2330), Expect = 0.0
 Identities = 438/582 (75%), Positives = 499/582 (85%), Gaps = 3/582 (0%)

Query: 7   SHADSNSSAAPEMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHE 66
           S A +  S   E++G+E+LV AL  EGV+Y+WGYPGGAVLYIYD L+KQ   +H+LVRHE
Sbjct: 10  SAAAATGSQTQELMGSEVLVKALQAEGVKYIWGYPGGAVLYIYDALYKQDTMQHVLVRHE 69

Query: 67  QAAVHAADGYARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQD 126
           QAAVHAADGYARATG VGVALVTSGPG+TNAVTGIATAY+DSIPMV+I G VPT AIGQD
Sbjct: 70  QAAVHAADGYARATGDVGVALVTSGPGLTNAVTGIATAYMDSIPMVIIAGQVPTPAIGQD 129

Query: 127 AFQECDTVGITRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACK 186
           AFQECDTVGITRPIVKHNFLVKD +D+A T+KKAF IA +GRPGPVVVDIPKDVS     
Sbjct: 130 AFQECDTVGITRPIVKHNFLVKDAKDIALTMKKAFHIARSGRPGPVVVDIPKDVSFKKVA 189

Query: 187 YE-YPKSIDMRSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAAL 245
           Y  YP+ ++MRSYNPV KGH GQIRKA+ LL GA+RPYIYTGGGV+L NA +ELR L  +
Sbjct: 190 YHGYPEKVEMRSYNPVKKGHGGQIRKALQLLLGAKRPYIYTGGGVLLGNACNELRTLVDM 249

Query: 246 TGHPVTNTLMGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPA 305
            G+PVTNTLMGLGA+P + ++F+GMLGMHGT EAN AMQNCDVL+A+GARFDDRVIGNP 
Sbjct: 250 LGYPVTNTLMGLGAYPASDRKFLGMLGMHGTIEANNAMQNCDVLLAVGARFDDRVIGNPK 309

Query: 306 HFTSQARKIIHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWW 365
           HF    RKIIH+DIDPSSISKRVKVDIPIVG+VKDVL ELI+ ++ S  KP    LA WW
Sbjct: 310 HFAQNERKIIHVDIDPSSISKRVKVDIPIVGDVKDVLTELISMVRESSTKPDAATLADWW 369

Query: 366 EQIEQWRSVDCLKYDRSS-EIIKPQYVVEKIWELTKG-DAFICSDVGQHQMWAAQFYKFD 423
           + IE WRS DCLKYD  + ++IKPQ VVE +W +TK  + +ICSDVGQHQMWAAQ+Y+FD
Sbjct: 370 KTIEGWRSRDCLKYDSDNKQVIKPQKVVETLWNMTKDTETYICSDVGQHQMWAAQYYRFD 429

Query: 424 EPRRWINSGGLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVK 483
           EPRRWINSGGLGTMGVG+PYAMGIK A PE EV TITGEGS+QMCIQELSTCLQY+TP+K
Sbjct: 430 EPRRWINSGGLGTMGVGIPYAMGIKLAKPEAEVFTITGEGSVQMCIQELSTCLQYNTPIK 489

Query: 484 ICSLNNGYLGMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALR 543
           I SLNN YLGMVRQWQEIEY  RYSHSYMDALP+FVKLAEAYGHVGM +E+  DVEPALR
Sbjct: 490 IVSLNNRYLGMVRQWQEIEYSGRYSHSYMDALPNFVKLAEAYGHVGMLIERPEDVEPALR 549

Query: 544 EAFRLKDRTVFLDFQTDPTENVWPMVQAGKGISEMLLGAEDL 585
           EA +LKDRTVF+DF+TDPTENV+PMVQAGKGI+EMLLG+EDL
Sbjct: 550 EARKLKDRTVFMDFRTDPTENVFPMVQAGKGITEMLLGSEDL 591


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: 1119
Number of extensions: 30
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: 585
Length of database: 591
Length adjustment: 37
Effective length of query: 548
Effective length of database: 554
Effective search space:   303592
Effective search space used:   303592
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_038215894.1 Q392_RS26710 (acetolactate synthase 3 catalytic 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.9096.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.5e-252  823.1   0.3   6.5e-252  822.8   0.3    1.0  1  lcl|NCBI__GCF_000745855.1:WP_038215894.1  Q392_RS26710 acetolactate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000745855.1:WP_038215894.1  Q392_RS26710 acetolactate synthase 3 catalytic subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  822.8   0.3  6.5e-252  6.5e-252       2     554 ..      23     585 ..      22     588 .. 0.97

  Alignments for each domain:
  == domain 1  score: 822.8 bits;  conditional E-value: 6.5e-252
                                 TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvla 69 
                                                g+e+lv++l++egv++++GyPGGavl iydaly ++ ++h+lvrheqaa+haadGyara+G vGv+l+
  lcl|NCBI__GCF_000745855.1:WP_038215894.1  23 MGSEVLVKALQAEGVKYIWGYPGGAVLYIYDALYkQDTMQHVLVRHEQAAVHAADGYARATGDVGVALV 91 
                                               699*******************************9999******************************* PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPG tn+vtgiatay+ds+P+v+++Gqv+t +iG+dafqe+d +Git+p++kh+flvk+a+d++ ++
  lcl|NCBI__GCF_000745855.1:WP_038215894.1  92 TSGPGLTNAVTGIATAYMDSIPMVIIAGQVPTPAIGQDAFQECDTVGITRPIVKHNFLVKDAKDIALTM 160
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleve.ekvelpgykptvkghklqikkaleliekakkPvll 206
                                               k+af+ia +GrPGPv+vd+Pkdv+ +++ ++ + ekve+++y+p +kgh  qi+kal+l+  ak+P ++
  lcl|NCBI__GCF_000745855.1:WP_038215894.1 161 KKAFHIARSGRPGPVVVDIPKDVSFKKVAYHGYpEKVEMRSYNPVKKGHGGQIRKALQLLLGAKRPYIY 229
                                               *************************999998655*********************************** PP

                                 TIGR00118 207 vGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGa 275
                                                GgGv+ ++a +el+ l+++l  pvt tl+GlGa+p+ ++++lgmlGmhGt ean a++++d+l+avGa
  lcl|NCBI__GCF_000745855.1:WP_038215894.1 230 TGGGVLLGNACNELRTLVDMLGYPVTNTLMGLGAYPASDRKFLGMLGMHGTIEANNAMQNCDVLLAVGA 298
                                               ********************************************************************* PP

                                 TIGR00118 276 rfddrvtgnlakfapea.kiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke. 338
                                               rfddrv gn ++fa++  kiih+didP++i+k vkvdipivGd+k vl+el++ ++e     +  +   
  lcl|NCBI__GCF_000745855.1:WP_038215894.1 299 RFDDRVIGNPKHFAQNErKIIHVDIDPSSISKRVKVDIPIVGDVKDVLTELISMVRESstkpDAATLAd 367
                                               **************87527***********************************999866553334445 PP

                                 TIGR00118 339 Wlekieewkkeyilkldeeees.ikPqkvikelskllkd.eaivttdvGqhqmwaaqfyktkkprkfit 405
                                               W++ ie w+++ +lk+d+++++ ikPqkv+++l++++kd e+++ +dvGqhqmwaaq+y++++pr++i+
  lcl|NCBI__GCF_000745855.1:WP_038215894.1 368 WWKTIEGWRSRDCLKYDSDNKQvIKPQKVVETLWNMTKDtETYICSDVGQHQMWAAQYYRFDEPRRWIN 436
                                               ***************99988776***************989**************************** PP

                                 TIGR00118 406 sgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWq 474
                                               sgGlGtmG G+P a+G+k+akpe++v ++tG+gs+qm +qelst+ +y++p+kiv lnn++lGmv+qWq
  lcl|NCBI__GCF_000745855.1:WP_038215894.1 437 SGGLGTMGVGIPYAMGIKLAKPEAEVFTITGEGSVQMCIQELSTCLQYNTPIKIVSLNNRYLGMVRQWQ 505
                                               ********************************************************************* PP

                                 TIGR00118 475 elfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevlP 542
                                               e+ y++rys++++ + lp+fvklaeayG++g+ ie+pe++e +l+ea + k + v++d++ d +e+v+P
  lcl|NCBI__GCF_000745855.1:WP_038215894.1 506 EIEYSGRYSHSYMDA-LPNFVKLAEAYGHVGMLIERPEDVEPALREARKLKdRTVFMDFRTDPTENVFP 573
                                               **************5.*******************************9987699*************** PP

                                 TIGR00118 543 mvapGagldelv 554
                                               mv  G+g++e++
  lcl|NCBI__GCF_000745855.1:WP_038215894.1 574 MVQAGKGITEML 585
                                               **********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (591 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 12.33
//
[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