Alignments for a candidate for ilvI in Alicycliphilus denitrificans K601

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Alicycliphilus denitrificans K601

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_013518618.1 ALIDE2_RS15530 acetolactate synthase 3 large subunit

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



>NCBI__GCF_000204645.1:WP_013518618.1
          Length = 597

 Score =  903 bits (2334), Expect = 0.0
 Identities = 441/577 (76%), Positives = 502/577 (87%), Gaps = 3/577 (0%)

Query: 12  NSSAAPEMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVH 71
           ++S   E++GAEILV AL  E V+Y+WGYPGGAVLYIYD L+KQ   +H+LVRHEQAAVH
Sbjct: 21  HASGTQELMGAEILVKALQAENVQYMWGYPGGAVLYIYDALYKQESIQHVLVRHEQAAVH 80

Query: 72  AADGYARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQEC 131
           AADGYARATG+VGVALVTSGPG+TNAVTGIATAY+DSIPMV+I+G VPT AIG DAFQEC
Sbjct: 81  AADGYARATGEVGVALVTSGPGLTNAVTGIATAYMDSIPMVIISGQVPTPAIGLDAFQEC 140

Query: 132 DTVGITRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYE-YP 190
           DTVGITRPIVKHNFLVKDVRDLA T+KKAF IA TGRPGPVVVDIPKDVS     Y  YP
Sbjct: 141 DTVGITRPIVKHNFLVKDVRDLALTLKKAFHIARTGRPGPVVVDIPKDVSFKKTAYHGYP 200

Query: 191 KSIDMRSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPV 250
           +S++MRSYNPV KGH+GQIRKA+ LL GA+RPYIYTGGGV+L NA+ ELR L  + G+PV
Sbjct: 201 QSVEMRSYNPVKKGHAGQIRKALQLLLGAKRPYIYTGGGVLLGNATQELRALVDMLGYPV 260

Query: 251 TNTLMGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQ 310
           TNTLMGLGA+P T ++F+GMLGMHGT EAN  MQNCDVL+A+GARFDDRVIGNP HF   
Sbjct: 261 TNTLMGLGAYPATDRKFLGMLGMHGTIEANNTMQNCDVLLAVGARFDDRVIGNPKHFAQN 320

Query: 311 ARKIIHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQ 370
            RKIIHIDIDPSSISKRVKVDIPIVG+VK+VL ELI+ I+ S  +P   AL+ WW+QIE 
Sbjct: 321 DRKIIHIDIDPSSISKRVKVDIPIVGDVKEVLTELISMIRESTTRPDAGALSAWWDQIEA 380

Query: 371 WRSVDCLKYDR-SSEIIKPQYVVEKIWELTK-GDAFICSDVGQHQMWAAQFYKFDEPRRW 428
           WR  DCLKYDR ++E+IKPQ+V+E +W +TK  DA+I SDVGQHQMWAAQ+YKFDEPRRW
Sbjct: 381 WRGRDCLKYDRGNTEVIKPQHVIETLWNMTKDADAYITSDVGQHQMWAAQYYKFDEPRRW 440

Query: 429 INSGGLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLN 488
           INSGGLGTMGVG+PYAMGIK A P+ EV  +TGEGS+QM IQELSTCLQY+TP+KI SLN
Sbjct: 441 INSGGLGTMGVGIPYAMGIKLAKPDAEVFCVTGEGSVQMNIQELSTCLQYNTPIKILSLN 500

Query: 489 NGYLGMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRL 548
           N YLGMVRQWQEIEY  RYSHSYMDALP+FVKLAEAYGHVGM +E+  DVEPALREA +L
Sbjct: 501 NRYLGMVRQWQEIEYSGRYSHSYMDALPNFVKLAEAYGHVGMLIERPQDVEPALREARKL 560

Query: 549 KDRTVFLDFQTDPTENVWPMVQAGKGISEMLLGAEDL 585
           KDRTVFLDF+TDPTENV+PMVQAGKGI+EMLLG+EDL
Sbjct: 561 KDRTVFLDFRTDPTENVFPMVQAGKGITEMLLGSEDL 597


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: 1139
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: 597
Length adjustment: 37
Effective length of query: 548
Effective length of database: 560
Effective search space:   306880
Effective search space used:   306880
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_013518618.1 ALIDE2_RS15530 (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.25826.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-254  829.1   0.2   9.8e-254  828.8   0.2    1.0  1  lcl|NCBI__GCF_000204645.1:WP_013518618.1  ALIDE2_RS15530 acetolactate synt


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000204645.1:WP_013518618.1  ALIDE2_RS15530 acetolactate synthase 3 large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  828.8   0.2  9.8e-254  9.8e-254       2     554 ..      29     591 ..      28     594 .. 0.97

  Alignments for each domain:
  == domain 1  score: 828.8 bits;  conditional E-value: 9.8e-254
                                 TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvla 69 
                                                gaeilv++l++e+v++++GyPGGavl iydaly ++ ++h+lvrheqaa+haadGyara+G+vGv+l+
  lcl|NCBI__GCF_000204645.1:WP_013518618.1  29 MGAEILVKALQAENVQYMWGYPGGAVLYIYDALYkQESIQHVLVRHEQAAVHAADGYARATGEVGVALV 97 
                                               79********************************8899******************************* PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPG tn+vtgiatay+ds+P+v+++Gqv+t +iG dafqe+d +Git+p++kh+flvk+++dl+ +l
  lcl|NCBI__GCF_000204645.1:WP_013518618.1  98 TSGPGLTNAVTGIATAYMDSIPMVIISGQVPTPAIGLDAFQECDTVGITRPIVKHNFLVKDVRDLALTL 166
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleve.ekvelpgykptvkghklqikkaleliekakkPvll 206
                                               k+af+ia tGrPGPv+vd+Pkdv+ +++ ++ + ++ve+++y+p +kgh  qi+kal+l+  ak+P ++
  lcl|NCBI__GCF_000204645.1:WP_013518618.1 167 KKAFHIARTGRPGPVVVDIPKDVSFKKTAYHGYpQSVEMRSYNPVKKGHAGQIRKALQLLLGAKRPYIY 235
                                               ************************9998887555*********************************** PP

                                 TIGR00118 207 vGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGa 275
                                                GgGv+ ++a++el+ l+++l  pvt tl+GlGa+p++++++lgmlGmhGt ean +++++d+l+avGa
  lcl|NCBI__GCF_000204645.1:WP_013518618.1 236 TGGGVLLGNATQELRALVDMLGYPVTNTLMGLGAYPATDRKFLGMLGMHGTIEANNTMQNCDVLLAVGA 304
                                               ********************************************************************* PP

                                 TIGR00118 276 rfddrvtgnlakfapea.kiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke. 338
                                               rfddrv gn ++fa++  kiihididP++i+k vkvdipivGd+k+vl+el++ ++e     +      
  lcl|NCBI__GCF_000204645.1:WP_013518618.1 305 RFDDRVIGNPKHFAQNDrKIIHIDIDPSSISKRVKVDIPIVGDVKEVLTELISMIRESttrpDAGALSa 373
                                               **************98626************************************99976553333346 PP

                                 TIGR00118 339 Wlekieewkkeyilkldeeees.ikPqkvikelskllkd.eaivttdvGqhqmwaaqfyktkkprkfit 405
                                               W+++ie w+ + +lk+d+ +++ ikPq+vi++l++++kd +a++t+dvGqhqmwaaq+yk+++pr++i+
  lcl|NCBI__GCF_000204645.1:WP_013518618.1 374 WWDQIEAWRGRDCLKYDRGNTEvIKPQHVIETLWNMTKDaDAYITSDVGQHQMWAAQYYKFDEPRRWIN 442
                                               ***************99876544***************999**************************** PP

                                 TIGR00118 406 sgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWq 474
                                               sgGlGtmG G+P a+G+k+akp+++v +vtG+gs+qmn+qelst+ +y++p+ki+ lnn++lGmv+qWq
  lcl|NCBI__GCF_000204645.1:WP_013518618.1 443 SGGLGTMGVGIPYAMGIKLAKPDAEVFCVTGEGSVQMNIQELSTCLQYNTPIKILSLNNRYLGMVRQWQ 511
                                               ********************************************************************* PP

                                 TIGR00118 475 elfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevlP 542
                                               e+ y++rys++++ + lp+fvklaeayG++g+ ie+p+++e +l+ea + k + v+ld++ d +e+v+P
  lcl|NCBI__GCF_000204645.1:WP_013518618.1 512 EIEYSGRYSHSYMDA-LPNFVKLAEAYGHVGMLIERPQDVEPALREARKLKdRTVFLDFRTDPTENVFP 579
                                               **************5.*******************************9987699*************** PP

                                 TIGR00118 543 mvapGagldelv 554
                                               mv  G+g++e++
  lcl|NCBI__GCF_000204645.1:WP_013518618.1 580 MVQAGKGITEML 591
                                               **********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (597 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: 00:00:00.02
# Mc/sec: 12.35
//
[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