Alignments for a candidate for ilvI in Dechloromonas agitata is5

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Dechloromonas agitata is5

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_027459069.1 K420_RS0116805 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_000519045.1:WP_027459069.1
          Length = 566

 Score =  797 bits (2058), Expect = 0.0
 Identities = 394/566 (69%), Positives = 469/566 (82%), Gaps = 5/566 (0%)

Query: 21  GAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYARAT 80
           GAEI++  L EE V+YV+GYPGG+VL+IYD L KQ + +HILVRHEQAAVHAAD Y+R++
Sbjct: 5   GAEIVIRCLQEEKVDYVFGYPGGSVLHIYDALFKQEEVKHILVRHEQAAVHAADAYSRSS 64

Query: 81  GKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGITRPI 140
            KVGVALVTSGPGVTN VTGIATAY+DSIPMVV+ G VPT  IGQDAFQECDTVGITRP 
Sbjct: 65  QKVGVALVTSGPGVTNTVTGIATAYMDSIPMVVLCGQVPTAYIGQDAFQECDTVGITRPC 124

Query: 141 VKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRSYNP 200
           VKHNFLVKDV+DLA+TIKKAF IA+TGRPGPVVVDIPKD++   C+++YPKS+ MRSYNP
Sbjct: 125 VKHNFLVKDVKDLASTIKKAFHIASTGRPGPVVVDIPKDITAQVCEFDYPKSVQMRSYNP 184

Query: 201 VNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGLGAF 260
           V KGH GQI+KAV +LQ A+RP IYTGGGV+L++A+++L QLA     PVTNTLMGLG +
Sbjct: 185 VVKGHLGQIKKAVQILQEAKRPIIYTGGGVILSDAAEKLTQLARKLNFPVTNTLMGLGGY 244

Query: 261 PGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHIDID 320
           P T KQFVGMLGMHGT+EAN AM   DV++A+GARFDDRVIGNP HF  + R++IHIDID
Sbjct: 245 PATDKQFVGMLGMHGTFEANNAMHYADVILAVGARFDDRVIGNPEHFGEEKRRVIHIDID 304

Query: 321 PSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDCLKYD 380
           PSSISKRVKVD+PIVGNV DV+ E++ ++     K   E +A WW+QI++WR  + L Y 
Sbjct: 305 PSSISKRVKVDVPIVGNVTDVIDEIL-KLLDGGFKADPE-VADWWKQIDEWRGRNSLAY- 361

Query: 381 RSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGTMGVG 440
           R S  I PQYVVEK++E+T GDAFI SDVGQHQM+AAQ+YKFD+PRRWINSGGLGTMGVG
Sbjct: 362 RQSNHIMPQYVVEKLYEVTGGDAFITSDVGQHQMFAAQYYKFDKPRRWINSGGLGTMGVG 421

Query: 441 LPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVRQWQE 500
           LPY MG+  A P  +V  +TGEGSIQMCIQELSTC QY+ P+KI +LNNG LGMVRQWQE
Sbjct: 422 LPYGMGVLLANPGAQVACVTGEGSIQMCIQELSTCKQYELPIKIINLNNGMLGMVRQWQE 481

Query: 501 IEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAF-RLKDRTVFLDFQT 559
           + Y  RYS SY+ +LPDFVKLAE+YGHVGMR+EK  DVEPALR+AF   K+  VF+DF  
Sbjct: 482 MFYSKRYSQSYVTSLPDFVKLAESYGHVGMRIEKPEDVEPALRKAFTEHKNDLVFMDFII 541

Query: 560 DPTENVWPMVQAGKGISEMLLGAEDL 585
           DP  NV+PMV AGKG++EM+L AED+
Sbjct: 542 DPAANVFPMVAAGKGLTEMIL-AEDI 566


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: 1016
Number of extensions: 38
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: 566
Length adjustment: 36
Effective length of query: 549
Effective length of database: 530
Effective search space:   290970
Effective search space used:   290970
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_027459069.1 K420_RS0116805 (acetolactate synthase, large subunit, biosynthetic type)
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.27568.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.6e-253  826.1   2.1   7.8e-253  825.9   2.1    1.0  1  lcl|NCBI__GCF_000519045.1:WP_027459069.1  K420_RS0116805 acetolactate synt


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000519045.1:WP_027459069.1  K420_RS0116805 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  825.9   2.1  7.8e-253  7.8e-253       2     555 ..       4     562 ..       3     564 .. 0.97

  Alignments for each domain:
  == domain 1  score: 825.9 bits;  conditional E-value: 7.8e-253
                                 TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               +gaei+++ l++e+v++vfGyPGG+vl+iydal+ ++e++hilvrheqaa+haad y+r+s kvGv+l+
  lcl|NCBI__GCF_000519045.1:WP_027459069.1   4 SGAEIVIRCLQEEKVDYVFGYPGGSVLHIYDALFkQEEVKHILVRHEQAAVHAADAYSRSSQKVGVALV 72 
                                               89********************************999******************************** PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPG tn+vtgiatay+ds+P+vvl Gqv+t+ iG+dafqe+d +Git+p++kh+flvk+++dl++++
  lcl|NCBI__GCF_000519045.1:WP_027459069.1  73 TSGPGVTNTVTGIATAYMDSIPMVVLCGQVPTAYIGQDAFQECDTVGITRPCVKHNFLVKDVKDLASTI 141
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207
                                               k+af+iastGrPGPv+vd+Pkd+t++ +e++++++v++++y+p vkgh  qikka++++++ak+P+++ 
  lcl|NCBI__GCF_000519045.1:WP_027459069.1 142 KKAFHIASTGRPGPVVVDIPKDITAQVCEFDYPKSVQMRSYNPVVKGHLGQIKKAVQILQEAKRPIIYT 210
                                               ********************************************************************* PP

                                 TIGR00118 208 GgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGar 276
                                               GgGvi ++a e+l++la +l+ pvt tl+GlG++p+++++++gmlGmhGt ean a++ ad+++avGar
  lcl|NCBI__GCF_000519045.1:WP_027459069.1 211 GGGVILSDAAEKLTQLARKLNFPVTNTLMGLGGYPATDKQFVGMLGMHGTFEANNAMHYADVILAVGAR 279
                                               ********************************************************************* PP

                                 TIGR00118 277 fddrvtgnlakfapeak.iihididPaeigknvkvdipivGdakkvleellkklkee...ekkekeWle 341
                                               fddrv gn ++f +e + +ihididP++i+k vkvd+pivG+++ v++e+lk l      + +  +W++
  lcl|NCBI__GCF_000519045.1:WP_027459069.1 280 FDDRVIGNPEHFGEEKRrVIHIDIDPSSISKRVKVDVPIVGNVTDVIDEILKLLDGGfkaDPEVADWWK 348
                                               ************987644*********************************999876442444445*** PP

                                 TIGR00118 342 kieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlG 410
                                               +i+ew+ ++ l++  ++++i Pq+v+++l++++ ++a++t+dvGqhqm+aaq+yk++kpr++i+sgGlG
  lcl|NCBI__GCF_000519045.1:WP_027459069.1 349 QIDEWRGRNSLAYR-QSNHIMPQYVVEKLYEVTGGDAFITSDVGQHQMFAAQYYKFDKPRRWINSGGLG 416
                                               *********98875.56789************************************************* PP

                                 TIGR00118 411 tmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfye 479
                                               tmG GlP  +G+ +a+p ++v +vtG+gs+qm +qelst+++y++p+ki++lnn +lGmv+qWqe+fy+
  lcl|NCBI__GCF_000519045.1:WP_027459069.1 417 TMGVGLPYGMGVLLANPGAQVACVTGEGSIQMCIQELSTCKQYELPIKIINLNNGMLGMVRQWQEMFYS 485
                                               ********************************************************************* PP

                                 TIGR00118 480 erysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk..epvlldvevdkeeevlPmvap 546
                                               +rys+++++s lpdfvklae+yG++g+riekpe++e +l++a++++  ++v++d+ +d  ++v+Pmva 
  lcl|NCBI__GCF_000519045.1:WP_027459069.1 486 KRYSQSYVTS-LPDFVKLAESYGHVGMRIEKPEDVEPALRKAFTEHknDLVFMDFIIDPAANVFPMVAA 553
                                               *********5.******************************998654589******************* PP

                                 TIGR00118 547 Gagldelve 555
                                               G+gl+e++ 
  lcl|NCBI__GCF_000519045.1:WP_027459069.1 554 GKGLTEMIL 562
                                               *******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (566 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 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 9.17
//
[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