Alignments for a candidate for ilvI in Dehalococcoides mccartyi 195

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Dehalococcoides mccartyi 195

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_010936561.1 DET_RS04345 acetolactate synthase, large subunit, biosynthetic type

Query= BRENDA::P9WG41
         (618 letters)



>NCBI__GCF_000011905.1:WP_010936561.1
          Length = 569

 Score =  554 bits (1428), Expect = e-162
 Identities = 292/564 (51%), Positives = 373/564 (66%), Gaps = 13/564 (2%)

Query: 37  QLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVRHEQGAGHAASGYA 96
           +LTGAQ V  SL + G DVIFG PGG +LP+YD       LRH+L RHEQGA HAA G+A
Sbjct: 2   KLTGAQIVCESLLKEGADVIFGYPGGVLLPLYDTFPQYPALRHILTRHEQGAAHAADGFA 61

Query: 97  HVTGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADISGIT 156
            VTG+VGVC+ATSGPGATNL+T +A+A MDSIP+VAITGQV R LIG DAFQE DI+GIT
Sbjct: 62  RVTGKVGVCLATSGPGATNLITGIANAYMDSIPMVAITGQVTRNLIGKDAFQEIDITGIT 121

Query: 157 MPITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFSWPPRMELPG 216
           +PITK N+LV     +   + EAF++A +GRPG VL+DIPKDV   Q  F +P   +LPG
Sbjct: 122 LPITKQNYLVTRASALADTIKEAFYLARTGRPGPVLIDIPKDVFIEQAEFEYPDEPDLPG 181

Query: 217 YKPNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVTTLMAR 276
           YKP  K +  Q+++AAKLI  A KPV+  G GV    A E+L+ LAE   +PV+TTL+  
Sbjct: 182 YKPVIKGNLMQIQKAAKLIETAEKPVIIAGHGVNISGANEELKTLAENCQLPVITTLLGV 241

Query: 277 GAFPDSHRQNLGMPGMHGTVAAVAALQRSDLLIALGTRFDDRVTGKLDSFAPEAKVIHAD 336
            +FP+ H  + GM GMHG   A  A+  +DL++A+G RFDDRVTGKL +FAP A VIH D
Sbjct: 242 SSFPEDHILSYGMLGMHGMAYANMAVAATDLIVAIGMRFDDRVTGKLSAFAPHASVIHID 301

Query: 337 IDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPGTIEMADWWAYLNGVRKTYPLSY 396
           IDPAEIGKN   DVPIVGDVK V+  L   +        ++ ++W   L   R+ +P   
Sbjct: 302 IDPAEIGKNIRVDVPIVGDVKTVLKSLNKQVE------CVQHSEWLRQLENWRREHPPLS 355

Query: 397 GPQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFIRYEKPRSWLNSGGLGTMG 456
              +D  + P+Y+++++ E    +A+ V GVGQHQMWAAQ   Y +P S + SGGLGTMG
Sbjct: 356 IRHTD-LILPQYIVQQISEATSGNAIVVTGVGQHQMWAAQHYTYIRPNSLVTSGGLGTMG 414

Query: 457 FAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATCAVEGIPVKVALINNGNLGMVRQW 516
           F +PAA+GAK+  P   VW I GDG FQM  QELAT   E   VK+A+ NNG LGMVRQW
Sbjct: 415 FDLPAALGAKVGCPDETVWCIAGDGGFQMNMQELATIVQERAAVKIAVFNNGYLGMVRQW 474

Query: 517 QSLFYAERYSQTDLATHSHRIPDFVKLAEALGCVGLRCEREEDVVDVINQARAINDCPVV 576
           Q LFY + Y  T L       PDF+K+AEA     L  +R+E+V   I QA A  + P +
Sbjct: 475 QDLFYNKNYVATPLG-----CPDFIKIAEAYDIPALNVKRKEEVRPAIEQAMA-TEGPFL 528

Query: 577 IDFIVGADAQVWPMVAAGTSNDEI 600
           I+FI+  +  V+PMV  G +  E+
Sbjct: 529 INFIIEPEENVYPMVPPGAALHEV 552


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: 1037
Number of extensions: 48
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: 569
Length adjustment: 37
Effective length of query: 581
Effective length of database: 532
Effective search space:   309092
Effective search space used:   309092
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_010936561.1 DET_RS04345 (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.20379.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.5e-244  797.0   0.2   5.2e-244  796.7   0.2    1.0  1  lcl|NCBI__GCF_000011905.1:WP_010936561.1  DET_RS04345 acetolactate synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000011905.1:WP_010936561.1  DET_RS04345 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  796.7   0.2  5.2e-244  5.2e-244       1     555 [.       3     554 ..       3     556 .. 0.99

  Alignments for each domain:
  == domain 1  score: 796.7 bits;  conditional E-value: 5.2e-244
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 
                                               l+ga+i+ esl keg +++fGyPGG +lp+yd++     l+hil+rheq+aahaadG+ar++GkvGv+l
  lcl|NCBI__GCF_000011905.1:WP_010936561.1   3 LTGAQIVCESLLKEGADVIFGYPGGVLLPLYDTFPqYPALRHILTRHEQGAAHAADGFARVTGKVGVCL 71 
                                               68*******************************987889****************************** PP

                                 TIGR00118  69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137
                                               atsGPGatnl+tgia+ay+ds+P+v++tGqv+++liG+dafqeidi+Gitlp+tk ++lv++a+ l+ +
  lcl|NCBI__GCF_000011905.1:WP_010936561.1  72 ATSGPGATNLITGIANAYMDSIPMVAITGQVTRNLIGKDAFQEIDITGITLPITKQNYLVTRASALADT 140
                                               ********************************************************************* PP

                                 TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvll 206
                                               +keaf++a tGrPGPvl+d+Pkdv  ++ e+e++++ +lpgykp +kg+ +qi+ka++lie+a+kPv++
  lcl|NCBI__GCF_000011905.1:WP_010936561.1 141 IKEAFYLARTGRPGPVLIDIPKDVFIEQAEFEYPDEPDLPGYKPVIKGNLMQIQKAAKLIETAEKPVII 209
                                               ********************************************************************* PP

                                 TIGR00118 207 vGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGa 275
                                               +G Gv i++a+eelk lae++++pv+ttllG+ +fpedh l+ gmlGmhG+++an+av  +dl++a+G+
  lcl|NCBI__GCF_000011905.1:WP_010936561.1 210 AGHGVNISGANEELKTLAENCQLPVITTLLGVSSFPEDHILSYGMLGMHGMAYANMAVAATDLIVAIGM 278
                                               ********************************************************************* PP

                                 TIGR00118 276 rfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekie 344
                                               rfddrvtg+l+ fap+a +ihididPaeigkn++vd+pivGd+k+vl+ l k+++ ++++e  Wl+++e
  lcl|NCBI__GCF_000011905.1:WP_010936561.1 279 RFDDRVTGKLSAFAPHASVIHIDIDPAEIGKNIRVDVPIVGDVKTVLKSLNKQVECVQHSE--WLRQLE 345
                                               *******************************************************999998..****** PP

                                 TIGR00118 345 ewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmG 413
                                               +w++e+++   ++ + i Pq++++++s+ ++++aiv t+vGqhqmwaaq+y++ +p++ +tsgGlGtmG
  lcl|NCBI__GCF_000011905.1:WP_010936561.1 346 NWRREHPPLSIRHTDLILPQYIVQQISEATSGNAIVVTGVGQHQMWAAQHYTYIRPNSLVTSGGLGTMG 414
                                               *******99999999****************************************************** PP

                                 TIGR00118 414 fGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeery 482
                                               f lPaalGakv+ p+etv +++Gdg+fqmn+qel+tiv+    vki ++nn +lGmv+qWq+lfy++ y
  lcl|NCBI__GCF_000011905.1:WP_010936561.1 415 FDLPAALGAKVGCPDETVWCIAGDGGFQMNMQELATIVQERAAVKIAVFNNGYLGMVRQWQDLFYNKNY 483
                                               ********************************************************************* PP

                                 TIGR00118 483 setklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagld 551
                                                +t l++  pdf+k+aeay + +++++++ee+  ++++a+++++p l+++ ++ ee+v+Pmv+pGa+l+
  lcl|NCBI__GCF_000011905.1:WP_010936561.1 484 VATPLGC--PDFIKIAEAYDIPALNVKRKEEVRPAIEQAMATEGPFLINFIIEPEENVYPMVPPGAALH 550
                                               ******8..************************************************************ PP

                                 TIGR00118 552 elve 555
                                               e++e
  lcl|NCBI__GCF_000011905.1:WP_010936561.1 551 EVLE 554
                                               *987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (569 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: 7.70
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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