Alignments for a candidate for ilvI in Nitriliruptor alkaliphilus DSM 45188

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Nitriliruptor alkaliphilus DSM 45188

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_083441462.1 NITAL_RS11140 acetolactate synthase, large subunit, biosynthetic type

Query= BRENDA::P9WG41
         (618 letters)



>NCBI__GCF_000969705.1:WP_083441462.1
          Length = 617

 Score =  648 bits (1671), Expect = 0.0
 Identities = 333/583 (57%), Positives = 409/583 (70%), Gaps = 12/583 (2%)

Query: 26  PAA--RPKHVALQQLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVR 83
           PAA  RP   A + +TGAQAV+RSLE LGVDV+FG PGGA+LP YDPL ++    HVLVR
Sbjct: 7   PAADPRPHERAGEVVTGAQAVMRSLEALGVDVVFGYPGGAILPAYDPLIEAD-FTHVLVR 65

Query: 84  HEQGAGHAASGYAHVTGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIG 143
           HEQGA H A GYAH TGRVGVC+ TSGP ATNLVT LADA MDS+P++AITGQV    IG
Sbjct: 66  HEQGAIHMAEGYAHATGRVGVCIVTSGPAATNLVTGLADAHMDSVPILAITGQVATTAIG 125

Query: 144 TDAFQEADISGITMPITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQ 203
           +DAFQEAD++GITMPITKHN +V S + I   +AEAF+IA SGRPG VLVD+PKDVL  +
Sbjct: 126 SDAFQEADVTGITMPITKHNEIVYSAERIAGAIAEAFYIARSGRPGPVLVDLPKDVLNAK 185

Query: 204 CTFSWPPRMELPGYKPNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAE 263
             + WP  ++LPGY+P  + H + +REA  LIA A +PV+Y GGG++R  A E+LR  AE
Sbjct: 186 VAWQWPEHLDLPGYRPTVRGHGKMIREALDLIAGAERPVIYAGGGLVRAGADEELRAFAE 245

Query: 264 LTGIPVVTTLMARGAFPDSHRQNLGMPGMHGTVAAVAALQRSDLLIALGTRFDDRVTGKL 323
             G+PVVTTLMARG  PD+H   +GMPGMHG  AAV A Q +DLLI LG RFDDRVTG L
Sbjct: 246 TLGLPVVTTLMARGILPDTHELTVGMPGMHGHYAAVKAFQETDLLITLGARFDDRVTGHL 305

Query: 324 DSFAPEAKVIHADIDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPGTI-----EM 378
            SFAP AKVIH D+DPAEIGKNR  DVPIVGDVK V+ +L+ ++      GT+     ++
Sbjct: 306 ASFAPHAKVIHVDVDPAEIGKNREVDVPIVGDVKVVLGQLLKVIEDKRTKGTLAELIPDV 365

Query: 379 ADWWAYLNGVRKTYPLSYGPQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFI 438
             W  +L+ ++  +PL       G L P+  I  + E  G DAV+VAGVGQHQMWAAQ I
Sbjct: 366 TAWRGHLDQMKADHPLRVEQPETGVLKPQTAIRAIHETWGDDAVYVAGVGQHQMWAAQHI 425

Query: 439 RYEKPRSWLNSGGLGTMGFAIPAAMGAKIAL-PGTEVWAIDGDGCFQMTNQELATCAVEG 497
            Y + R W+NSGGLGTMGFA+PAA+GAK+ +     V AIDGDGCFQMT QELA      
Sbjct: 426 PYTRGRQWINSGGLGTMGFAVPAAIGAKVGVGRDVPVVAIDGDGCFQMTFQELAAAVQHD 485

Query: 498 IPVKVALINNGNLGMVRQWQSLFYAERYSQTDLATHSHRIPDFVKLAEALGCVGLRCERE 557
           IPV   +INNG LGMVRQWQ LFY +R SQ  L      +PD +KLA+A    G R    
Sbjct: 486 IPVVFCVINNGYLGMVRQWQHLFYEDRLSQVAL---PQDLPDLMKLADAYQMPGFRISSV 542

Query: 558 EDVVDVINQARAINDCPVVIDFIVGADAQVWPMVAAGTSNDEI 600
           +++   + +A+ I D P++++F V  D  V+PMV +G SNDEI
Sbjct: 543 DELDATLAKAKQITDQPILVEFRVDPDEMVFPMVPSGASNDEI 585


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: 1240
Number of extensions: 48
Number of successful extensions: 5
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: 617
Length adjustment: 37
Effective length of query: 581
Effective length of database: 580
Effective search space:   336980
Effective search space used:   336980
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_083441462.1 NITAL_RS11140 (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.30787.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.1e-232  757.9   1.9   3.6e-232  757.7   1.9    1.0  1  lcl|NCBI__GCF_000969705.1:WP_083441462.1  NITAL_RS11140 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000969705.1:WP_083441462.1  NITAL_RS11140 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  757.7   1.9  3.6e-232  3.6e-232       2     556 ..      22     588 ..      21     589 .. 0.97

  Alignments for each domain:
  == domain 1  score: 757.7 bits;  conditional E-value: 3.6e-232
                                 TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvlat 70 
                                               +ga+++++sl++ gv++vfGyPGGa+lp yd l + +++h+lvrheq+a+h+a+Gya a+G+vGv+++t
  lcl|NCBI__GCF_000969705.1:WP_083441462.1  22 TGAQAVMRSLEALGVDVVFGYPGGAILPAYDPLIEADFTHVLVRHEQGAIHMAEGYAHATGRVGVCIVT 90 
                                               79******************************************************************* PP

                                 TIGR00118  71 sGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilk 139
                                               sGP atnlvtg+a+a++dsvP++++tGqvat++iGsdafqe+d++Git+p+tkh+ +v +ae ++  + 
  lcl|NCBI__GCF_000969705.1:WP_083441462.1  91 SGPAATNLVTGLADAHMDSVPILAITGQVATTAIGSDAFQEADVTGITMPITKHNEIVYSAERIAGAIA 159
                                               ********************************************************************* PP

                                 TIGR00118 140 eafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvG 208
                                               eaf+ia +GrPGPvlvdlPkdv +a++  + +e+++lpgy+ptv+gh + i++al+li+ a++Pv+++G
  lcl|NCBI__GCF_000969705.1:WP_083441462.1 160 EAFYIARSGRPGPVLVDLPKDVLNAKVAWQWPEHLDLPGYRPTVRGHGKMIREALDLIAGAERPVIYAG 228
                                               ********************************************************************* PP

                                 TIGR00118 209 gGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarf 277
                                               gG++ a+a+eel+ +ae+l +pv+ttl+  G +p++h+l++gm GmhG ++a  a +e+dlli++Garf
  lcl|NCBI__GCF_000969705.1:WP_083441462.1 229 GGLVRAGADEELRAFAETLGLPVVTTLMARGILPDTHELTVGMPGMHGHYAAVKAFQETDLLITLGARF 297
                                               ********************************************************************* PP

                                 TIGR00118 278 ddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee.........ekkek 337
                                               ddrvtg+la+fap+ak+ih+d+dPaeigkn++vd+pivGd+k vl +llk ++++            + 
  lcl|NCBI__GCF_000969705.1:WP_083441462.1 298 DDRVTGHLASFAPHAKVIHVDVDPAEIGKNREVDVPIVGDVKVVLGQLLKVIEDKrtkgtlaelI-PDV 365
                                               **************************************************999987777766532.344 PP

                                 TIGR00118 338 e.Wlekieewkkeyilkldeeees.ikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfi 404
                                                 W  +++++k++++l++++ e+  +kPq+ i+++++   d+a++ ++vGqhqmwaaq+ ++++ r++i
  lcl|NCBI__GCF_000969705.1:WP_083441462.1 366 TaWRGHLDQMKADHPLRVEQPETGvLKPQTAIRAIHETWGDDAVYVAGVGQHQMWAAQHIPYTRGRQWI 434
                                               45***************999877659******************************************* PP

                                 TIGR00118 405 tsgGlGtmGfGlPaalGakvakp.eetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkq 472
                                               +sgGlGtmGf +Paa+Gakv++  +  vva++Gdg fqm+ qel+++v+ dipv+ +++nn +lGmv+q
  lcl|NCBI__GCF_000969705.1:WP_083441462.1 435 NSGGLGTMGFAVPAAIGAKVGVGrDVPVVAIDGDGCFQMTFQELAAAVQHDIPVVFCVINNGYLGMVRQ 503
                                               *********************972567****************************************** PP

                                 TIGR00118 473 WqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeev 540
                                               Wq+lfye+r s++ l ++lpd++kla+ay + g ri++ +el++ l++a + + +p+l++++vd +e v
  lcl|NCBI__GCF_000969705.1:WP_083441462.1 504 WQHLFYEDRLSQVALPQDLPDLMKLADAYQMPGFRISSVDELDATLAKAKQITdQPILVEFRVDPDEMV 572
                                               *************************************************997669************** PP

                                 TIGR00118 541 lPmvapGagldelvee 556
                                               +Pmv++Ga++de++e+
  lcl|NCBI__GCF_000969705.1:WP_083441462.1 573 FPMVPSGASNDEILES 588
                                               ************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (617 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: 8.48
//
[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