Alignments for a candidate for ilvI in Nostoc punctiforme ATCC 29133; PCC 73102

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Nostoc punctiforme ATCC 29133; PCC 73102

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_012408418.1 NPUN_RS08810 acetolactate synthase, large subunit, biosynthetic type

Query= BRENDA::P9WG41
         (618 letters)



>NCBI__GCF_000020025.1:WP_012408418.1
          Length = 637

 Score =  544 bits (1401), Expect = e-159
 Identities = 297/583 (50%), Positives = 382/583 (65%), Gaps = 13/583 (2%)

Query: 24  KHPAARPKHVALQQLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKK---LRHV 80
           K   A    V  ++ +G  A++ SL   GVD IFG PGGA+LP+YD L+  +    ++H+
Sbjct: 24  KQSRASSPPVLPKRASGGFALLDSLHRHGVDYIFGYPGGAILPIYDDLYKVEATGAIKHI 83

Query: 81  LVRHEQGAGHAASGYAHVTGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRG 140
           LVRHEQGA HAA GYA  TG+VGVC  TSGPGATNLVT +A A MDSIP++ +TGQV R 
Sbjct: 84  LVRHEQGAAHAADGYARATGKVGVCFGTSGPGATNLVTGIATAYMDSIPMIVVTGQVARP 143

Query: 141 LIGTDAFQEADISGITMPITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVL 200
            IGTDAFQE DI GIT+PI KH+++VR   D+ R++AEAFHIA++GRPG VL+D+PKDV 
Sbjct: 144 SIGTDAFQETDIYGITLPIVKHSYVVRDPKDMARIVAEAFHIASTGRPGPVLIDVPKDVA 203

Query: 201 QGQCTF--SWPPRMELPGYKPNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQL 258
             +  +    P  ++L GY+P  K + RQ+  A +LI  +R+P+LY+GGG I   A E++
Sbjct: 204 LEEFDYVPVKPGSVKLRGYRPTVKGNPRQINAAIQLITESRRPLLYIGGGAIAAGAHEEI 263

Query: 259 RELAELTGIPVVTTLMARGAFPDSHRQNLGMPGMHGTVAAVAALQRSDLLIALGTRFDDR 318
           +ELAEL  IPV TTLM  GAF + H   LGM GMHGT  A  A+   DLLI +G RFDDR
Sbjct: 264 KELAELFNIPVTTTLMGIGAFDEHHPLALGMLGMHGTAYANFAVSDCDLLICVGARFDDR 323

Query: 319 VTGKLDSFAPEAKVIHADIDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPGT-IE 377
           VTGKLD FA  AKVIH DIDPAE+GKNR  +VPIVGDV+ V+ +L+   +   +  T  +
Sbjct: 324 VTGKLDEFASRAKVIHIDIDPAEVGKNRIPEVPIVGDVRNVLVDLLRRCKETGVKATPNQ 383

Query: 378 MADWWAYLNGVRKTYPLSYGPQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQF 437
             +W   +N  R  YPL   PQ   S+SP+ VI ++   A P+A +   VGQHQMWAAQF
Sbjct: 384 NQEWLNLVNRWRDEYPLIV-PQHPDSISPQEVIVEVNSQA-PNAFYTTDVGQHQMWAAQF 441

Query: 438 IRYEKPRSWLNSGGLGTMGFAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATCAVEG 497
           ++   PR W++S GLGTMGF +PAAMGAK+A P  EV  I GD  FQM  QEL T A  G
Sbjct: 442 LK-NGPRRWISSAGLGTMGFGLPAAMGAKVAFPDEEVICISGDASFQMCLQELGTLAQYG 500

Query: 498 IPVKVALINNGNLGMVRQWQSLFYAERYSQTDLATHSHRIPDFVKLAEALGCVGLRCERE 557
           I VK  +INNG  GMVRQWQ  FY ERYS +++      +PD   LA+A G  G+     
Sbjct: 501 INVKTIIINNGWQGMVRQWQQAFYGERYSCSNMEV---GMPDVELLAKAYGIKGMVISDR 557

Query: 558 EDVVDVINQARAINDCPVVIDFIVGADAQVWPMVAAGTSNDEI 600
             + D I +  A +  PV+++  V  D   +PMVA G SN ++
Sbjct: 558 SQLKDAIAEMLA-HKGPVILNVHVTRDENCYPMVAPGKSNAQM 599


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: 1141
Number of extensions: 60
Number of successful extensions: 6
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: 637
Length adjustment: 38
Effective length of query: 580
Effective length of database: 599
Effective search space:   347420
Effective search space used:   347420
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: 54 (25.4 bits)

Align candidate WP_012408418.1 NPUN_RS08810 (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.25246.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.5e-265  865.5   0.1   8.9e-265  865.3   0.1    1.0  1  lcl|NCBI__GCF_000020025.1:WP_012408418.1  NPUN_RS08810 acetolactate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020025.1:WP_012408418.1  NPUN_RS08810 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  865.3   0.1  8.9e-265  8.9e-265       2     555 ..      39     601 ..      38     603 .. 0.98

  Alignments for each domain:
  == domain 1  score: 865.3 bits;  conditional E-value: 8.9e-265
                                 TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly....dselehilvrheqaaahaadGyarasGkvGv 66 
                                               +g+ +l++sl+++gv+++fGyPGGa+lpiyd ly    ++ ++hilvrheq+aahaadGyara+GkvGv
  lcl|NCBI__GCF_000020025.1:WP_012408418.1  39 SGGFALLDSLHRHGVDYIFGYPGGAILPIYDDLYkveaTGAIKHILVRHEQGAAHAADGYARATGKVGV 107
                                               688899****************************9887789**************************** PP

                                 TIGR00118  67 vlatsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlp 135
                                               +++tsGPGatnlvtgiatay+ds+P++v+tGqva+  iG+dafqe di Gitlp++khs++v++++d++
  lcl|NCBI__GCF_000020025.1:WP_012408418.1 108 CFGTSGPGATNLVTGIATAYMDSIPMIVVTGQVARPSIGTDAFQETDIYGITLPIVKHSYVVRDPKDMA 176
                                               ********************************************************************* PP

                                 TIGR00118 136 eilkeafeiastGrPGPvlvdlPkdvteaeieleve..ekvelpgykptvkghklqikkaleliekakk 202
                                               +i+ eaf+iastGrPGPvl+d+Pkdv+ +e+++      +v+l+gy+ptvkg+++qi++a++li+++++
  lcl|NCBI__GCF_000020025.1:WP_012408418.1 177 RIVAEAFHIASTGRPGPVLIDVPKDVALEEFDYVPVkpGSVKLRGYRPTVKGNPRQINAAIQLITESRR 245
                                               ********************************9876579****************************** PP

                                 TIGR00118 203 PvllvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlli 271
                                               P+l++GgG+i+a+a+ee+kelae ++ipvtttl+G+Gaf+e+hplalgmlGmhGt++an+avs++dlli
  lcl|NCBI__GCF_000020025.1:WP_012408418.1 246 PLLYIGGGAIAAGAHEEIKELAELFNIPVTTTLMGIGAFDEHHPLALGMLGMHGTAYANFAVSDCDLLI 314
                                               ********************************************************************* PP

                                 TIGR00118 272 avGarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee.....ekk 335
                                               +vGarfddrvtg+l++fa++ak+ihididPae+gkn+  ++pivGd+++vl +ll++ ke+      ++
  lcl|NCBI__GCF_000020025.1:WP_012408418.1 315 CVGARFDDRVTGKLDEFASRAKVIHIDIDPAEVGKNRIPEVPIVGDVRNVLVDLLRRCKETgvkatPNQ 383
                                               *********************************************************999888886566 PP

                                 TIGR00118 336 ekeWlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfi 404
                                               ++eWl+ +++w++ey+l + ++ +si Pq+vi e+  +++ +a++ttdvGqhqmwaaqf+k+  pr++i
  lcl|NCBI__GCF_000020025.1:WP_012408418.1 384 NQEWLNLVNRWRDEYPLIVPQHPDSISPQEVIVEVNSQAP-NAFYTTDVGQHQMWAAQFLKNG-PRRWI 450
                                               667***********************************99.6*******************98.***** PP

                                 TIGR00118 405 tsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqW 473
                                               +s+GlGtmGfGlPaa+Gakva p+e+v++++Gd+sfqm lqel t+++y+i+vk++i+nn ++Gmv+qW
  lcl|NCBI__GCF_000020025.1:WP_012408418.1 451 SSAGLGTMGFGLPAAMGAKVAFPDEEVICISGDASFQMCLQELGTLAQYGINVKTIIINNGWQGMVRQW 519
                                               ********************************************************************* PP

                                 TIGR00118 474 qelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlP 542
                                               q+ fy erys ++++ ++pd++ la+ayG+kg+ i+++++l+++++e+l++k+pv+l+v+v ++e+++P
  lcl|NCBI__GCF_000020025.1:WP_012408418.1 520 QQAFYGERYSCSNMEVGMPDVELLAKAYGIKGMVISDRSQLKDAIAEMLAHKGPVILNVHVTRDENCYP 588
                                               ********************************************************************* PP

                                 TIGR00118 543 mvapGagldelve 555
                                               mvapG++++++v+
  lcl|NCBI__GCF_000020025.1:WP_012408418.1 589 MVAPGKSNAQMVG 601
                                               ***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (637 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: 12.98
//
[ok]

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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