Alignments for a candidate for ilvI in Methanobacterium lacus AL-21

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Methanobacterium lacus AL-21

Align acetohydroxy-acid synthase large subunit (EC 2.2.1.6) (characterized)
to candidate WP_013643696.1 METBO_RS00450 acetolactate synthase, large subunit, biosynthetic type

Query= metacyc::MONOMER-11900
         (599 letters)



>NCBI__GCF_000191585.1:WP_013643696.1
          Length = 577

 Score =  701 bits (1809), Expect = 0.0
 Identities = 343/585 (58%), Positives = 436/585 (74%), Gaps = 21/585 (3%)

Query: 1   MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARA 60
           M G EA+IK+L  + VEI+FGYPGG LLP YD L+ SDL H+L RHEQ AAHAADG+ARA
Sbjct: 1   MKGGEAIIKSLTDQGVEIVFGYPGGVLLPLYDVLYDSDLKHILVRHEQCAAHAADGFARA 60

Query: 61  SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMP 120
           SGKVGVCIGTSGPGATNL+TG+ATA+ DSSP++A+ GQV + LIGNDAFQE+D +G+ MP
Sbjct: 61  SGKVGVCIGTSGPGATNLITGIATAYMDSSPILAIAGQVSSHLIGNDAFQEVDTIGITMP 120

Query: 121 IVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLI 180
           I KHN+Q  K  +IP + +SAF IA TGRPGPV +DLPKDVQE E + +       ++L 
Sbjct: 121 ITKHNYQPMKANEIPGMVKSAFYIAGTGRPGPVVLDLPKDVQEEEFEFES---AKDIELP 177

Query: 181 GYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMG 240
           GY PT  GHP+Q+K+A KLI  +K+P+ILAGGG++LSGA EELL+   ++N PV T+LMG
Sbjct: 178 GYKPTMKGHPKQLKRAAKLIQESKKPVILAGGGIILSGATEELLQFANIINAPVSTSLMG 237

Query: 241 KGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKIIHI 300
           KG   E++ L+LGM+GMHG K +N+ + E D LI+IGCRFSDR TG +  FA NAKI+HI
Sbjct: 238 KGSFPEDNSLSLGMLGMHGRKVSNFIVDECDCLIAIGCRFSDRTTGLLSGFAKNAKILHI 297

Query: 301 DIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVNSLK 360
           D+DPAEIGKNV+VDVPIVGDAK IL ++IK +D           + E   +W+  V   K
Sbjct: 298 DVDPAEIGKNVDVDVPIVGDAKTILGDLIKIID----------PEPEQKQEWLNYVKDFK 347

Query: 361 KSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQTPRS 420
            S IP + ++++P+KPQ+++KEL   + D     +TI+TTDVGQNQMWMAHYF    PR 
Sbjct: 348 NSCIPRLSFNEVPLKPQQVIKELSEAVTD-----DTIVTTDVGQNQMWMAHYFDVNNPRK 402

Query: 421 FLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVICIF 480
           F+SSGGLGTMGFGFP+AIGAK+AKP++ VI + GDGGF+M CQ+L TI EY+IPV+I + 
Sbjct: 403 FISSGGLGTMGFGFPAAIGAKIAKPNNDVIAVCGDGGFLMVCQDLATIKEYDIPVIIVVL 462

Query: 481 DNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKEAIN 540
           DNR LGMV QWQ LFY +R    + G +P+F+KLAES+G+KA RIE P E+ EA++ AI 
Sbjct: 463 DNRHLGMVAQWQKLFYDERMSHTHLGESPNFVKLAESFGVKAERIEKPGEMKEAIERAIK 522

Query: 541 CDEPYLLDFAIDPSSALSMVPPGAKLTNII---DAVQEHPNEKIV 582
             EPYLLD  IDP   L MVPPG  LT I+      +E+P+E IV
Sbjct: 523 SGEPYLLDVIIDPDEILPMVPPGCSLTEIVGEYKVEREYPDEIIV 567


Lambda     K      H
   0.319    0.137    0.405 

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: 1033
Number of extensions: 43
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: 599
Length of database: 577
Length adjustment: 37
Effective length of query: 562
Effective length of database: 540
Effective search space:   303480
Effective search space used:   303480
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 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate WP_013643696.1 METBO_RS00450 (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.16016.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.5e-273  892.4   0.0   6.3e-273  892.2   0.0    1.0  1  lcl|NCBI__GCF_000191585.1:WP_013643696.1  METBO_RS00450 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000191585.1:WP_013643696.1  METBO_RS00450 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  892.2   0.0  6.3e-273  6.3e-273       1     556 [.       1     554 [.       1     555 [. 0.99

  Alignments for each domain:
  == domain 1  score: 892.2 bits;  conditional E-value: 6.3e-273
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               +kg+e++++sl+++gve+vfGyPGG +lp+yd lyds+l+hilvrheq+aahaadG+arasGkvGv+++
  lcl|NCBI__GCF_000191585.1:WP_013643696.1   1 MKGGEAIIKSLTDQGVEIVFGYPGGVLLPLYDVLYDSDLKHILVRHEQCAAHAADGFARASGKVGVCIG 69 
                                               89******************************************************************* PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPGatnl+tgiatay+ds+P+++++Gqv+++liG+dafqe+d +Git+p+tkh+++  ka+++p ++
  lcl|NCBI__GCF_000191585.1:WP_013643696.1  70 TSGPGATNLITGIATAYMDSSPILAIAGQVSSHLIGNDAFQEVDTIGITMPITKHNYQPMKANEIPGMV 138
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207
                                               k af+ia tGrPGPv++dlPkdv+e+e+e+e  +++elpgykpt+kgh++q+k+a++li+++kkPv+l+
  lcl|NCBI__GCF_000191585.1:WP_013643696.1 139 KSAFYIAGTGRPGPVVLDLPKDVQEEEFEFESAKDIELPGYKPTMKGHPKQLKRAAKLIQESKKPVILA 207
                                               ********************************************************************* PP

                                 TIGR00118 208 GgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGar 276
                                               GgG+i ++a+eel ++a+ +++pv t+l+G+G+fped+ l+lgmlGmhG+k++n+ v+e+d+lia+G+r
  lcl|NCBI__GCF_000191585.1:WP_013643696.1 208 GGGIILSGATEELLQFANIINAPVSTSLMGKGSFPEDNSLSLGMLGMHGRKVSNFIVDECDCLIAIGCR 276
                                               ********************************************************************* PP

                                 TIGR00118 277 fddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekiee 345
                                               f+dr+tg l+ fa++aki+hid+dPaeigknv vd+pivGdak++l +l+k +  e ++++eWl+ +++
  lcl|NCBI__GCF_000191585.1:WP_013643696.1 277 FSDRTTGLLSGFAKNAKILHIDVDPAEIGKNVDVDVPIVGDAKTILGDLIKIIDPEPEQKQEWLNYVKD 345
                                               ********************************************************999989******* PP

                                 TIGR00118 346 wkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGf 414
                                               +k+++i++l+ +e ++kPq+vikels+ + d++ivttdvGq+qmw+a+++++++prkfi+sgGlGtmGf
  lcl|NCBI__GCF_000191585.1:WP_013643696.1 346 FKNSCIPRLSFNEVPLKPQQVIKELSEAVTDDTIVTTDVGQNQMWMAHYFDVNNPRKFISSGGLGTMGF 414
                                               ********************************************************************* PP

                                 TIGR00118 415 GlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerys 483
                                               G+Paa+Gak+akp+++v+av+Gdg+f m++q+l+ti+eydipv+iv+l+n++lGmv+qWq+lfy+er+s
  lcl|NCBI__GCF_000191585.1:WP_013643696.1 415 GFPAAIGAKIAKPNNDVIAVCGDGGFLMVCQDLATIKEYDIPVIIVVLDNRHLGMVAQWQKLFYDERMS 483
                                               ********************************************************************* PP

                                 TIGR00118 484 etklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGaglde 552
                                               +t+l+ e+p+fvklae++Gvk++riekp e++e++++a++s ep+lldv +d ++e+lPmv+pG++l+e
  lcl|NCBI__GCF_000191585.1:WP_013643696.1 484 HTHLG-ESPNFVKLAESFGVKAERIEKPGEMKEAIERAIKSGEPYLLDVIID-PDEILPMVPPGCSLTE 550
                                               *****.7*********************************************.99************** PP

                                 TIGR00118 553 lvee 556
                                               +v+e
  lcl|NCBI__GCF_000191585.1:WP_013643696.1 551 IVGE 554
                                               *975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (577 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 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 7.22
//
[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