Alignments for a candidate for ilvI in Methanococcus maripaludis C5

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Methanococcus maripaludis C5

Align acetohydroxy-acid synthase large subunit (EC 2.2.1.6) (characterized)
to candidate WP_011868714.1 MMARC5_RS04835 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_000016125.1:WP_011868714.1
          Length = 587

 Score =  843 bits (2179), Expect = 0.0
 Identities = 405/592 (68%), Positives = 490/592 (82%), Gaps = 14/592 (2%)

Query: 1   MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARA 60
           M GAEAM+KAL+AE V++LFGYPGG LLPFYDAL+HSDL+H+LTRHEQAAAHAADGYARA
Sbjct: 1   MKGAEAMMKALDAENVKVLFGYPGGQLLPFYDALYHSDLVHILTRHEQAAAHAADGYARA 60

Query: 61  SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMP 120
           SG+VGVC+ TSGPGATNLVTGVATAH+DSSP+VALTGQVPTKLIGNDAFQEIDALG+FM 
Sbjct: 61  SGEVGVCVATSGPGATNLVTGVATAHADSSPVVALTGQVPTKLIGNDAFQEIDALGMFMQ 120

Query: 121 IVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLI 180
           I KHNFQIQKT +IP+IFR AFEIA+TGRPG VH+DLPKDVQ+ ELD++K+PIP+ + L 
Sbjct: 121 ITKHNFQIQKTNEIPKIFRKAFEIAKTGRPGAVHVDLPKDVQDNELDLEKYPIPADINLQ 180

Query: 181 GYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMG 240
           GY PT  GHP QIKKA++L+  A+RP+I+AGGGV ++ A  EL+KL E   IPVCTTLMG
Sbjct: 181 GYKPTKFGHPLQIKKAVELMKIAQRPVIIAGGGVQIANATPELIKLSEYAQIPVCTTLMG 240

Query: 241 KGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKIIHI 300
           KG   E HPL+LG+VGMHGT+ +NY + ESDVLI+IGCRFSDRITGDI +FA NAKIIH+
Sbjct: 241 KGVFPEEHPLSLGLVGMHGTQASNYSVYESDVLIAIGCRFSDRITGDISTFAPNAKIIHV 300

Query: 301 DIDPAEIGKNVNVDVPIVGDAKLILKEVIKQL--DYIINKDSKENNDKENISQWIENVNS 358
           DIDPAEIGKNV  D+PIVGDAK ILK+V+  L    I+NK           ++W+ENV  
Sbjct: 301 DIDPAEIGKNVRADIPIVGDAKAILKDVLIHLMKKEIVNK-----------TEWMENVKK 349

Query: 359 LKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNIN-KNTIITTDVGQNQMWMAHYFKTQT 417
           L+K S+PVM++D+ PIKPQK++KE+M  + +++ +  NT+ITTDVGQNQMWMAHYF+T  
Sbjct: 350 LQKKSMPVMEFDNTPIKPQKVIKEMMNAVREIDPSLTNTVITTDVGQNQMWMAHYFQTSA 409

Query: 418 PRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVI 477
           P+SF+SSGG GTMGFGFP+AIGAK A+PD+ VI +TGDGGF+MN QEL TIAEY IPV++
Sbjct: 410 PKSFISSGGQGTMGFGFPAAIGAKFARPDANVIAVTGDGGFLMNSQELATIAEYEIPVIV 469

Query: 478 CIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKE 537
            IFDNRTLGMVYQWQNL+YGKRQC+V+ G  PDFIKLAESYGI A R+E P +INEA K 
Sbjct: 470 VIFDNRTLGMVYQWQNLYYGKRQCAVHLGETPDFIKLAESYGIGALRLEKPEDINEAFKT 529

Query: 538 AINCDEPYLLDFAIDPSSALSMVPPGAKLTNIIDAVQEHPNEKIVCFDEIKR 589
           A+N  +PYL+D  IDP+ AL MVPPG  +TNI+   ++ P  K  CF E+K+
Sbjct: 530 ALNSGKPYLIDIIIDPAEALHMVPPGGNMTNILFPERQEPTPKAQCFSEMKK 581


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: 1066
Number of extensions: 34
Number of successful extensions: 3
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: 587
Length adjustment: 37
Effective length of query: 562
Effective length of database: 550
Effective search space:   309100
Effective search space used:   309100
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_011868714.1 MMARC5_RS04835 (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.19953.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.2e-259  846.9   3.1   3.7e-259  846.7   3.1    1.0  1  lcl|NCBI__GCF_000016125.1:WP_011868714.1  MMARC5_RS04835 acetolactate synt


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016125.1:WP_011868714.1  MMARC5_RS04835 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  846.7   3.1  3.7e-259  3.7e-259       1     554 [.       1     562 [.       1     565 [. 0.98

  Alignments for each domain:
  == domain 1  score: 846.7 bits;  conditional E-value: 3.7e-259
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               +kgae+++++l +e+v+++fGyPGG++lp+ydaly+s+l hil+rheqaaahaadGyarasG+vGv++a
  lcl|NCBI__GCF_000016125.1:WP_011868714.1   1 MKGAEAMMKALDAENVKVLFGYPGGQLLPFYDALYHSDLVHILTRHEQAAAHAADGYARASGEVGVCVA 69 
                                               89******************************************************************* PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPGatnlvtg+ata++ds+P+v+ltGqv+t+liG+dafqeid lG+++ +tkh+f+++k++++p+i+
  lcl|NCBI__GCF_000016125.1:WP_011868714.1  70 TSGPGATNLVTGVATAHADSSPVVALTGQVPTKLIGNDAFQEIDALGMFMQITKHNFQIQKTNEIPKIF 138
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleve...ekvelpgykptvkghklqikkaleliekakkPv 204
                                               ++afeia+tGrPG v+vdlPkdv+++e++le++   ++++l+gykpt+ gh+lqikka+el++ a++Pv
  lcl|NCBI__GCF_000016125.1:WP_011868714.1 139 RKAFEIAKTGRPGAVHVDLPKDVQDNELDLEKYpipADINLQGYKPTKFGHPLQIKKAVELMKIAQRPV 207
                                               ***************************998776677********************************* PP

                                 TIGR00118 205 llvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliav 273
                                               +++GgGv ia+a+ el +l+e ++ipv+ttl+G+G fpe+hpl+lg++GmhGt+++n++v e+d+lia+
  lcl|NCBI__GCF_000016125.1:WP_011868714.1 208 IIAGGGVQIANATPELIKLSEYAQIPVCTTLMGKGVFPEEHPLSLGLVGMHGTQASNYSVYESDVLIAI 276
                                               ********************************************************************* PP

                                 TIGR00118 274 GarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkeke.Wle 341
                                               G+rf+dr+tg++++fap+akiih+didPaeigknv++dipivGdak +l+++l +l ++e  +k  W+e
  lcl|NCBI__GCF_000016125.1:WP_011868714.1 277 GCRFSDRITGDISTFAPNAKIIHVDIDPAEIGKNVRADIPIVGDAKAILKDVLIHLMKKEIVNKTeWME 345
                                               ***************************************************999888886655544*** PP

                                 TIGR00118 342 kieewkkeyilkldeeeesikPqkvikelskllkd......eaivttdvGqhqmwaaqfyktkkprkfi 404
                                               ++++++k++++ ++ ++++ikPqkvike+++ +++      ++++ttdvGq+qmw+a++++t++p++fi
  lcl|NCBI__GCF_000016125.1:WP_011868714.1 346 NVKKLQKKSMPVMEFDNTPIKPQKVIKEMMNAVREidpsltNTVITTDVGQNQMWMAHYFQTSAPKSFI 414
                                               ********************************9999999*9**************************** PP

                                 TIGR00118 405 tsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqW 473
                                               +sgG GtmGfG+Paa+Gak a p+++v+avtGdg+f mn qel+ti+ey+ipv++vi++n++lGmv+qW
  lcl|NCBI__GCF_000016125.1:WP_011868714.1 415 SSGGQGTMGFGFPAAIGAKFARPDANVIAVTGDGGFLMNSQELATIAEYEIPVIVVIFDNRTLGMVYQW 483
                                               ********************************************************************* PP

                                 TIGR00118 474 qelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlP 542
                                               q+l+y +r+ +++l+ e+pdf+klae+yG+ ++r+ekpe+++e++k al+s +p+l+d+ +d ++e+l 
  lcl|NCBI__GCF_000016125.1:WP_011868714.1 484 QNLYYGKRQCAVHLG-ETPDFIKLAESYGIGALRLEKPEDINEAFKTALNSGKPYLIDIIID-PAEALH 550
                                               ***************.7*********************************************.999*** PP

                                 TIGR00118 543 mvapGagldelv 554
                                               mv+pG+++++++
  lcl|NCBI__GCF_000016125.1:WP_011868714.1 551 MVPPGGNMTNIL 562
                                               *********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (587 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: 11.89
//
[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