Alignments for a candidate for ilvI in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Dyella japonica UNC79MFTsu3.2

Align Acetolactate synthase isozyme 2 large subunit; AHAS-II; ALS-II; Acetohydroxy-acid synthase II large subunit; EC 2.2.1.6 (characterized)
to candidate N515DRAFT_0567 N515DRAFT_0567 acetolactate synthase, large subunit

Query= SwissProt::P0DP90
         (548 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0567
          Length = 625

 Score =  424 bits (1091), Expect = e-123
 Identities = 240/580 (41%), Positives = 336/580 (57%), Gaps = 37/580 (6%)

Query: 1   MNGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGGVEHL-----------LCRHEQG 49
           M+GA+ VV  L  +GV+ +FGY GGAI+PVYDA++     H+           +  +EQG
Sbjct: 26  MSGAEVVVQVLADEGVDVLFGYSGGAILPVYDAVFRYNATHIGPSGGEPMPLIVPANEQG 85

Query: 50  AAMAAIGYARATGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAF 109
           A   A GYARA+GK GV I TSGPGATN++T + D++ DS+P+V + GQV    IG+DAF
Sbjct: 86  AGFMAAGYARASGKVGVAIVTSGPGATNMVTPVRDSMSDSVPMVVLCGQVPTTAIGSDAF 145

Query: 110 QEVDVLGLSLACTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQ------- 162
           QE  +  +  AC KH FLV   E+L   +  AF++A SGRPGPV+VDIPKD+Q       
Sbjct: 146 QEAPIANIMSACAKHVFLVTDAEKLEATLRTAFEIARSGRPGPVVVDIPKDVQNTLLPFH 205

Query: 163 ----LASGDLEPWFTTVENEVTFPHAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALRE 218
               L           +E   T   A+     + LA++++P++Y GGG   + A   LR 
Sbjct: 206 GEGLLPMPGYRARLQRLEQS-TLDDAQCVAFFEALAQSKRPLIYAGGGTIASGASHELRA 264

Query: 219 FLAATKMPATCTLKGLGAVEADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVT 278
           F+A   +P T TL GLGA +   P  L MLGMHGT  AN+AV++CD L  +GARFDDRV 
Sbjct: 265 FVADYGLPVTTTLMGLGAYDTTEPLALHMLGMHGTAYANYAVEDCDFLFTLGARFDDRVA 324

Query: 279 GKLNTFAPHASVI-HMDIDPAEMNKLRQAHVALQGDLNALLPAL-----------QQPLN 326
           G  + FAP A  I  +DIDPAE+ K++       GDL   L  L           Q    
Sbjct: 325 GVPDKFAPQAKFIAQIDIDPAEIGKVKSVDWHHTGDLTRTLAQLRAWGERHGWREQLSAR 384

Query: 327 QYDWQQHCAQLRDEHSWRYDHPGDAIYAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHI 386
              W +H A+L+  H+  YD     I    ++++++       V++T VGQHQMWAAQ+ 
Sbjct: 385 YAPWHRHVAELKQVHALDYDRASPLIQPYAVIEEINRHTQGHAVISTGVGQHQMWAAQYF 444

Query: 387 AHTRPENFITSSGLGTMGFGLPAAVGAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQL 446
               P ++++S  +GTMGFGLPAA+GAQ ARP   V+ I GD S  MN+ EL TV    L
Sbjct: 445 DFREPRHWLSSGSMGTMGFGLPAAIGAQFARPGAVVIDIDGDASIRMNLGELETVTTYGL 504

Query: 447 PLKIVLLDNQRLGMVRQWQQLFFQERYSETTLT-DNPDFLMLASAFGIH-GQHITRKDQV 504
           P+K+V+L+N   GMVRQWQ+LFF+ R++ +  +    DF+  A A G    + + R++++
Sbjct: 505 PVKVVVLNNIGDGMVRQWQKLFFRGRFASSDKSLHRKDFIKAAQADGFEWARRLERREEL 564

Query: 505 EAALDTMLNSDGPYLLHVSIDELENVWPLVPPGASNSEML 544
            A +   L   GP  L V ID    V+P+V PGA+ ++M+
Sbjct: 565 AATIADFLAHPGPAFLEVMIDPDAGVYPMVGPGATYAQMI 604


Lambda     K      H
   0.320    0.135    0.410 

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: 949
Number of extensions: 38
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: 548
Length of database: 625
Length adjustment: 37
Effective length of query: 511
Effective length of database: 588
Effective search space:   300468
Effective search space used:   300468
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 N515DRAFT_0567 N515DRAFT_0567 (acetolactate synthase, large subunit)
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.934.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   2.8e-199  649.1   0.0   3.3e-199  648.8   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_0567  N515DRAFT_0567 acetolactate synt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_0567  N515DRAFT_0567 acetolactate synthase, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  648.8   0.0  3.3e-199  3.3e-199       1     555 [.      26     605 ..      26     607 .. 0.94

  Alignments for each domain:
  == domain 1  score: 648.8 bits;  conditional E-value: 3.3e-199
                                    TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly...........dselehilvrheqaaahaad 55 
                                                  ++gae++v+ l +egv+++fGy GGa+lp+yda++            + +  i++  eq+a  +a 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0567  26 MSGAEVVVQVLADEGVDVLFGYSGGAILPVYDAVFrynathigpsgGEPMPLIVPANEQGAGFMAA 91 
                                                  79********************************9444322222111224457899********** PP

                                    TIGR00118  56 GyarasGkvGvvlatsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpv 121
                                                  GyarasGkvGv+++tsGPGatn+vt++ +++ dsvP+vvl Gqv+t++iGsdafqe+ i  i+ ++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0567  92 GYARASGKVGVAIVTSGPGATNMVTPVRDSMSDSVPMVVLCGQVPTTAIGSDAFQEAPIANIMSAC 157
                                                  ****************************************************************** PP

                                    TIGR00118 122 tkhsflvkkaedlpeilkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkg.. 185
                                                   kh flv++ae l ++l+ afeia +GrPGPv+vd+Pkdv+++ + ++ e  + +pgy+ +++   
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0567 158 AKHVFLVTDAEKLEATLRTAFEIARSGRPGPVVVDIPKDVQNTLLPFHGEGLLPMPGYRARLQRle 223
                                                  **********************************************************98765411 PP

                                    TIGR00118 186 ....hklqikkaleliekakkPvllvGgGviiaeaseelkelaerlkipvtttllGlGafpedhpl 247
                                                      + +q  +  e+++++k+P++++GgG i+++as+el+ ++    +pvtttl+GlGa++ ++pl
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0567 224 qstlDDAQCVAFFEALAQSKRPLIYAGGGTIASGASHELRAFVADYGLPVTTTLMGLGAYDTTEPL 289
                                                  1112456788999***************************************************** PP

                                    TIGR00118 248 algmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeak.iihididPaeigknvkvdi 312
                                                  al mlGmhGt++an+av+++d l+++Garfddrv+g  +kfap+ak i  ididPaeigk+ +vd 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0567 290 ALHMLGMHGTAYANYAVEDCDFLFTLGARFDDRVAGVPDKFAPQAKfIAQIDIDPAEIGKVKSVDW 355
                                                  **********************************************6679**************** PP

                                    TIGR00118 313 pivGdakkvleellkklkee......ekkeke.WlekieewkkeyilkldeeeesikPqkvikels 371
                                                     Gd ++ l++l +  +++      + +    W ++++e+k+ + l +d+ +  i+P +vi+e+ 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0567 356 HHTGDLTRTLAQLRAWGERHgwreqlSARY-ApWHRHVAELKQVHALDYDRASPLIQPYAVIEEIN 420
                                                  *************98877766664333344.26********************************* PP

                                    TIGR00118 372 kllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGd 437
                                                  + ++++a+++t+vGqhqmwaaq++++++pr++++sg +GtmGfGlPaa+Ga+ a p + v++++Gd
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0567 421 RHTQGHAVISTGVGQHQMWAAQYFDFREPRHWLSSGSMGTMGFGLPAAIGAQFARPGAVVIDIDGD 486
                                                  ****************************************************************** PP

                                    TIGR00118 438 gsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGv 503
                                                  +s+ mnl el+t++ y++pvk+v+lnn   Gmv+qWq+lf+++r++++  + +  df+k a+a G 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0567 487 ASIRMNLGELETVTTYGLPVKVVVLNNIGDGMVRQWQKLFFRGRFASSDKSLHRKDFIKAAQADGF 552
                                                  ************************************************99999************9 PP

                                    TIGR00118 504 k.giriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldelve 555
                                                  + + r+e++eel++ ++++l++ +p++l+v +d ++ v+Pmv pGa+ +++++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0567 553 EwARRLERREELAATIADFLAHPGPAFLEVMIDPDAGVYPMVGPGATYAQMIT 605
                                                  75889*********************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (625 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: 13.05
//
[ok]

This GapMind analysis is from Apr 09 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