Alignments for a candidate for ilvH in Bacteroides thetaiotaomicron VPI-5482

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvH in Bacteroides thetaiotaomicron VPI-5482

Align acetolactate synthase isozyme 2 large subunit; EC 2.2.1.6 (characterized)
to candidate 351605 BT2077 acetolactate synthase large subunit (NCBI ptt file)

Query= CharProtDB::CH_003896
         (548 letters)



>FitnessBrowser__Btheta:351605
          Length = 565

 Score =  478 bits (1231), Expect = e-139
 Identities = 253/558 (45%), Positives = 360/558 (64%), Gaps = 15/558 (2%)

Query: 1   MNGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYD--GGVEHLLCRHEQGAAMAAIGYA 58
           + GA+ ++ +L  QGV T+FGYPGG+IMP +DALYD    + H+L RHEQGAA AA GYA
Sbjct: 6   ITGAEAMMRSLEHQGVTTIFGYPGGSIMPTFDALYDHQNTLNHILVRHEQGAAHAAQGYA 65

Query: 59  RATGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLS 118
           R +GK GVC+ TSGPGATN ITG+ADA++DS P+V I GQV   F+GTDAFQEVD++G++
Sbjct: 66  RVSGKVGVCLVTSGPGATNTITGIADAMIDSTPIVVIAGQVGTGFLGTDAFQEVDLVGIT 125

Query: 119 LACTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTT-VEN 177
               K S+ ++  E++   +A AF +A SGRPGPV++D  K+ Q+     EP     + +
Sbjct: 126 QPIAKWSYQIRRAEDVAWAIARAFYIASSGRPGPVVLDFAKNAQVEKTKYEPTKQEFIRS 185

Query: 178 EVTFPHAE---VEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGL 234
            V  P  +   V+ A +++  A++P++ VG GV +  A   LR F+    MPA CTL GL
Sbjct: 186 YVPVPDTDEESVKAAAELINNAERPLVLVGQGVELGSAQEELRIFIEKADMPAGCTLLGL 245

Query: 235 GAVEADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPHASVIHMD 294
            A+  D+P   GMLGMHG    N    +CD+LIAVG RFDDRVTG L T+A  A VIH D
Sbjct: 246 SALPTDHPLNKGMLGMHGNLGPNINTNKCDVLIAVGMRFDDRVTGNLATYAKQAKVIHFD 305

Query: 295 IDPAEMNKLRQAHVALQGDLNALLPALQQPLNQ------YDWQQHCAQLRDEHSWRYD-H 347
           IDPAE+NK  +  +A+ GD    L A+   L +       D  +    + +E   R + H
Sbjct: 306 IDPAEVNKNVKVDIAVLGDCKKTLAAVTGLLKKNRHTEWVDSFKEYEAVEEEKVIRPELH 365

Query: 348 PG-DAIYAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFG 406
           P  D++    +++ +S+    + ++ TDVGQ+QM +A++  +TR  + +TS GLGTMGFG
Sbjct: 366 PATDSLSMGEVVRAVSEATRHEAILVTDVGQNQMISARYFKYTRERSIVTSGGLGTMGFG 425

Query: 407 LPAAVGAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQ 466
           LPAA+GA   RP+ TV    GDG   MN+QELGT+  ++ P+KI+ L+N  LG VRQWQ 
Sbjct: 426 LPAAIGATFGRPDRTVCVFMGDGGLQMNIQELGTIMEQKAPVKIICLNNNYLGNVRQWQA 485

Query: 467 LFFQERYSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSIDE 526
           +FF  RYS T +  NPD++ +ASA+ I  + +  +++++AA+D ML++DG +LL   + E
Sbjct: 486 MFFNRRYSFTPML-NPDYMKIASAYDIPSKRVFSREELKAAIDEMLSTDGAFLLEACVVE 544

Query: 527 LENVWPLVPPGASNSEML 544
             NV P+ PPG S ++ML
Sbjct: 545 EGNVLPMTPPGGSVNQML 562


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: 771
Number of extensions: 32
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: 548
Length of database: 565
Length adjustment: 36
Effective length of query: 512
Effective length of database: 529
Effective search space:   270848
Effective search space used:   270848
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 351605 BT2077 (acetolactate synthase large subunit (NCBI ptt file))
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.4939.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   1.8e-211  689.3   0.3     2e-211  689.2   0.3    1.0  1  lcl|FitnessBrowser__Btheta:351605  BT2077 acetolactate synthase lar


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:351605  BT2077 acetolactate synthase large subunit (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  689.2   0.3    2e-211    2e-211       2     555 ..       7     563 ..       6     565 .] 0.97

  Alignments for each domain:
  == domain 1  score: 689.2 bits;  conditional E-value: 2e-211
                          TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly..dselehilvrheqaaahaadGyarasGkvGvvlatsGPGa 75 
                                        +gae++++sl+++gv t+fGyPGG+++p +daly  ++ l+hilvrheq+aahaa+Gyar+sGkvGv+l+tsGPGa
  lcl|FitnessBrowser__Btheta:351605   7 TGAEAMMRSLEHQGVTTIFGYPGGSIMPTFDALYdhQNTLNHILVRHEQGAAHAAQGYARVSGKVGVCLVTSGPGA 82 
                                        89********************************88899************************************* PP

                          TIGR00118  76 tnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGrPG 151
                                        tn++tgia+a++ds+P+vv++Gqv t  +G+dafqe+d++Git+p+ k+s+++++aed++  + +af+ias+GrPG
  lcl|FitnessBrowser__Btheta:351605  83 TNTITGIADAMIDSTPIVVIAGQVGTGFLGTDAFQEVDLVGITQPIAKWSYQIRRAEDVAWAIARAFYIASSGRPG 158
                                        **************************************************************************** PP

                          TIGR00118 152 PvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeaseelkelaerl 227
                                        Pv++d+ k+ + +++++e +++  +++y p   +++  +k+a+eli++a++P++lvG Gv  + a+eel+ + e++
  lcl|FitnessBrowser__Btheta:351605 159 PVVLDFAKNAQVEKTKYEPTKQEFIRSYVPVPDTDEESVKAAAELINNAERPLVLVGQGVELGSAQEELRIFIEKA 234
                                        **************************************************************************** PP

                          TIGR00118 228 kipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihididPae 303
                                        ++p  +tllGl a+p dhpl  gmlGmhG    n+  +++d+liavG+rfddrvtgnla++a++ak+ih+didPae
  lcl|FitnessBrowser__Btheta:351605 235 DMPAGCTLLGLSALPTDHPLNKGMLGMHGNLGPNINTNKCDVLIAVGMRFDDRVTGNLATYAKQAKVIHFDIDPAE 310
                                        **************************************************************************** PP

                          TIGR00118 304 igknvkvdipivGdakkvleellkklkeeekkekeWlekieewkk...eyilk..ldeeeesikPqkvikelskll 374
                                        ++knvkvdi++ Gd+kk l+ +   lk+++++e  W+++ +e+ +   e++++  l+   +s+   +v++++s+ +
  lcl|FitnessBrowser__Btheta:351605 311 VNKNVKVDIAVLGDCKKTLAAVTGLLKKNRHTE--WVDSFKEYEAveeEKVIRpeLHPATDSLSMGEVVRAVSEAT 384
                                        ***********************9999887777..999999987521144444337777889************** PP

                          TIGR00118 375 kdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelsti 450
                                        ++eai+ tdvGq+qm +a+++k+++ r+ +tsgGlGtmGfGlPaa+Ga  + p+ tv   +Gdg++qmn+qel ti
  lcl|FitnessBrowser__Btheta:351605 385 RHEAILVTDVGQNQMISARYFKYTRERSIVTSGGLGTMGFGLPAAIGATFGRPDRTVCVFMGDGGLQMNIQELGTI 460
                                        **************************************************************************** PP

                          TIGR00118 451 veydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeske 526
                                        +e + pvki++lnn++lG v+qWq +f+++rys t + +  pd++k+a ay + + r+ ++eel+++++e+l++++
  lcl|FitnessBrowser__Btheta:351605 461 MEQKAPVKIICLNNNYLGNVRQWQAMFFNRRYSFTPMLN--PDYMKIASAYDIPSKRVFSREELKAAIDEMLSTDG 534
                                        **************************************7..*********************************** PP

                          TIGR00118 527 pvlldvevdkeeevlPmvapGagldelve 555
                                          ll+  v +e +vlPm +pG+++++++ 
  lcl|FitnessBrowser__Btheta:351605 535 AFLLEACVVEEGNVLPMTPPGGSVNQMLL 563
                                        **************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (565 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 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.93
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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