Aligments for a candidate for ilvH in Dechlorosoma suillum PS

GapMind for Amino acid biosynthesis

Aligments for a candidate for ilvH in Dechlorosoma suillum PS

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate Dsui_1925 Dsui_1925 acetolactate synthase, large subunit, biosynthetic type

Query= BRENDA::P08142
         (562 letters)



>FitnessBrowser__PS:Dsui_1925
          Length = 572

 Score =  720 bits (1858), Expect = 0.0
 Identities = 358/550 (65%), Positives = 430/550 (78%), Gaps = 2/550 (0%)

Query: 14  TGAEFIVHFLEQQGIKIVTGIPGGSILPVYDALSQSTQIRHILARHEQGAGFIAQGMART 73
           TGA+ +V  LE+QG+  V+GIPGG+ILP YDALS S +IRH+LARHEQGAGFIAQGMAR 
Sbjct: 22  TGAQIVVRLLERQGVTTVSGIPGGAILPFYDALSASEKIRHVLARHEQGAGFIAQGMARA 81

Query: 74  DGKPAVCMACSGPGATNLVTAIADARLDSIPLICITGQVPASMIGTDAFQEVDTYGISIP 133
            G+PAVC+A SGPGATNL+TAIADA+LDSIPL+ ITGQVP SMIGTDAFQEVDTYG+SIP
Sbjct: 82  SGQPAVCLASSGPGATNLLTAIADAKLDSIPLVAITGQVPRSMIGTDAFQEVDTYGLSIP 141

Query: 134 ITKHNYLVRHIEELPQVMSDAFRIAQSGRPGPVWIDIPKDVQTAVFEIETQPAMAEKAAA 193
           ITKHN+LV   EEL +V+  AF +A SGRPGPV +DIPKDVQ    E+   PA   + A 
Sbjct: 142 ITKHNFLVNSAEELLEVIPRAFTLAASGRPGPVLVDIPKDVQAQAIEVSQWPAPGGRQAP 201

Query: 194 PAFSEESIRDAAAMINAAKRPVLYLGGGVINAPARVRE--LAEKAQLPTTMTLMALGMLP 251
           PA    +I  AAAMINAA+RP+LYLGGGV+++ A      LAEKA LPTTMTLMALG +P
Sbjct: 202 PAPDMAAIEKAAAMINAAERPILYLGGGVVHSGAAEAAVALAEKASLPTTMTLMALGAMP 261

Query: 252 KAHPLSLGMLGMHGVRSTNYILQEADLLIVLGARFDDRAIGKTEQFCPNAKIIHVDIDRA 311
             HPLS+ MLGMHG R TN +L+E DLLI +GARFDDRA GK   FCP A+IIH+DID +
Sbjct: 262 VDHPLSIHMLGMHGARYTNLLLEECDLLIAVGARFDDRATGKVAAFCPKAQIIHIDIDPS 321

Query: 312 ELGKIKQPHVAIQADVDDVLAQLIPLVEAQPRAEWHQLVADLQREFPCPIPKACDPLSHY 371
           EL KIK  HV I  DV +VL +L PLVEA  R  W   + DL+  F    P   DP SHY
Sbjct: 322 ELDKIKNAHVGIAGDVGEVLEKLSPLVEAHLRKRWLTHMGDLRSRFRLQRPNLEDPRSHY 381

Query: 372 GLINAVAACVDDNAIITTDVGQHQMWTAQAYPLNRPRQWLTSGGLGTMGFGLPAAIGAAL 431
           GLI AVA C+DD+A I TDVGQHQMW AQAYPL RPRQWLTSGGLGTMGFG+PAA+GAAL
Sbjct: 382 GLIQAVADCLDDSAAIATDVGQHQMWVAQAYPLRRPRQWLTSGGLGTMGFGVPAALGAAL 441

Query: 432 ANPDRKVLCFSGDGSLMMNIQEMATASENQLDVKIILMNNEALGLVHQQQSLFYEQGVFA 491
           A P+R V+CF+GDGS++MNIQE+AT +E   ++KI+LMNN+ALGLV+QQQ LFY +  FA
Sbjct: 442 AEPERTVVCFTGDGSILMNIQELATIAEAGANLKIVLMNNDALGLVYQQQELFYGKRYFA 501

Query: 492 ATYPGKINFMQIAAGFGLETCDLNNEADPQASLQEIINRPGPALIHVRIDAEEKVYPMVP 551
           + + G+ +F++IA GFG++T DL+  ADP+A+L++ + RPGP LIH  ID  EKVYPMVP
Sbjct: 502 SKFAGQPDFLKIAEGFGIDTLDLDTAADPRAALRQALQRPGPCLIHAFIDMNEKVYPMVP 561

Query: 552 PGAANTEMVG 561
           PGAANT+M+G
Sbjct: 562 PGAANTDMIG 571


Lambda     K      H
   0.320    0.135    0.400 

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: 986
Number of extensions: 38
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: 562
Length of database: 572
Length adjustment: 36
Effective length of query: 526
Effective length of database: 536
Effective search space:   281936
Effective search space used:   281936
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 Dsui_1925 Dsui_1925 (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.30027.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-210  685.4   0.0   3.1e-210  685.2   0.0    1.0  1  lcl|FitnessBrowser__PS:Dsui_1925  Dsui_1925 acetolactate synthase,


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_1925  Dsui_1925 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  685.2   0.0  3.1e-210  3.1e-210       1     555 [.      21     571 ..      21     572 .] 0.98

  Alignments for each domain:
  == domain 1  score: 685.2 bits;  conditional E-value: 3.1e-210
                         TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGPGat 76 
                                       l+ga+i+v+ l+++gv tv G+PGGa+lp+ydal  +++++h+l+rheq+a  +a+G+arasG++ v+la sGPGat
  lcl|FitnessBrowser__PS:Dsui_1925  21 LTGAQIVVRLLERQGVTTVSGIPGGAILPFYDALSaSEKIRHVLARHEQGAGFIAQGMARASGQPAVCLASSGPGAT 97 
                                       68*********************************8899************************************** PP

                         TIGR00118  77 nlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGrPGPv 153
                                       nl+t+ia+a lds+Plv++tGqv++s+iG+dafqe+d  G+++p+tkh+flv++ae+l e++ +af++a++GrPGPv
  lcl|FitnessBrowser__PS:Dsui_1925  98 NLLTAIADAKLDSIPLVAITGQVPRSMIGTDAFQEVDTYGLSIPITKHNFLVNSAEELLEVIPRAFTLAASGRPGPV 174
                                       ***************************************************************************** PP

                         TIGR00118 154 lvdlPkdvteaeieleveekvelp.gykptvkghklqikkaleliekakkPvllvGgGviiaeaseelkelaerlki 229
                                       lvd+Pkdv++++ie+++      p g +    ++ + i+ka+ +i++a++P+l+ GgGv++++a e  + lae++ +
  lcl|FitnessBrowser__PS:Dsui_1925 175 LVDIPKDVQAQAIEVSQW---PAPgGRQAPPAPDMAAIEKAAAMINAAERPILYLGGGVVHSGAAEAAVALAEKASL 248
                                       ************998876...4441555667889999**************************************** PP

                         TIGR00118 230 pvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihididPaeigk 306
                                       p t+tl+ lGa+p dhpl++ mlGmhG++++nl ++e+dlliavGarfddr tg++a f+p+a+iihididP+e++k
  lcl|FitnessBrowser__PS:Dsui_1925 249 PTTMTLMALGAMPVDHPLSIHMLGMHGARYTNLLLEECDLLIAVGARFDDRATGKVAAFCPKAQIIHIDIDPSELDK 325
                                       ***************************************************************************** PP

                         TIGR00118 307 nvkvdipivGdakkvleellkklkeeekkekeWlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttd 383
                                       + ++++ i Gd+ +vle+l   ++++ +k   Wl ++ +++++  l+  + e++     +i+++   l+d+a ++td
  lcl|FitnessBrowser__PS:Dsui_1925 326 IKNAHVGIAGDVGEVLEKLSPLVEAHLRKR--WLTHMGDLRSRFRLQRPNLEDPRSHYGLIQAVADCLDDSAAIATD 400
                                       *******************99998877666..********************************************* PP

                         TIGR00118 384 vGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkiv 460
                                       vGqhqmw+aq y+ ++pr+++tsgGlGtmGfG+PaalGa +a+pe tvv+ tGdgs+ mn+qel+ti+e++ ++kiv
  lcl|FitnessBrowser__PS:Dsui_1925 401 VGQHQMWVAQAYPLRRPRQWLTSGGLGTMGFGVPAALGAALAEPERTVVCFTGDGSILMNIQELATIAEAGANLKIV 477
                                       ***************************************************************************** PP

                         TIGR00118 461 ilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdke 537
                                       ++nn+ lG+v+q qelfy +ry ++k+a ++pdf k+ae++G+ ++ + + ++  ++l++al+  +p l+   +d +
  lcl|FitnessBrowser__PS:Dsui_1925 478 LMNNDALGLVYQQQELFYGKRYFASKFA-GQPDFLKIAEGFGIDTLDLDTAADPRAALRQALQRPGPCLIHAFIDMN 553
                                       ****************************.6*********************************************** PP

                         TIGR00118 538 eevlPmvapGagldelve 555
                                       e+v+Pmv+pGa+++++++
  lcl|FitnessBrowser__PS:Dsui_1925 554 EKVYPMVPPGAANTDMIG 571
                                       ***************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (572 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 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 7.67
//
[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