GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Shewanella loihica PV-4

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 5207768 Shew_0289 acetolactate synthase 2 catalytic subunit (RefSeq)

Query= SwissProt::P0DP90
         (548 letters)



>FitnessBrowser__PV4:5207768
          Length = 557

 Score =  722 bits (1864), Expect = 0.0
 Identities = 352/547 (64%), Positives = 437/547 (79%)

Query: 1   MNGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARA 60
           + GA  V+ AL A GV TVFGYPGGAIMP+YDAL    VEHLL RHEQGAA AA+GYARA
Sbjct: 7   IRGADAVIKALAAHGVTTVFGYPGGAIMPIYDALVGAPVEHLLSRHEQGAAFAAVGYARA 66

Query: 61  TGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSLA 120
           +GKTGVC ATSGPGATNL+T LADALLDS+P+VAITGQVS   IGTDAFQE+DVLG+SL+
Sbjct: 67  SGKTGVCFATSGPGATNLVTVLADALLDSVPLVAITGQVSTAVIGTDAFQEIDVLGMSLS 126

Query: 121 CTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVENEVT 180
           CTKHSF+V  +EEL   +  AF++A SGRPGPVLVDIPKDIQ+A  D +     ++ E  
Sbjct: 127 CTKHSFMVTDVEELVPTLYRAFEIAASGRPGPVLVDIPKDIQIALLDYKAPLQAIQPEPQ 186

Query: 181 FPHAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGAVEAD 240
              + +E A+ ++A+AQ+PMLYVGGGVGMA AV  LR+F+  + MP+  TLKGLG++  D
Sbjct: 187 VDPSLLESAKNLIAQAQRPMLYVGGGVGMAGAVEQLRDFINQSGMPSVATLKGLGSIAHD 246

Query: 241 YPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPHASVIHMDIDPAEM 300
           +P YLGMLGMHG KAAN AVQECDLL+ VGARFDDRVTG+L +FA HA V+H+DID AE+
Sbjct: 247 HPGYLGMLGMHGGKAANLAVQECDLLLVVGARFDDRVTGRLASFAEHAKVVHLDIDIAEL 306

Query: 301 NKLRQAHVALQGDLNALLPALQQPLNQYDWQQHCAQLRDEHSWRYDHPGDAIYAPLLLKQ 360
            KLR+  VA+ GDL  +LPAL QPL    W    A+L+ +H+W YD PG+ I+AP LL +
Sbjct: 307 GKLRRPDVAIAGDLREILPALAQPLEIAPWLAEVARLKAQHAWSYDRPGELIFAPKLLNR 366

Query: 361 LSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGLPAAVGAQVARPND 420
           L+ + P D VV  DVGQHQMW AQH+   RPE+ ++S+GLGTMGFGLPAA+GA+VARP+ 
Sbjct: 367 LAAKLPEDSVVACDVGQHQMWVAQHMWFRRPEDHLSSAGLGTMGFGLPAAIGAKVARPDA 426

Query: 421 TVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQERYSETTLTD 480
            VV +SGDGSFMMNVQEL T+KR+Q+PLKI+L+DNQ+LGMV+QWQQLFF+ER+SET L+D
Sbjct: 427 CVVAVSGDGSFMMNVQELTTIKRRQIPLKILLIDNQKLGMVKQWQQLFFEERFSETDLSD 486

Query: 481 NPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSIDELENVWPLVPPGASN 540
           NPDF+ +ASAF I G+ IT+  +VE+ALD ML++ GP+LLHV IDE  NVWPLVPPGASN
Sbjct: 487 NPDFVTMASAFDIPGRTITQAGEVESALDEMLDAKGPFLLHVRIDEAHNVWPLVPPGASN 546

Query: 541 SEMLEKL 547
            +M++++
Sbjct: 547 RDMMDEM 553


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: 944
Number of extensions: 32
Number of successful extensions: 1
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: 557
Length adjustment: 36
Effective length of query: 512
Effective length of database: 521
Effective search space:   266752
Effective search space used:   266752
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 5207768 Shew_0289 (acetolactate synthase 2 catalytic subunit (RefSeq))
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.12500.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   6.8e-214  697.3   0.0     8e-214  697.1   0.0    1.0  1  lcl|FitnessBrowser__PV4:5207768  Shew_0289 acetolactate synthase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5207768  Shew_0289 acetolactate synthase 2 catalytic subunit (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  697.1   0.0    8e-214    8e-214       2     556 ..       8     552 ..       7     553 .. 0.98

  Alignments for each domain:
  == domain 1  score: 697.1 bits;  conditional E-value: 8e-214
                        TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvlatsGPGatnlv 79 
                                      +ga++++++l ++gv tvfGyPGGa++piydal    +eh+l rheq+aa aa GyarasGk+Gv++atsGPGatnlv
  lcl|FitnessBrowser__PV4:5207768   8 RGADAVIKALAAHGVTTVFGYPGGAIMPIYDALVGAPVEHLLSRHEQGAAFAAVGYARASGKTGVCFATSGPGATNLV 85 
                                      79**************************************************************************** PP

                        TIGR00118  80 tgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGrPGPvlvdl 157
                                      t +a+a ldsvPlv++tGqv+t++iG+dafqeid+lG++l++tkhsf+v+++e+l  +l +afeia++GrPGPvlvd+
  lcl|FitnessBrowser__PV4:5207768  86 TVLADALLDSVPLVAITGQVSTAVIGTDAFQEIDVLGMSLSCTKHSFMVTDVEELVPTLYRAFEIAASGRPGPVLVDI 163
                                      ****************************************************************************** PP

                        TIGR00118 158 PkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeaseelkelaerlkipvtttl 235
                                      Pkd++ a ++++ +    l++ +p+ + ++  ++ a +li++a++P+l+vGgGv +a+a e+l+++ ++  +p ++tl
  lcl|FitnessBrowser__PV4:5207768 164 PKDIQIALLDYKAP----LQAIQPEPQVDPSLLESAKNLIAQAQRPMLYVGGGVGMAGAVEQLRDFINQSGMPSVATL 237
                                      ******99999887....999********************************************************* PP

                        TIGR00118 236 lGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihididPaeigknvkvdip 313
                                       GlG++ +dhp  lgmlGmhG k+anlav+e+dll+ vGarfddrvtg la+fa++ak++h+did ae+gk ++ d++
  lcl|FitnessBrowser__PV4:5207768 238 KGLGSIAHDHPGYLGMLGMHGGKAANLAVQECDLLLVVGARFDDRVTGRLASFAEHAKVVHLDIDIAELGKLRRPDVA 315
                                      ****************************************************************************** PP

                        TIGR00118 314 ivGdakkvleellkklkeeekkekeWlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwa 391
                                      i Gd +++l  l + l+        Wl++++++k+++  ++d+  e i   k++++l   l+++++v+ dvGqhqmw+
  lcl|FitnessBrowser__PV4:5207768 316 IAGDLREILPALAQPLE---IAP--WLAEVARLKAQHAWSYDRPGELIFAPKLLNRLAAKLPEDSVVACDVGQHQMWV 388
                                      ******99999877654...333..*********************99888999************************ PP

                        TIGR00118 392 aqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGm 469
                                      aq+  +++p+ +++s+GlGtmGfGlPaa+Gakva p++ vvav+Gdgsf+mn+qel+ti++ +ip+ki++++n+ lGm
  lcl|FitnessBrowser__PV4:5207768 389 AQHMWFRRPEDHLSSAGLGTMGFGLPAAIGAKVARPDACVVAVSGDGSFMMNVQELTTIKRRQIPLKILLIDNQKLGM 466
                                      ****************************************************************************** PP

                        TIGR00118 470 vkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapG 547
                                      vkqWq+lf+eer+set l+ ++pdfv +a a+ + g +i++  e+e++l+e+l  k+p ll v++d+ ++v+P+v+pG
  lcl|FitnessBrowser__PV4:5207768 467 VKQWQQLFFEERFSETDLS-DNPDFVTMASAFDIPGRTITQAGEVESALDEMLDAKGPFLLHVRIDEAHNVWPLVPPG 543
                                      *******************.6********************************************************* PP

                        TIGR00118 548 agldelvee 556
                                      a++ ++++e
  lcl|FitnessBrowser__PV4:5207768 544 ASNRDMMDE 552
                                      *****9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (557 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: 11.23
//
[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:

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:

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:

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:

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