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

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.25474.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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 11.65
//
[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