Alignments for a candidate for ilvI in Shewanella sp. ANA-3

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Shewanella sp. ANA-3

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 7023118 Shewana3_0356 acetolactate synthase 2 catalytic subunit (RefSeq)

Query= SwissProt::P0DP90
         (548 letters)



>FitnessBrowser__ANA3:7023118
          Length = 557

 Score =  723 bits (1866), Expect = 0.0
 Identities = 357/547 (65%), Positives = 429/547 (78%)

Query: 1   MNGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARA 60
           + GA  V+  L A GV TVFGYPGGAIMP+YDALY   VEHLL RHEQGAA AA+GYARA
Sbjct: 7   IRGADAVIKVLAAHGVTTVFGYPGGAIMPIYDALYGSPVEHLLSRHEQGAAFAAVGYARA 66

Query: 61  TGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSLA 120
           +GKTGVC ATSGPGATNLIT LADALLDS+PVVAITGQVS   IGTDAFQE+DVLG+SL+
Sbjct: 67  SGKTGVCFATSGPGATNLITSLADALLDSVPVVAITGQVSTAVIGTDAFQEIDVLGMSLS 126

Query: 121 CTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVENEVT 180
           CTKHSF+V  + +L   + +AF++A SGRPGPVLVDIPKDIQ+A  +       V NE  
Sbjct: 127 CTKHSFMVTDVNDLIPTLYQAFEIAASGRPGPVLVDIPKDIQIAQLEYRTPLLAVTNEPQ 186

Query: 181 FPHAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGAVEAD 240
              +E++ AR +LA+A++PMLYVGGGVGMA AV  LREF+ AT MP+  TLKGLG++   
Sbjct: 187 ASASEIDAARALLAEAKQPMLYVGGGVGMAGAVDQLREFIKATGMPSVATLKGLGSIAHG 246

Query: 241 YPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPHASVIHMDIDPAEM 300
            P YLGMLGMHG KAAN AVQ+CDLL+  GARFDDRVTG+L TFA  A VIH+DID AE+
Sbjct: 247 TPGYLGMLGMHGGKAANLAVQDCDLLVVAGARFDDRVTGRLATFANKAKVIHLDIDAAEL 306

Query: 301 NKLRQAHVALQGDLNALLPALQQPLNQYDWQQHCAQLRDEHSWRYDHPGDAIYAPLLLKQ 360
            KLRQ  VA+ GDL  + PAL   LN   WQ     L  +H W Y HPG  IYAP +L++
Sbjct: 307 GKLRQPDVAIAGDLRQIFPALAMALNITPWQAEVEHLARKHQWDYQHPGSLIYAPAMLRR 366

Query: 361 LSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGLPAAVGAQVARPND 420
           L+++ P D VV  DVGQHQMW AQH+   RPE+ ++S+GLGTMGFGLPAA+GAQVARP+ 
Sbjct: 367 LANKLPEDSVVCCDVGQHQMWVAQHMWFRRPEDHLSSAGLGTMGFGLPAAIGAQVARPDA 426

Query: 421 TVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQERYSETTLTD 480
           TVV +SGDGSFMMNVQEL T+KR++LP+KI+L+DNQ+LGMV+QWQQLFF+ERYSET L+D
Sbjct: 427 TVVTVSGDGSFMMNVQELTTIKRRKLPVKILLIDNQKLGMVKQWQQLFFEERYSETDLSD 486

Query: 481 NPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSIDELENVWPLVPPGASN 540
           NPDF+ LASAF I G+ I   D+VE AL  ML + GPYLLHV+ID+  NVWPLVPPGASN
Sbjct: 487 NPDFVQLASAFDIPGRTIFSSDEVEEALTEMLAAKGPYLLHVAIDDAFNVWPLVPPGASN 546

Query: 541 SEMLEKL 547
           S+M++++
Sbjct: 547 SDMMDEM 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: 925
Number of extensions: 29
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 7023118 Shewana3_0356 (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.11109.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.9e-212  692.0   0.2   3.4e-212  691.7   0.2    1.0  1  lcl|FitnessBrowser__ANA3:7023118  Shewana3_0356 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7023118  Shewana3_0356 acetolactate synthase 2 catalytic subunit (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  691.7   0.2  3.4e-212  3.4e-212       2     556 ..       8     552 ..       7     553 .. 0.97

  Alignments for each domain:
  == domain 1  score: 691.7 bits;  conditional E-value: 3.4e-212
                         TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvlatsGPGatnl 78 
                                       +ga+++++ l ++gv tvfGyPGGa++piydaly s +eh+l rheq+aa aa GyarasGk+Gv++atsGPGatnl
  lcl|FitnessBrowser__ANA3:7023118   8 RGADAVIKVLAAHGVTTVFGYPGGAIMPIYDALYGSPVEHLLSRHEQGAAFAAVGYARASGKTGVCFATSGPGATNL 84 
                                       79*************************************************************************** PP

                         TIGR00118  79 vtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGrPGPvlv 155
                                       +t++a+a ldsvP+v++tGqv+t++iG+dafqeid+lG++l++tkhsf+v++++dl  +l +afeia++GrPGPvlv
  lcl|FitnessBrowser__ANA3:7023118  85 ITSLADALLDSVPVVAITGQVSTAVIGTDAFQEIDVLGMSLSCTKHSFMVTDVNDLIPTLYQAFEIAASGRPGPVLV 161
                                       ***************************************************************************** PP

                         TIGR00118 156 dlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeaseelkelaerlkipvt 232
                                       d+Pkd++ a++e++++    l +   + +++   i +a  l+++ak+P+l+vGgGv +a+a ++l+e+ +++ +p +
  lcl|FitnessBrowser__ANA3:7023118 162 DIPKDIQIAQLEYRTP----LLAVTNEPQASASEIDAARALLAEAKQPMLYVGGGVGMAGAVDQLREFIKATGMPSV 234
                                       ********99998877....5555566667788999999************************************** PP

                         TIGR00118 233 ttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihididPaeigknvk 309
                                       +tl GlG++ +  p  lgmlGmhG k+anlav+++dll+  Garfddrvtg la+fa++ak+ih+did ae+gk ++
  lcl|FitnessBrowser__ANA3:7023118 235 ATLKGLGSIAHGTPGYLGMLGMHGGKAANLAVQDCDLLVVAGARFDDRVTGRLATFANKAKVIHLDIDAAELGKLRQ 311
                                       ***************************************************************************** PP

                         TIGR00118 310 vdipivGdakkvleellkklkeeekkekeWlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGq 386
                                        d++i Gd ++++  l  +l+    +   W +++e++ +++   +++  + i   +++++l + l+++++v  dvGq
  lcl|FitnessBrowser__ANA3:7023118 312 PDVAIAGDLRQIFPALAMALNI---T--PWQAEVEHLARKHQWDYQHPGSLIYAPAMLRRLANKLPEDSVVCCDVGQ 383
                                       **********999998877654...3..3999*****9999999999999999999********************* PP

                         TIGR00118 387 hqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkiviln 463
                                       hqmw+aq+  +++p+ +++s+GlGtmGfGlPaa+Ga+va p++tvv+v+Gdgsf+mn+qel+ti++ ++pvki++++
  lcl|FitnessBrowser__ANA3:7023118 384 HQMWVAQHMWFRRPEDHLSSAGLGTMGFGLPAAIGAQVARPDATVVTVSGDGSFMMNVQELTTIKRRKLPVKILLID 460
                                       ***************************************************************************** PP

                         TIGR00118 464 nellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeev 540
                                       n+ lGmvkqWq+lf+eeryset l+ ++pdfv+la a+ + g +i + +e+ee+l+e+l+ k+p+ll v +d+  +v
  lcl|FitnessBrowser__ANA3:7023118 461 NQKLGMVKQWQQLFFEERYSETDLS-DNPDFVQLASAFDIPGRTIFSSDEVEEALTEMLAAKGPYLLHVAIDDAFNV 536
                                       *************************.6************************************************** PP

                         TIGR00118 541 lPmvapGagldelvee 556
                                       +P+v+pGa+++++++e
  lcl|FitnessBrowser__ANA3:7023118 537 WPLVPPGASNSDMMDE 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 7.43
//
[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