GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Klebsiella michiganensis M5al

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 BWI76_RS00960 BWI76_RS00960 acetolactate synthase 2 catalytic subunit

Query= SwissProt::P0DP90
         (548 letters)



>FitnessBrowser__Koxy:BWI76_RS00960
          Length = 548

 Score =  990 bits (2559), Expect = 0.0
 Identities = 488/548 (89%), Positives = 518/548 (94%)

Query: 1   MNGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARA 60
           MNGA+WVVHALRAQGV+TVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARA
Sbjct: 1   MNGARWVVHALRAQGVDTVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARA 60

Query: 61  TGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSLA 120
           TGKTGVCIATSGPGATNLITGLADALLDS+PVVAITGQV+APFIGTDAFQEVDVLGLSLA
Sbjct: 61  TGKTGVCIATSGPGATNLITGLADALLDSVPVVAITGQVAAPFIGTDAFQEVDVLGLSLA 120

Query: 121 CTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVENEVT 180
           CTKHSFLVQSLEELPRI+AEAF VA SGRPGPVLVDIPKDIQLA GDL+P F+ V ++V 
Sbjct: 121 CTKHSFLVQSLEELPRIIAEAFHVANSGRPGPVLVDIPKDIQLAQGDLDPHFSMVADDVD 180

Query: 181 FPHAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGAVEAD 240
           FP+A++E A QML ++QKPMLYVGGGVGMAQAVPALREFL  T+MPAT TLKGLG V AD
Sbjct: 181 FPYADIEYALQMLTQSQKPMLYVGGGVGMAQAVPALREFLTVTQMPATATLKGLGVVAAD 240

Query: 241 YPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPHASVIHMDIDPAEM 300
           YPYYLGMLGMHGTKAAN AVQECDLLIAVGARFDDRVTGKLNTFAPHA VIHMDIDPAE+
Sbjct: 241 YPYYLGMLGMHGTKAANLAVQECDLLIAVGARFDDRVTGKLNTFAPHAKVIHMDIDPAEL 300

Query: 301 NKLRQAHVALQGDLNALLPALQQPLNQYDWQQHCAQLRDEHSWRYDHPGDAIYAPLLLKQ 360
           NKLRQAH+ L GDLN +LPALQQPL+   W+Q  AQLR EH+WRYDHPG+AIYAPLLLKQ
Sbjct: 301 NKLRQAHIGLTGDLNVMLPALQQPLSIDAWRQRNAQLRAEHAWRYDHPGEAIYAPLLLKQ 360

Query: 361 LSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGLPAAVGAQVARPND 420
           LS+RKPADCVVTTDVGQHQMW+AQH+ +TRPENFITSSGLGTMGFGLPAAVGAQVARP+D
Sbjct: 361 LSERKPADCVVTTDVGQHQMWSAQHMTYTRPENFITSSGLGTMGFGLPAAVGAQVARPDD 420

Query: 421 TVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQERYSETTLTD 480
           TV+CISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQERYSETTLTD
Sbjct: 421 TVICISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQERYSETTLTD 480

Query: 481 NPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSIDELENVWPLVPPGASN 540
           NPDFL LASAFGI GQHITRKDQVEAALDTML+S GPYLLHVSIDELENVWPLVPPGASN
Sbjct: 481 NPDFLTLASAFGIPGQHITRKDQVEAALDTMLSSQGPYLLHVSIDELENVWPLVPPGASN 540

Query: 541 SEMLEKLS 548
           +EMLEKLS
Sbjct: 541 AEMLEKLS 548


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: 1059
Number of extensions: 27
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: 548
Length adjustment: 36
Effective length of query: 512
Effective length of database: 512
Effective search space:   262144
Effective search space used:   262144
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 BWI76_RS00960 BWI76_RS00960 (acetolactate synthase 2 catalytic subunit)
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.24293.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   3.7e-221  721.3   0.0   4.1e-221  721.1   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS00960  BWI76_RS00960 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS00960  BWI76_RS00960 acetolactate synthase 2 catalytic subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  721.1   0.0  4.1e-221  4.1e-221       1     555 [.       1     545 [.       1     547 [. 0.97

  Alignments for each domain:
  == domain 1  score: 721.1 bits;  conditional E-value: 4.1e-221
                               TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvlats 71 
                                             ++ga+ +v++l+++gv+tvfGyPGGa++p+ydalyd+++eh+l rheq+aa aa Gyara+Gk+Gv++ats
  lcl|FitnessBrowser__Koxy:BWI76_RS00960   1 MNGARWVVHALRAQGVDTVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARATGKTGVCIATS 71 
                                             789******************************************************************** PP

                               TIGR00118  72 GPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeaf 142
                                             GPGatnl+tg+a+a ldsvP+v++tGqva+  iG+dafqe+d+lG++l++tkhsflv++ e+lp+i+ eaf
  lcl|FitnessBrowser__Koxy:BWI76_RS00960  72 GPGATNLITGLADALLDSVPVVAITGQVAAPFIGTDAFQEVDVLGLSLACTKHSFLVQSLEELPRIIAEAF 142
                                             *********************************************************************** PP

                               TIGR00118 143 eiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGvii 213
                                             ++a++GrPGPvlvd+Pkd++ a+ +l+ +   ++   + +v   ++ i+ al+++++++kP+l+vGgGv +
  lcl|FitnessBrowser__Koxy:BWI76_RS00960 143 HVANSGRPGPVLVDIPKDIQLAQGDLDPH--FSM--VADDVDFPYADIEYALQMLTQSQKPMLYVGGGVGM 209
                                             ***********************999887..444..4567778899************************* PP

                               TIGR00118 214 aeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgn 284
                                             a+a   l+e+   +++p t+tl GlG + +d p  lgmlGmhGtk+anlav+e+dlliavGarfddrvtg+
  lcl|FitnessBrowser__Koxy:BWI76_RS00960 210 AQAVPALREFLTVTQMPATATLKGLGVVAADYPYYLGMLGMHGTKAANLAVQECDLLIAVGARFDDRVTGK 280
                                             *********************************************************************** PP

                               TIGR00118 285 lakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekieewkkeyilkld 355
                                             l++fap+ak+ih+didPae++k ++++i + Gd + +l  l + l    + +  W ++ +++++e+  ++d
  lcl|FitnessBrowser__Koxy:BWI76_RS00960 281 LNTFAPHAKVIHMDIDPAELNKLRQAHIGLTGDLNVMLPALQQPL----SID-AWRQRNAQLRAEHAWRYD 346
                                             *********************************877776665444....333.4***************** PP

                               TIGR00118 356 eeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvak 426
                                             +  e+i    ++k+ls+  + + +vttdvGqhqmw+aq+ ++++p++fits+GlGtmGfGlPaa+Ga+va 
  lcl|FitnessBrowser__Koxy:BWI76_RS00960 347 HPGEAIYAPLLLKQLSERKPADCVVTTDVGQHQMWSAQHMTYTRPENFITSSGLGTMGFGLPAAVGAQVAR 417
                                             *******99************************************************************** PP

                               TIGR00118 427 peetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvkl 497
                                             p++tv++++Gdgsf+mn+qel t+++ ++p+kiv+l+n+ lGmv+qWq+lf++eryset+l+ ++pdf  l
  lcl|FitnessBrowser__Koxy:BWI76_RS00960 418 PDDTVICISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQERYSETTLT-DNPDFLTL 487
                                             **************************************************************.6******* PP

                               TIGR00118 498 aeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldelve 555
                                             a a+G+ g++i++++++e++l+ +l+s++p+ll v++d+ e+v+P+v+pGa+++e++e
  lcl|FitnessBrowser__Koxy:BWI76_RS00960 488 ASAFGIPGQHITRKDQVEAALDTMLSSQGPYLLHVSIDELENVWPLVPPGASNAEMLE 545
                                             ********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (548 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 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 7.55
//
[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