GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Thermus aquaticus YT-1

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_053767937.1 BVI061214_RS07970 biosynthetic-type acetolactate synthase large subunit

Query= BRENDA::P9WG41
         (618 letters)



>NCBI__GCF_001280255.1:WP_053767937.1
          Length = 561

 Score =  563 bits (1451), Expect = e-165
 Identities = 301/564 (53%), Positives = 387/564 (68%), Gaps = 16/564 (2%)

Query: 38  LTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVRHEQGAGHAASGYAH 97
           + GA+A++++LE  GV+VIFG PGGA++P YD L+DS  +RH+LVRHEQG  HAA+ YA 
Sbjct: 1   MKGAEALLKALEREGVEVIFGHPGGAIMPTYDALYDSP-IRHILVRHEQGGIHAATAYAR 59

Query: 98  VTGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADISGITM 157
            +GRVGV MATSGPGA NLVT LADA MDS PVVAITG V R LIGTDAFQEAD++G+TM
Sbjct: 60  ASGRVGVVMATSGPGALNLVTGLADALMDSTPVVAITGNVPRALIGTDAFQEADVTGVTM 119

Query: 158 PITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFSWPPRMELPGY 217
           PITKHN+LV+  ++IPRV+ EAFHIA++GRPG VL+D+PKDV   + T  +   ++LPGY
Sbjct: 120 PITKHNYLVQDVNEIPRVVKEAFHIASTGRPGPVLIDLPKDVQLAEFTGEFDVELDLPGY 179

Query: 218 KPNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVTTLMARG 277
           KP  + H +Q+  A   +  A +P+L VGGG     A  +L   AE TG+PV+TTLM  G
Sbjct: 180 KPTLRGHPKQIERALDALEKAERPILMVGGGAQHAHA--ELLAFAEKTGLPVITTLMGLG 237

Query: 278 AFPDSHRQNLGMPGMHGTVAAVAALQRSDLLIALGTRFDDRVTGKLDSFAPEA-KVIHAD 336
           AFP +H   LGMPGMHGTVAA  A+  +D+++A+G RFDDRVTGK+  FAP A  +IH D
Sbjct: 238 AFPGNHPLWLGMPGMHGTVAANRAIHHADVILAIGLRFDDRVTGKVSRFAPHAHTIIHVD 297

Query: 337 IDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPGTIEMADWWAYLNGVRKTYPLSY 396
           IDPAEIGK     +PIVGD + V+ E++   +       + +A WW  L   R  YPL Y
Sbjct: 298 IDPAEIGKVVRTHIPIVGDSRLVLKEMLKGAK------PLRLAAWWRELEEWRTRYPLRY 351

Query: 397 GPQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFIRYEKPRSWLNSGGLGTMG 456
            P+    L    VI    E  G +A+   GVGQHQM+AAQ+    +PRS+L SGGLGTMG
Sbjct: 352 RPRP--HLQAPEVIRAFHEATGGNAIVTTGVGQHQMFAAQYFTVTRPRSFLTSGGLGTMG 409

Query: 457 FAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATCAVEGIPVKVALINNGNLGMVRQW 516
             +P A+GA+IA P   V   DGDG FQMT QELAT     +PVKV ++NNG LGMVRQW
Sbjct: 410 VGLPFAIGAQIARPEELVIDFDGDGSFQMTLQELATVVKYRLPVKVVILNNGYLGMVRQW 469

Query: 517 QSLFYAERYSQTDLATHSHRIPDFVKLAEALGCVGLRCEREEDVVDVINQARAINDCPVV 576
           Q LF+A+RYS+  LA  +   PDF KLAEA G  G+R ER+ED+   + +A    D PVV
Sbjct: 470 QDLFHAKRYSEVYLADSN---PDFAKLAEAYGIKGVRVERKEDLKKGV-EAVLNADGPVV 525

Query: 577 IDFIVGADAQVWPMVAAGTSNDEI 600
            +F V  +  V+PM+ AG + +++
Sbjct: 526 AEFKVYHEEGVFPMIPAGGAAEDM 549


Lambda     K      H
   0.319    0.136    0.414 

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: 1107
Number of extensions: 60
Number of successful extensions: 8
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: 618
Length of database: 561
Length adjustment: 37
Effective length of query: 581
Effective length of database: 524
Effective search space:   304444
Effective search space used:   304444
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 WP_053767937.1 BVI061214_RS07970 (biosynthetic-type acetolactate synthase large 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.910858.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.2e-244  797.9   0.0   2.6e-244  797.8   0.0    1.0  1  NCBI__GCF_001280255.1:WP_053767937.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001280255.1:WP_053767937.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  797.8   0.0  2.6e-244  2.6e-244       1     555 [.       1     551 [.       1     553 [. 0.98

  Alignments for each domain:
  == domain 1  score: 797.8 bits;  conditional E-value: 2.6e-244
                             TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvlatsGP 73 
                                           +kgae+l+++l++egve++fG+PGGa++p ydalyds ++hilvrheq+ +haa  yarasG+vGvv+atsGP
  NCBI__GCF_001280255.1:WP_053767937.1   1 MKGAEALLKALEREGVEVIFGHPGGAIMPTYDALYDSPIRHILVRHEQGGIHAATAYARASGRVGVVMATSGP 73 
                                           89*********************************************************************** PP

                             TIGR00118  74 GatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeias 146
                                           Ga nlvtg+a+a +ds+P+v++tG v+++liG+dafqe+d++G+t+p+tkh++lv++++++p+++keaf+ias
  NCBI__GCF_001280255.1:WP_053767937.1  74 GALNLVTGLADALMDSTPVVAITGNVPRALIGTDAFQEADVTGVTMPITKHNYLVQDVNEIPRVVKEAFHIAS 146
                                           ************************************************************************* PP

                             TIGR00118 147 tGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeasee 219
                                           tGrPGPvl+dlPkdv+ ae++ e + +++lpgykpt++gh++qi++al+++eka++P+l+vGgG+ +  a++e
  NCBI__GCF_001280255.1:WP_053767937.1 147 TGRPGPVLIDLPKDVQLAEFTGEFDVELDLPGYKPTLRGHPKQIERALDALEKAERPILMVGGGAQH--AHAE 217
                                           ****************************************************************976..5679 PP

                             TIGR00118 220 lkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapea 292
                                           l  +ae++ +pv+ttl+GlGafp +hpl lgm GmhGt +an a+++ad+++a+G rfddrvtg++++fap+a
  NCBI__GCF_001280255.1:WP_053767937.1 218 LLAFAEKTGLPVITTLMGLGAFPGNHPLWLGMPGMHGTVAANRAIHHADVILAIGLRFDDRVTGKVSRFAPHA 290
                                           ************************************************************************9 PP

                             TIGR00118 293 k.iihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekieewkkeyilkldeeeesikPq 364
                                           + iih+didPaeigk+v+++ipivGd++ vl+e+lk +k  +     W++++eew+++y+l++  + +  +  
  NCBI__GCF_001280255.1:WP_053767937.1 291 HtIIHVDIDPAEIGKVVRTHIPIVGDSRLVLKEMLKGAKPLRLAA--WWRELEEWRTRYPLRYRPRPHLQA-P 360
                                           769**********************************99999888..*************99988776555.5 PP

                             TIGR00118 365 kvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGd 437
                                           +vi++ ++ + ++aivtt+vGqhqm+aaq++++++pr+f+tsgGlGtmG GlP a+Ga++a pee v++ +Gd
  NCBI__GCF_001280255.1:WP_053767937.1 361 EVIRAFHEATGGNAIVTTGVGQHQMFAAQYFTVTRPRSFLTSGGLGTMGVGLPFAIGAQIARPEELVIDFDGD 433
                                           8************************************************************************ PP

                             TIGR00118 438 gsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriek 510
                                           gsfqm+lqel+t+v+y +pvk+vilnn +lGmv+qWq+lf+ +ryse++la ++pdf+klaeayG+kg+r+e+
  NCBI__GCF_001280255.1:WP_053767937.1 434 GSFQMTLQELATVVKYRLPVKVVILNNGYLGMVRQWQDLFHAKRYSEVYLADSNPDFAKLAEAYGIKGVRVER 506
                                           ************************************************************************* PP

                             TIGR00118 511 peeleeklkealeskepvlldvevdkeeevlPmvapGagldelve 555
                                           +e+l++ ++ +l+ ++pv+ +++v +ee v+Pm++ G++ ++++ 
  NCBI__GCF_001280255.1:WP_053767937.1 507 KEDLKKGVEAVLNADGPVVAEFKVYHEEGVFPMIPAGGAAEDMIL 551
                                           ******************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (561 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 34.62
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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