GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Marivita geojedonensis DPG-138

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_085635848.1 MGEO_RS06270 acetolactate synthase 3 large subunit

Query= metacyc::MONOMER-18810
         (585 letters)



>NCBI__GCF_002115805.1:WP_085635848.1
          Length = 584

 Score =  601 bits (1549), Expect = e-176
 Identities = 303/567 (53%), Positives = 400/567 (70%), Gaps = 5/567 (0%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           +M GA+++V AL ++GV+ V+GYPGGAVL IYDE+ +Q    H LVRHEQ AVHAA+GYA
Sbjct: 4   QMTGAKMVVQALKDQGVDTVFGYPGGAVLPIYDEIFQQNGIRHYLVRHEQGAVHAAEGYA 63

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           RATGK GV LVTSGPG TNAVTG+  A +DSIP+VV+TG VPT  IG DAFQE DTVGIT
Sbjct: 64  RATGKPGVVLVTSGPGATNAVTGLTDALMDSIPIVVLTGQVPTFMIGSDAFQEADTVGIT 123

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
           RP  KHN+LVKD   L+  I +AF +A +GRPGPV++DIPKDV   +  Y       +  
Sbjct: 124 RPCTKHNWLVKDTDTLSGIIHEAFHVATSGRPGPVLIDIPKDVQFASGAYTEKAKASVSH 183

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLA--NASDELRQLAALTGHPVTNTLM 255
           Y P  KG    I + V  ++ AERP  YTGGGVV +   AS  LR+L   TG P+T+TLM
Sbjct: 184 YQPQVKGDMETITQLVEAIETAERPVFYTGGGVVNSGPGASQLLRELVDATGIPITSTLM 243

Query: 256 GLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKII 315
           GLG +P + K ++GMLGMHG YEAN+AM  CD++I +GARFDDR+ G    F+ ++RK  
Sbjct: 244 GLGCYPASGKNWLGMLGMHGLYEANLAMHGCDLMINVGARFDDRITGRLDAFSPKSRK-A 302

Query: 316 HIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVD 375
           HIDIDPSSI+K ++VD+PI+G+V  VL++++   KA   K  REA+ KWW +IE+WR VD
Sbjct: 303 HIDIDPSSINKVIRVDMPIIGDVGHVLEDVLKVWKARGRKVNREAIQKWWARIEEWRKVD 362

Query: 376 CLKYDRSSEIIKPQYVVEKIWELTKG-DAFICSDVGQHQMWAAQFYKFDEPRRWINSGGL 434
           CLKY  S + I+PQ+ ++++  LTKG D +IC++VGQHQMWAAQ+  F++P RW+ SGGL
Sbjct: 363 CLKYKPSGKTIRPQHALDRLEALTKGRDRYICTEVGQHQMWAAQYLGFEDPNRWMTSGGL 422

Query: 435 GTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGM 494
           GTMG G P ++G++ A P+  V+ + GE S  M +QE+ T +QY  PVK   LNN  LGM
Sbjct: 423 GTMGYGTPASIGVQVAHPDALVINVAGEASWLMNMQEMGTAVQYRLPVKQFILNNERLGM 482

Query: 495 VRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVF 554
           VRQWQE+ +  RYSHS+ +ALPDFVKLAEA+G  G+     +D++ A+ E     D  V 
Sbjct: 483 VRQWQELLHGERYSHSWSEALPDFVKLAEAFGCKGILCSDPADLDDAIMEMLDY-DGPVI 541

Query: 555 LDFQTDPTENVWPMVQAGKGISEMLLG 581
            D   +  EN +PM+ +G+  ++MLLG
Sbjct: 542 FDCLVEKHENCFPMIPSGEPHNKMLLG 568


Lambda     K      H
   0.319    0.135    0.407 

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: 989
Number of extensions: 31
Number of successful extensions: 5
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: 585
Length of database: 584
Length adjustment: 37
Effective length of query: 548
Effective length of database: 547
Effective search space:   299756
Effective search space used:   299756
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_085635848.1 MGEO_RS06270 (acetolactate synthase 3 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.2982043.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.9e-236  769.9   0.0     8e-236  769.7   0.0    1.0  1  NCBI__GCF_002115805.1:WP_085635848.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002115805.1:WP_085635848.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  769.7   0.0    8e-236    8e-236       1     554 [.       5     566 ..       5     569 .. 0.98

  Alignments for each domain:
  == domain 1  score: 769.7 bits;  conditional E-value: 8e-236
                             TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsG 72 
                                           ++ga+++v++lk++gv+tvfGyPGGavlpiyd+++ +++++h lvrheq+a+haa+Gyara+Gk+Gvvl+tsG
  NCBI__GCF_002115805.1:WP_085635848.1   5 MTGAKMVVQALKDQGVDTVFGYPGGAVLPIYDEIFqQNGIRHYLVRHEQGAVHAAEGYARATGKPGVVLVTSG 77 
                                           79*********************************999*********************************** PP

                             TIGR00118  73 PGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeia 145
                                           PGatn+vtg+++a +ds+P+vvltGqv+t +iGsdafqe+d +Git+p+tkh++lvk+++ l+ i++eaf++a
  NCBI__GCF_002115805.1:WP_085635848.1  78 PGATNAVTGLTDALMDSIPIVVLTGQVPTFMIGSDAFQEADTVGITRPCTKHNWLVKDTDTLSGIIHEAFHVA 150
                                           ************************************************************************* PP

                             TIGR00118 146 stGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviia..ea 216
                                           ++GrPGPvl+d+Pkdv+ a+  ++ ++k ++  y+p+vkg+   i +++e+ie+a++Pv + GgGv+ +  +a
  NCBI__GCF_002115805.1:WP_085635848.1 151 TSGRPGPVLIDIPKDVQFASGAYTEKAKASVSHYQPQVKGDMETITQLVEAIETAERPVFYTGGGVVNSgpGA 223
                                           *******************************************************************873369 PP

                             TIGR00118 217 seelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfa 289
                                           s+ l+el++++ ip+t+tl+GlG++p+  ++ lgmlGmhG +eanla++ +dl+i vGarfddr+tg l+ f+
  NCBI__GCF_002115805.1:WP_085635848.1 224 SQLLRELVDATGIPITSTLMGLGCYPASGKNWLGMLGMHGLYEANLAMHGCDLMINVGARFDDRITGRLDAFS 296
                                           9************************************************************************ PP

                             TIGR00118 290 peakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke.Wlekieewkkeyilkldee 357
                                           p+++  hididP++i+k+++vd+pi+Gd+ +vle++lk  k++    +++ ++ W+++ieew+k  +lk++ +
  NCBI__GCF_002115805.1:WP_085635848.1 297 PKSRKAHIDIDPSSINKVIRVDMPIIGDVGHVLEDVLKVWKARgrkvNREAIQkWWARIEEWRKVDCLKYKPS 369
                                           *************************************98877766666666677******************* PP

                             TIGR00118 358 eesikPqkvikelskllkd.eaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpee 429
                                            ++i+Pq+ +++l  l+k+ + ++ t+vGqhqmwaaq++ ++ p++++tsgGlGtmG+G Pa++G++va+p++
  NCBI__GCF_002115805.1:WP_085635848.1 370 GKTIRPQHALDRLEALTKGrDRYICTEVGQHQMWAAQYLGFEDPNRWMTSGGLGTMGYGTPASIGVQVAHPDA 442
                                           ******************9899*************************************************** PP

                             TIGR00118 430 tvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayG 502
                                            v++v+G++s  mn+qe+ t+v+y +pvk  ilnne lGmv+qWqel++ erys++  ++ lpdfvklaea+G
  NCBI__GCF_002115805.1:WP_085635848.1 443 LVINVAGEASWLMNMQEMGTAVQYRLPVKQFILNNERLGMVRQWQELLHGERYSHSWSEA-LPDFVKLAEAFG 514
                                           ********************************************************9995.************ PP

                             TIGR00118 503 vkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldelv 554
                                            kgi  ++p++l++++ e+l  ++pv++d  v+k+e+++Pm+++G   ++++
  NCBI__GCF_002115805.1:WP_085635848.1 515 CKGILCSDPADLDDAIMEMLDYDGPVIFDCLVEKHENCFPMIPSGEPHNKML 566
                                           **********************************************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (584 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 24.84
//
[ok]

This GapMind analysis is from Jul 26 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