GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Xenophilus azovorans DSM 13620

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_038215894.1 Q392_RS26710 acetolactate synthase 3 catalytic subunit

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



>NCBI__GCF_000745855.1:WP_038215894.1
          Length = 591

 Score =  902 bits (2330), Expect = 0.0
 Identities = 438/582 (75%), Positives = 499/582 (85%), Gaps = 3/582 (0%)

Query: 7   SHADSNSSAAPEMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHE 66
           S A +  S   E++G+E+LV AL  EGV+Y+WGYPGGAVLYIYD L+KQ   +H+LVRHE
Sbjct: 10  SAAAATGSQTQELMGSEVLVKALQAEGVKYIWGYPGGAVLYIYDALYKQDTMQHVLVRHE 69

Query: 67  QAAVHAADGYARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQD 126
           QAAVHAADGYARATG VGVALVTSGPG+TNAVTGIATAY+DSIPMV+I G VPT AIGQD
Sbjct: 70  QAAVHAADGYARATGDVGVALVTSGPGLTNAVTGIATAYMDSIPMVIIAGQVPTPAIGQD 129

Query: 127 AFQECDTVGITRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACK 186
           AFQECDTVGITRPIVKHNFLVKD +D+A T+KKAF IA +GRPGPVVVDIPKDVS     
Sbjct: 130 AFQECDTVGITRPIVKHNFLVKDAKDIALTMKKAFHIARSGRPGPVVVDIPKDVSFKKVA 189

Query: 187 YE-YPKSIDMRSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAAL 245
           Y  YP+ ++MRSYNPV KGH GQIRKA+ LL GA+RPYIYTGGGV+L NA +ELR L  +
Sbjct: 190 YHGYPEKVEMRSYNPVKKGHGGQIRKALQLLLGAKRPYIYTGGGVLLGNACNELRTLVDM 249

Query: 246 TGHPVTNTLMGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPA 305
            G+PVTNTLMGLGA+P + ++F+GMLGMHGT EAN AMQNCDVL+A+GARFDDRVIGNP 
Sbjct: 250 LGYPVTNTLMGLGAYPASDRKFLGMLGMHGTIEANNAMQNCDVLLAVGARFDDRVIGNPK 309

Query: 306 HFTSQARKIIHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWW 365
           HF    RKIIH+DIDPSSISKRVKVDIPIVG+VKDVL ELI+ ++ S  KP    LA WW
Sbjct: 310 HFAQNERKIIHVDIDPSSISKRVKVDIPIVGDVKDVLTELISMVRESSTKPDAATLADWW 369

Query: 366 EQIEQWRSVDCLKYDRSS-EIIKPQYVVEKIWELTKG-DAFICSDVGQHQMWAAQFYKFD 423
           + IE WRS DCLKYD  + ++IKPQ VVE +W +TK  + +ICSDVGQHQMWAAQ+Y+FD
Sbjct: 370 KTIEGWRSRDCLKYDSDNKQVIKPQKVVETLWNMTKDTETYICSDVGQHQMWAAQYYRFD 429

Query: 424 EPRRWINSGGLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVK 483
           EPRRWINSGGLGTMGVG+PYAMGIK A PE EV TITGEGS+QMCIQELSTCLQY+TP+K
Sbjct: 430 EPRRWINSGGLGTMGVGIPYAMGIKLAKPEAEVFTITGEGSVQMCIQELSTCLQYNTPIK 489

Query: 484 ICSLNNGYLGMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALR 543
           I SLNN YLGMVRQWQEIEY  RYSHSYMDALP+FVKLAEAYGHVGM +E+  DVEPALR
Sbjct: 490 IVSLNNRYLGMVRQWQEIEYSGRYSHSYMDALPNFVKLAEAYGHVGMLIERPEDVEPALR 549

Query: 544 EAFRLKDRTVFLDFQTDPTENVWPMVQAGKGISEMLLGAEDL 585
           EA +LKDRTVF+DF+TDPTENV+PMVQAGKGI+EMLLG+EDL
Sbjct: 550 EARKLKDRTVFMDFRTDPTENVFPMVQAGKGITEMLLGSEDL 591


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: 1119
Number of extensions: 30
Number of successful extensions: 4
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: 591
Length adjustment: 37
Effective length of query: 548
Effective length of database: 554
Effective search space:   303592
Effective search space used:   303592
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_038215894.1 Q392_RS26710 (acetolactate synthase 3 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.3923118.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.5e-252  823.1   0.3   6.5e-252  822.8   0.3    1.0  1  NCBI__GCF_000745855.1:WP_038215894.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000745855.1:WP_038215894.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  822.8   0.3  6.5e-252  6.5e-252       2     554 ..      23     585 ..      22     588 .. 0.97

  Alignments for each domain:
  == domain 1  score: 822.8 bits;  conditional E-value: 6.5e-252
                             TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGP 73 
                                            g+e+lv++l++egv++++GyPGGavl iydaly ++ ++h+lvrheqaa+haadGyara+G vGv+l+tsGP
  NCBI__GCF_000745855.1:WP_038215894.1  23 MGSEVLVKALQAEGVKYIWGYPGGAVLYIYDALYkQDTMQHVLVRHEQAAVHAADGYARATGDVGVALVTSGP 95 
                                           699*******************************9999*********************************** PP

                             TIGR00118  74 GatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeias 146
                                           G tn+vtgiatay+ds+P+v+++Gqv+t +iG+dafqe+d +Git+p++kh+flvk+a+d++ ++k+af+ia 
  NCBI__GCF_000745855.1:WP_038215894.1  96 GLTNAVTGIATAYMDSIPMVIIAGQVPTPAIGQDAFQECDTVGITRPIVKHNFLVKDAKDIALTMKKAFHIAR 168
                                           ************************************************************************* PP

                             TIGR00118 147 tGrPGPvlvdlPkdvteaeieleve.ekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaease 218
                                           +GrPGPv+vd+Pkdv+ +++ ++ + ekve+++y+p +kgh  qi+kal+l+  ak+P ++ GgGv+ ++a +
  NCBI__GCF_000745855.1:WP_038215894.1 169 SGRPGPVVVDIPKDVSFKKVAYHGYpEKVEMRSYNPVKKGHGGQIRKALQLLLGAKRPYIYTGGGVLLGNACN 241
                                           *****************999998655*********************************************** PP

                             TIGR00118 219 elkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfape 291
                                           el+ l+++l  pvt tl+GlGa+p+ ++++lgmlGmhGt ean a++++d+l+avGarfddrv gn ++fa++
  NCBI__GCF_000745855.1:WP_038215894.1 242 ELRTLVDMLGYPVTNTLMGLGAYPASDRKFLGMLGMHGTIEANNAMQNCDVLLAVGARFDDRVIGNPKHFAQN 314
                                           ***********************************************************************87 PP

                             TIGR00118 292 a.kiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke.Wlekieewkkeyilkldeee 358
                                             kiih+didP++i+k vkvdipivGd+k vl+el++ ++e     +  +   W++ ie w+++ +lk+d+++
  NCBI__GCF_000745855.1:WP_038215894.1 315 ErKIIHVDIDPSSISKRVKVDIPIVGDVKDVLTELISMVRESstkpDAATLAdWWKTIEGWRSRDCLKYDSDN 387
                                           527***********************************999866553334445***************99988 PP

                             TIGR00118 359 es.ikPqkvikelskllkd.eaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpee 429
                                           ++ ikPqkv+++l++++kd e+++ +dvGqhqmwaaq+y++++pr++i+sgGlGtmG G+P a+G+k+akpe+
  NCBI__GCF_000745855.1:WP_038215894.1 388 KQvIKPQKVVETLWNMTKDtETYICSDVGQHQMWAAQYYRFDEPRRWINSGGLGTMGVGIPYAMGIKLAKPEA 460
                                           776***************989**************************************************** PP

                             TIGR00118 430 tvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayG 502
                                           +v ++tG+gs+qm +qelst+ +y++p+kiv lnn++lGmv+qWqe+ y++rys++++ + lp+fvklaeayG
  NCBI__GCF_000745855.1:WP_038215894.1 461 EVFTITGEGSVQMCIQELSTCLQYNTPIKIVSLNNRYLGMVRQWQEIEYSGRYSHSYMDA-LPNFVKLAEAYG 532
                                           ***********************************************************5.************ PP

                             TIGR00118 503 vkgiriekpeeleeklkealesk.epvlldvevdkeeevlPmvapGagldelv 554
                                           ++g+ ie+pe++e +l+ea + k + v++d++ d +e+v+Pmv  G+g++e++
  NCBI__GCF_000745855.1:WP_038215894.1 533 HVGMLIERPEDVEPALREARKLKdRTVFMDFRTDPTENVFPMVQAGKGITEML 585
                                           *******************9987699*************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (591 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: 31.55
//
[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