GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Ruegeria conchae TW15

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_029622025.1 G7G_RS0114505 acetolactate synthase 3 large subunit

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



>NCBI__GCF_000192475.1:WP_029622025.1
          Length = 583

 Score =  598 bits (1542), Expect = e-175
 Identities = 306/567 (53%), Positives = 400/567 (70%), Gaps = 6/567 (1%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           EM GA+++V AL ++GV+ V+GYPGGAVL IYDE+  Q    HILVRHEQ AVHAA+GYA
Sbjct: 4   EMTGAKMVVQALKDQGVDTVFGYPGGAVLPIYDEIFLQNDIRHILVRHEQGAVHAAEGYA 63

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           R+TGK GVALVTSGPG TNAVTG+  A LDSIP+VV+TG VPT  IG DAFQE DTVGIT
Sbjct: 64  RSTGKPGVALVTSGPGATNAVTGLTDALLDSIPIVVLTGQVPTFMIGSDAFQEADTVGIT 123

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
           RP  KHN+LVKD   LAAT+ +AF +A  GRPGPV+VDIPKDV   + +Y  PK      
Sbjct: 124 RPCTKHNWLVKDTDSLAATMHEAFHVATAGRPGPVLVDIPKDVQFASGEYTTPKP-STSH 182

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLAN--ASDELRQLAALTGHPVTNTLM 255
           Y PV KG   +I + VA ++ A++P  YTGGGV+ +   AS  LR+L   TG P+T+TLM
Sbjct: 183 YQPVLKGDLEEITELVAAIETAKKPVFYTGGGVINSGPAASQLLRELVDATGFPITSTLM 242

Query: 256 GLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKII 315
           GLGA+P + + ++GMLGMHG YEANMAM +CD++I IGARFDDR+ G    F+  + K  
Sbjct: 243 GLGAYPASGENWIGMLGMHGLYEANMAMHDCDLMINIGARFDDRITGRIDAFSPNSIK-A 301

Query: 316 HIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVD 375
           H+DIDPSSI+K ++VDIPIVG+V  VL++++   KA   K     + +W +QI +WR V+
Sbjct: 302 HVDIDPSSINKVIRVDIPIVGDVAHVLEDILKVWKARGRKTDAANIKQWQDQINKWRKVN 361

Query: 376 CLKYDRSSEIIKPQYVVEKIWELTKG-DAFICSDVGQHQMWAAQFYKFDEPRRWINSGGL 434
           CL +  S + IKPQY ++++ ELTK  D ++ ++VGQHQMWAAQ+  F++P RW+ SGGL
Sbjct: 362 CLAFTNSEKTIKPQYALQRLEELTKNHDRYVTTEVGQHQMWAAQYLGFEDPNRWMTSGGL 421

Query: 435 GTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGM 494
           GTMG G P ++G++ A P+  V+ + GE S  M +QE+ T  QY  PVK   LNN  LGM
Sbjct: 422 GTMGYGFPASIGVQMAHPDALVINVAGEASWLMNMQEMGTAAQYRLPVKQFILNNERLGM 481

Query: 495 VRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVF 554
           VRQWQE+ +  RYSHS+ +ALPDFVKLAEA+G  G+     +D++ A+ E     D  V 
Sbjct: 482 VRQWQELLHGERYSHSWSEALPDFVKLAEAFGAKGILCSDPADLDDAIMEMIDY-DGPVI 540

Query: 555 LDFQTDPTENVWPMVQAGKGISEMLLG 581
            D   +  EN +PM+ +GK  +EMLLG
Sbjct: 541 FDCVVEKHENCFPMIPSGKAHNEMLLG 567


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: 978
Number of extensions: 36
Number of successful extensions: 6
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: 583
Length adjustment: 36
Effective length of query: 549
Effective length of database: 547
Effective search space:   300303
Effective search space used:   300303
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_029622025.1 G7G_RS0114505 (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.3196982.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.3e-238  778.1   0.2   2.6e-238  777.9   0.2    1.0  1  NCBI__GCF_000192475.1:WP_029622025.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000192475.1:WP_029622025.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  777.9   0.2  2.6e-238  2.6e-238       1     554 [.       5     565 ..       5     568 .. 0.97

  Alignments for each domain:
  == domain 1  score: 777.9 bits;  conditional E-value: 2.6e-238
                             TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsG 72 
                                           ++ga+++v++lk++gv+tvfGyPGGavlpiyd+++ +++++hilvrheq+a+haa+Gyar++Gk+Gv+l+tsG
  NCBI__GCF_000192475.1:WP_029622025.1   5 MTGAKMVVQALKDQGVDTVFGYPGGAVLPIYDEIFlQNDIRHILVRHEQGAVHAAEGYARSTGKPGVALVTSG 77 
                                           79*********************************99************************************ PP

                             TIGR00118  73 PGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeia 145
                                           PGatn+vtg+++a lds+P+vvltGqv+t +iGsdafqe+d +Git+p+tkh++lvk+++ l+++++eaf++a
  NCBI__GCF_000192475.1:WP_029622025.1  78 PGATNAVTGLTDALLDSIPIVVLTGQVPTFMIGSDAFQEADTVGITRPCTKHNWLVKDTDSLAATMHEAFHVA 150
                                           ************************************************************************* PP

                             TIGR00118 146 stGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiae..a 216
                                           ++GrPGPvlvd+Pkdv+ a+ e++++ k +   y+p +kg+   i +++ +ie+akkPv + GgGvi ++  a
  NCBI__GCF_000192475.1:WP_029622025.1 151 TAGRPGPVLVDIPKDVQFASGEYTTP-KPSTSHYQPVLKGDLEEITELVAAIETAKKPVFYTGGGVINSGpaA 222
                                           **********************9999.778899**********************************885448 PP

                             TIGR00118 217 seelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfa 289
                                           s+ l+el++++  p+t+tl+GlGa+p+  ++ +gmlGmhG +ean+a++++dl+i +Garfddr+tg ++ f+
  NCBI__GCF_000192475.1:WP_029622025.1 223 SQLLRELVDATGFPITSTLMGLGAYPASGENWIGMLGMHGLYEANMAMHDCDLMINIGARFDDRITGRIDAFS 295
                                           999********************************************************************** PP

                             TIGR00118 290 peakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke.Wlekieewkkeyilkldee 357
                                           p++   h+didP++i+k+++vdipivGd+ +vle++lk  k++    +  +++ W ++i++w+k ++l++ ++
  NCBI__GCF_000192475.1:WP_029622025.1 296 PNSIKAHVDIDPSSINKVIRVDIPIVGDVAHVLEDILKVWKARgrktDAANIKqWQDQINKWRKVNCLAFTNS 368
                                           *************************************99888765553444445******************* PP

                             TIGR00118 358 eesikPqkvikelskllkd.eaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpee 429
                                           e++ikPq+ +++l +l+k+ + +vtt+vGqhqmwaaq++ ++ p++++tsgGlGtmG+G+Pa++G+++a+p++
  NCBI__GCF_000192475.1:WP_029622025.1 369 EKTIKPQYALQRLEELTKNhDRYVTTEVGQHQMWAAQYLGFEDPNRWMTSGGLGTMGYGFPASIGVQMAHPDA 441
                                           ****************998689*************************************************** PP

                             TIGR00118 430 tvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayG 502
                                            v++v+G++s  mn+qe+ t+++y +pvk  ilnne lGmv+qWqel++ erys++  ++ lpdfvklaea+G
  NCBI__GCF_000192475.1:WP_029622025.1 442 LVINVAGEASWLMNMQEMGTAAQYRLPVKQFILNNERLGMVRQWQELLHGERYSHSWSEA-LPDFVKLAEAFG 513
                                           ********************************************************9995.************ PP

                             TIGR00118 503 vkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldelv 554
                                           +kgi  ++p++l++++ e++  ++pv++d +v+k+e+++Pm+++G++ +e++
  NCBI__GCF_000192475.1:WP_029622025.1 514 AKGILCSDPADLDDAIMEMIDYDGPVIFDCVVEKHENCFPMIPSGKAHNEML 565
                                           **************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (583 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: 34.11
//
[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