Alignments for a candidate for ilvI in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Dinoroseobacter shibae DFL-12

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate 3608378 Dshi_1779 acetolactate synthase, large subunit, biosynthetic type (RefSeq)

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



>FitnessBrowser__Dino:3608378
          Length = 585

 Score =  609 bits (1571), Expect = e-179
 Identities = 310/571 (54%), Positives = 400/571 (70%), Gaps = 6/571 (1%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           +M GA+++V AL ++GV+ V+GYPGGAVL IYDE+ +Q + +HILVRHEQAA HAA+GYA
Sbjct: 4   QMTGAQMVVQALKDQGVDTVFGYPGGAVLPIYDEIFQQNEIKHILVRHEQAATHAAEGYA 63

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           R+TGK GV LVTSGPG TNAVTGI  A +DSIPMVV++G VPT  IG DAFQE DTVGIT
Sbjct: 64  RSTGKPGVVLVTSGPGATNAVTGITDALMDSIPMVVLSGQVPTFMIGNDAFQEADTVGIT 123

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
           RP  KHN+LVK+   LA TI +AF +A +GRPGPV+VDIPKDV   +  Y  P   D R 
Sbjct: 124 RPCTKHNWLVKETDLLADTIHQAFHVATSGRPGPVLVDIPKDVQFASGTYVPPAKADTRH 183

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLAN--ASDELRQLAALTGHPVTNTLM 255
           Y P  KG    I   V L++ AERP  YTGGGV+ +   AS  LR+  A TG P+T+TLM
Sbjct: 184 YQPRVKGDVAAITAMVELMETAERPIFYTGGGVINSGPAASQLLREFVAETGFPITSTLM 243

Query: 256 GLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKII 315
           GLGA+P + + ++GMLGMHG YEAN+AM  CDV+I IGARFDDR+ G  A F+ +++K I
Sbjct: 244 GLGAYPASGENWIGMLGMHGLYEANLAMHGCDVMINIGARFDDRITGRVADFSPESKK-I 302

Query: 316 HIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVD 375
           HIDIDPSSI+K ++ D+PI+G++  VL++ +   KA   K  + A+  WW QIE+WR+V 
Sbjct: 303 HIDIDPSSINKVIRTDVPIIGDIAHVLEDALRIWKARGRKTNKAAVKAWWTQIEEWRTVR 362

Query: 376 CLKYDRSSEIIKPQYVVEKIWELTKG--DAFICSDVGQHQMWAAQFYKFDEPRRWINSGG 433
           CL +  S   IKPQY ++++  LTK     FI ++VGQHQMWAAQ+  FDEP RW+ SGG
Sbjct: 363 CLDFKNSETTIKPQYAMQRLEALTKDHPKRFIATEVGQHQMWAAQYLGFDEPNRWMTSGG 422

Query: 434 LGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLG 493
           LGTMG G P ++G++ A P+  V+ + GE S  M +QE+ T +QY  PVK   LNN  LG
Sbjct: 423 LGTMGYGFPASIGVQVAHPDALVINVAGEASWLMNMQEMGTAIQYMLPVKQFILNNERLG 482

Query: 494 MVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTV 553
           MVRQWQE+ +  RYSHS+ DALPDFVKLAEA+G  G+  +   D++ A+ E     D  V
Sbjct: 483 MVRQWQELLHGERYSHSWSDALPDFVKLAEAFGAKGILCKDPKDLDDAIMEMLEY-DGPV 541

Query: 554 FLDFQTDPTENVWPMVQAGKGISEMLLGAED 584
             D   +  EN +PM+ +G   +EMLLG  D
Sbjct: 542 IFDCLVEKHENCFPMIPSGAPHNEMLLGEAD 572


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: 952
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: 585
Length adjustment: 37
Effective length of query: 548
Effective length of database: 548
Effective search space:   300304
Effective search space used:   300304
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 3608378 Dshi_1779 (acetolactate synthase, large subunit, biosynthetic type (RefSeq))
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.16039.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.3e-237  775.6   0.2   1.5e-237  775.4   0.2    1.0  1  lcl|FitnessBrowser__Dino:3608378  Dshi_1779 acetolactate synthase,


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3608378  Dshi_1779 acetolactate synthase, large subunit, biosynthetic type (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  775.4   0.2  1.5e-237  1.5e-237       1     554 [.       5     567 ..       5     570 .. 0.97

  Alignments for each domain:
  == domain 1  score: 775.4 bits;  conditional E-value: 1.5e-237
                         TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGPGat 76 
                                       ++ga+++v++lk++gv+tvfGyPGGavlpiyd+++ ++e++hilvrheqaa+haa+Gyar++Gk+Gvvl+tsGPGat
  lcl|FitnessBrowser__Dino:3608378   5 MTGAQMVVQALKDQGVDTVFGYPGGAVLPIYDEIFqQNEIKHILVRHEQAATHAAEGYARSTGKPGVVLVTSGPGAT 81 
                                       79*********************************999*************************************** PP

                         TIGR00118  77 nlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGrPGPv 153
                                       n+vtgi++a +ds+P+vvl+Gqv+t +iG+dafqe+d +Git+p+tkh++lvk+++ l+ ++++af++a++GrPGPv
  lcl|FitnessBrowser__Dino:3608378  82 NAVTGITDALMDSIPMVVLSGQVPTFMIGNDAFQEADTVGITRPCTKHNWLVKETDLLADTIHQAFHVATSGRPGPV 158
                                       ***************************************************************************** PP

                         TIGR00118 154 lvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiae..aseelkelaerlk 228
                                       lvd+Pkdv+ a+ ++  ++k + + y+p+vkg+ + i + +el+e+a++P+ + GgGvi ++  as+ l+e++ ++ 
  lcl|FitnessBrowser__Dino:3608378 159 LVDIPKDVQFASGTYVPPAKADTRHYQPRVKGDVAAITAMVELMETAERPIFYTGGGVINSGpaASQLLREFVAETG 235
                                       ***********************************************************885448999********* PP

                         TIGR00118 229 ipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihididPaeig 305
                                        p+t+tl+GlGa+p+  ++ +gmlGmhG +eanla++ +d++i +Garfddr+tg +a f+pe+k ihididP++i+
  lcl|FitnessBrowser__Dino:3608378 236 FPITSTLMGLGAYPASGENWIGMLGMHGLYEANLAMHGCDVMINIGARFDDRITGRVADFSPESKKIHIDIDPSSIN 312
                                       ***************************************************************************** PP

                         TIGR00118 306 knvkvdipivGdakkvleellkklkee....ekkeke.WlekieewkkeyilkldeeeesikPqkvikelskllkd. 376
                                       k++++d+pi+Gd  +vle+ l+  k++    +k   + W+ +ieew++  +l ++++e++ikPq+ +++l  l+kd 
  lcl|FitnessBrowser__Dino:3608378 313 KVIRTDVPIIGDIAHVLEDALRIWKARgrktNKAAVKaWWTQIEEWRTVRCLDFKNSETTIKPQYAMQRLEALTKDh 389
                                       *******************9987776655545555567**************************************7 PP

                         TIGR00118 377 .eaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstive 452
                                        + +++t+vGqhqmwaaq++ +++p++++tsgGlGtmG+G+Pa++G++va+p++ v++v+G++s  mn+qe+ t+ +
  lcl|FitnessBrowser__Dino:3608378 390 pKRFIATEVGQHQMWAAQYLGFDEPNRWMTSGGLGTMGYGFPASIGVQVAHPDALVINVAGEASWLMNMQEMGTAIQ 466
                                       7789************************************************************************* PP

                         TIGR00118 453 ydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvl 529
                                       y +pvk  ilnne lGmv+qWqel++ erys++   + lpdfvklaea+G+kgi  ++p++l++++ e+le ++pv+
  lcl|FitnessBrowser__Dino:3608378 467 YMLPVKQFILNNERLGMVRQWQELLHGERYSHSWSDA-LPDFVKLAEAFGAKGILCKDPKDLDDAIMEMLEYDGPVI 542
                                       *********************************9995.*************************************** PP

                         TIGR00118 530 ldvevdkeeevlPmvapGagldelv 554
                                       +d  v+k+e+++Pm+++Ga  +e++
  lcl|FitnessBrowser__Dino:3608378 543 FDCLVEKHENCFPMIPSGAPHNEML 567
                                       ***********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (585 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: 00:00:00.02
# Mc/sec: 12.41
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis