Alignments for a candidate for ilvI in Rhodomicrobium vannielii ATCC 17100

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Rhodomicrobium vannielii ATCC 17100

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_013419888.1 RVAN_RS11500 acetolactate synthase 3 large subunit

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



>NCBI__GCF_000166055.1:WP_013419888.1
          Length = 587

 Score =  637 bits (1644), Expect = 0.0
 Identities = 317/571 (55%), Positives = 408/571 (71%), Gaps = 5/571 (0%)

Query: 16  APEMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADG 75
           A  M GAEI++ ALA++GVE+++GYPGGAVL IYDE+ KQ   +H LVRHEQ A HAA+G
Sbjct: 2   ARAMTGAEIVLQALADQGVEHIFGYPGGAVLPIYDEIFKQNGIKHFLVRHEQGATHAAEG 61

Query: 76  YARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVG 135
           YAR++GKVGV LVTSGPG TNAVTG+A A +DSIP+V ITG V T  IG DAFQECDTVG
Sbjct: 62  YARSSGKVGVVLVTSGPGATNAVTGLADALMDSIPLVCITGQVGTPLIGSDAFQECDTVG 121

Query: 136 ITRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDM 195
           ITRP  KHN+LVKDV DLA  + +AF++A  GRPGPVV+DIPKDV      Y  P  +  
Sbjct: 122 ITRPCTKHNYLVKDVSDLARILHEAFYVAQNGRPGPVVIDIPKDVQFAKGTYIGPNKVVH 181

Query: 196 RSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLAN--ASDELRQLAALTGHPVTNT 253
           ++Y P  KG    IR AV L+  A++P  YTGGGV+ +   AS  LR+    TG P+T+T
Sbjct: 182 KTYRPQVKGSPQAIRDAVDLIASAKKPIFYTGGGVINSGPAASKLLREFVDTTGFPITST 241

Query: 254 LMGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARK 313
           LMGLGA+P +SKQ++GMLGMHGTYEANMAM +CDV+I +GARFDDR+ G    F   ++K
Sbjct: 242 LMGLGAYPASSKQWLGMLGMHGTYEANMAMHDCDVMICVGARFDDRITGRLNAFAPNSKK 301

Query: 314 IIHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRS 373
            IHIDIDPSSISK V+ DIPI+G+   VL+E++   ++   +  ++A+  WW  I+ WRS
Sbjct: 302 -IHIDIDPSSISKTVRADIPIIGDCGYVLEEMLRVWRSRAPQIDKKAIKAWWTSIDGWRS 360

Query: 374 VDCLKYDRSSEIIKPQYVVEKIWELTKG-DAFICSDVGQHQMWAAQFYKFDEPRRWINSG 432
            DCLKY    ++I PQY +++++ELTK  D +I ++VGQHQMWAAQFY+FDEP  W+ SG
Sbjct: 361 RDCLKYKTRDDVIMPQYAIQRLYELTKNRDTYITTEVGQHQMWAAQFYRFDEPNHWMTSG 420

Query: 433 GLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYL 492
           GLGTMG GLP A+G++ A PE  V+ I GE S+ M +QE+ST  QY  P+KI  LNN Y+
Sbjct: 421 GLGTMGYGLPAAVGVQVAHPESLVIDIAGESSVMMTMQEMSTAAQYGLPIKIFILNNEYM 480

Query: 493 GMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRT 552
           GMVRQWQE+ +  RYS SY +ALPDFVKLAEAY  VG+R EK  +++  + E      + 
Sbjct: 481 GMVRQWQELMHGGRYSQSYAEALPDFVKLAEAYHGVGLRCEKPDELDDMIIEMIN-TPKP 539

Query: 553 VFLDFQTDPTENVWPMVQAGKGISEMLLGAE 583
           V  D +     N +PM+ +G+  + ML G E
Sbjct: 540 VLFDCRVSKLANCFPMIPSGEAHNNMLFGDE 570


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: 971
Number of extensions: 35
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: 587
Length adjustment: 37
Effective length of query: 548
Effective length of database: 550
Effective search space:   301400
Effective search space used:   301400
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_013419888.1 RVAN_RS11500 (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.18240.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.8e-247  806.1   0.0   9.1e-247  805.8   0.0    1.0  1  lcl|NCBI__GCF_000166055.1:WP_013419888.1  RVAN_RS11500 acetolactate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000166055.1:WP_013419888.1  RVAN_RS11500 acetolactate synthase 3 large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  805.8   0.0  9.1e-247  9.1e-247       1     554 [.       5     566 ..       5     569 .. 0.98

  Alignments for each domain:
  == domain 1  score: 805.8 bits;  conditional E-value: 9.1e-247
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 
                                               ++gaei++++l ++gve++fGyPGGavlpiyd+++ +++++h lvrheq+a+haa+Gyar+sGkvGvvl
  lcl|NCBI__GCF_000166055.1:WP_013419888.1   5 MTGAEIVLQALADQGVEHIFGYPGGAVLPIYDEIFkQNGIKHFLVRHEQGATHAAEGYARSSGKVGVVL 73 
                                               79*********************************999******************************* PP

                                 TIGR00118  69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137
                                               +tsGPGatn+vtg+a+a +ds+Plv +tGqv t liGsdafqe+d +Git+p+tkh++lvk+++dl++i
  lcl|NCBI__GCF_000166055.1:WP_013419888.1  74 VTSGPGATNAVTGLADALMDSIPLVCITGQVGTPLIGSDAFQECDTVGITRPCTKHNYLVKDVSDLARI 142
                                               ********************************************************************* PP

                                 TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvll 206
                                               l+eaf++a+ GrPGPv++d+Pkdv+ a+ ++  ++kv  ++y+p+vkg+++ i+ a++li++akkP+ +
  lcl|NCBI__GCF_000166055.1:WP_013419888.1 143 LHEAFYVAQNGRPGPVVIDIPKDVQFAKGTYIGPNKVVHKTYRPQVKGSPQAIRDAVDLIASAKKPIFY 211
                                               ********************************************************************* PP

                                 TIGR00118 207 vGgGviiae..aseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliav 273
                                                GgGvi ++  as+ l+e+++++  p+t+tl+GlGa+p+  ++ lgmlGmhGt+ean+a++++d++i+v
  lcl|NCBI__GCF_000166055.1:WP_013419888.1 212 TGGGVINSGpaASKLLREFVDTTGFPITSTLMGLGAYPASSKQWLGMLGMHGTYEANMAMHDCDVMICV 280
                                               ******885448999****************************************************** PP

                                 TIGR00118 274 GarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke 338
                                               Garfddr+tg l+ fap++k ihididP++i+k+v++dipi+Gd+  vlee+l+  +++    +kk ++
  lcl|NCBI__GCF_000166055.1:WP_013419888.1 281 GARFDDRITGRLNAFAPNSKKIHIDIDPSSISKTVRADIPIIGDCGYVLEEMLRVWRSRapqiDKKAIK 349
                                               *****************************************************9887776767677777 PP

                                 TIGR00118 339 .WlekieewkkeyilkldeeeesikPqkvikelskllkd.eaivttdvGqhqmwaaqfyktkkprkfit 405
                                                W+ +i+ w+++ +lk++++++ i Pq+ i++l++l+k+ ++++tt+vGqhqmwaaqfy++++p++++t
  lcl|NCBI__GCF_000166055.1:WP_013419888.1 350 aWWTSIDGWRSRDCLKYKTRDDVIMPQYAIQRLYELTKNrDTYITTEVGQHQMWAAQFYRFDEPNHWMT 418
                                               8************************************9889**************************** PP

                                 TIGR00118 406 sgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWq 474
                                               sgGlGtmG+GlPaa+G++va+pe+ v++++G++s++m++qe+st+++y++p+ki ilnne++Gmv+qWq
  lcl|NCBI__GCF_000166055.1:WP_013419888.1 419 SGGLGTMGYGLPAAVGVQVAHPESLVIDIAGESSVMMTMQEMSTAAQYGLPIKIFILNNEYMGMVRQWQ 487
                                               ********************************************************************* PP

                                 TIGR00118 475 elfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPm 543
                                               el++ +rys+++ ++ lpdfvklaeay  +g+r ekp+el++ + e++++ +pvl+d +v k ++++Pm
  lcl|NCBI__GCF_000166055.1:WP_013419888.1 488 ELMHGGRYSQSYAEA-LPDFVKLAEAYHGVGLRCEKPDELDDMIIEMINTPKPVLFDCRVSKLANCFPM 555
                                               *************95.***************************************************** PP

                                 TIGR00118 544 vapGagldelv 554
                                               +++G + ++++
  lcl|NCBI__GCF_000166055.1:WP_013419888.1 556 IPSGEAHNNML 566
                                               ********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (587 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 7.76
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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:

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