Alignments for a candidate for ilvI in Rhodospirillum rubrum ATCC 11170

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Rhodospirillum rubrum ATCC 11170

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate YP_425559.1 Rru_A0467 acetolactate synthase, large subunit

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



>NCBI__GCF_000013085.1:YP_425559.1
          Length = 586

 Score =  630 bits (1626), Expect = 0.0
 Identities = 315/567 (55%), Positives = 404/567 (71%), Gaps = 5/567 (0%)

Query: 21  GAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYARAT 80
           GAEI++ ALA++GVE ++GYPGGAVL +YDE+ KQ +  H+LVRHEQAAVHAA+GYAR+T
Sbjct: 8   GAEIVLKALADQGVEVIFGYPGGAVLPLYDEIFKQNQIRHVLVRHEQAAVHAAEGYARST 67

Query: 81  GKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGITRPI 140
           GK GV LVTSGPG TNAVTG+  A LDSIP+V +TG VPTH IG DAFQE DT GITR  
Sbjct: 68  GKTGVVLVTSGPGATNAVTGLTDAMLDSIPVVCLTGQVPTHLIGNDAFQEADTTGITRQC 127

Query: 141 VKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRSYNP 200
            KHN+LVK   DLA  I +AF +A +GRPGPVV+D+PKD+      Y  P  +  +SY P
Sbjct: 128 TKHNYLVKKGEDLARVIHEAFQVAGSGRPGPVVIDLPKDILMGPAPYVAPSRVKHKSYRP 187

Query: 201 VNKGHSGQIRKAVALLQGAERPYIYTGGGVVLA--NASDELRQLAALTGHPVTNTLMGLG 258
             KG    I KAV ++  A+RP  Y GGGVV +   AS  L Q   +TG+P+T TLMGLG
Sbjct: 188 QLKGDITAIEKAVEIIAKAKRPIFYCGGGVVNSGPQASQLLTQFVKMTGYPITLTLMGLG 247

Query: 259 AFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHID 318
            +P +  Q++GMLGMHGT+EAN AM +CDV++AIGARFDDRV G    F+  + K I ID
Sbjct: 248 IYPASDPQYLGMLGMHGTFEANHAMHDCDVMVAIGARFDDRVTGRLDAFSPNSTK-IQID 306

Query: 319 IDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDCLK 378
           IDPSSI+K V VD+ IVG+V  VL+++I   KA    P   AL  WW +I  W+  DCL 
Sbjct: 307 IDPSSINKNVAVDLGIVGDVGHVLEDMIKVWKARQYHPDVAALKNWWGRIADWQRRDCLH 366

Query: 379 YDRSSEIIKPQYVVEKIWELTKG-DAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGTM 437
           Y  S E+ KPQY +E+++ LT+  + FI ++VGQHQMWAAQ++KFD+P +W+ SGGLGTM
Sbjct: 367 YQPSDEVTKPQYAIERLYALTRDRETFITTEVGQHQMWAAQYFKFDKPNQWMTSGGLGTM 426

Query: 438 GVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVRQ 497
           G G P A+G++ A P   VV I+GE S  M +QEL+T +QY  PVK+  LNN Y+GMVRQ
Sbjct: 427 GYGFPAAIGVQMAHPGALVVDISGEASFMMNMQELATAVQYRLPVKVFILNNRYMGMVRQ 486

Query: 498 WQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFLDF 557
           WQE+ +  RYS SY + LPDFVKLAEA+G VG+R EK +D++  + E   + DR V +D 
Sbjct: 487 WQELLHGGRYSESYSECLPDFVKLAEAFGAVGLRSEKPADLDDVIAEMIAV-DRPVLVDV 545

Query: 558 QTDPTENVWPMVQAGKGISEMLLGAED 584
             DP+ENV+PM+ +G   ++MLLG ED
Sbjct: 546 AVDPSENVFPMIPSGAPHNQMLLGPED 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: 992
Number of extensions: 42
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: 586
Length adjustment: 37
Effective length of query: 548
Effective length of database: 549
Effective search space:   300852
Effective search space used:   300852
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 YP_425559.1 Rru_A0467 (acetolactate synthase, 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.30021.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
   7.1e-242  789.7   0.2   8.4e-242  789.5   0.2    1.0  1  lcl|NCBI__GCF_000013085.1:YP_425559.1  Rru_A0467 acetolactate synthase,


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000013085.1:YP_425559.1  Rru_A0467 acetolactate synthase, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  789.5   0.2  8.4e-242  8.4e-242       2     554 ..       7     567 ..       6     570 .. 0.98

  Alignments for each domain:
  == domain 1  score: 789.5 bits;  conditional E-value: 8.4e-242
                              TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsG 72 
                                            +gaei++++l ++gve++fGyPGGavlp+yd+++ +++++h+lvrheqaa+haa+Gyar++Gk+Gvvl+tsG
  lcl|NCBI__GCF_000013085.1:YP_425559.1   7 SGAEIVLKALADQGVEVIFGYPGGAVLPLYDEIFkQNQIRHVLVRHEQAAVHAAEGYARSTGKTGVVLVTSG 78 
                                            79********************************999*********************************** PP

                              TIGR00118  73 PGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafei 144
                                            PGatn+vtg+++a+lds+P+v ltGqv+t+liG+dafqe+d +Git+ +tkh++lvkk edl+++++eaf++
  lcl|NCBI__GCF_000013085.1:YP_425559.1  79 PGATNAVTGLTDAMLDSIPVVCLTGQVPTHLIGNDAFQEADTTGITRQCTKHNYLVKKGEDLARVIHEAFQV 150
                                            ************************************************************************ PP

                              TIGR00118 145 astGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviia.. 214
                                            a +GrPGPv++dlPkd+      +  +++v+ ++y+p++kg+ + i+ka+e+i+kak+P+ + GgGv+ +  
  lcl|NCBI__GCF_000013085.1:YP_425559.1 151 AGSGRPGPVVIDLPKDILMGPAPYVAPSRVKHKSYRPQLKGDITAIEKAVEIIAKAKRPIFYCGGGVVNSgp 222
                                            ********************************************************************8733 PP

                              TIGR00118 215 easeelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnla 286
                                            +as+ l+++++++  p+t tl+GlG +p+ +p+ lgmlGmhGt ean a++++d+++a+Garfddrvtg l+
  lcl|NCBI__GCF_000013085.1:YP_425559.1 223 QASQLLTQFVKMTGYPITLTLMGLGIYPASDPQYLGMLGMHGTFEANHAMHDCDVMVAIGARFDDRVTGRLD 294
                                            6999******************************************************************** PP

                              TIGR00118 287 kfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke.Wlekieewkkeyilk 353
                                             f+p+++ i ididP++i+knv+vd+ ivGd+ +vle+++k  k++    +    + W+ +i++w+++ +l+
  lcl|NCBI__GCF_000013085.1:YP_425559.1 295 AFSPNSTKIQIDIDPSSINKNVAVDLGIVGDVGHVLEDMIKVWKARqyhpDVAALKnWWGRIADWQRRDCLH 366
                                            ****************************************98877655553334445*************** PP

                              TIGR00118 354 ldeeeesikPqkvikelskllkd.eaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakv 424
                                            ++ ++e  kPq+ i++l+ l++d e+++tt+vGqhqmwaaq++k++kp++++tsgGlGtmG+G+Paa+G+++
  lcl|NCBI__GCF_000013085.1:YP_425559.1 367 YQPSDEVTKPQYAIERLYALTRDrETFITTEVGQHQMWAAQYFKFDKPNQWMTSGGLGTMGYGFPAAIGVQM 438
                                            *********************9989*********************************************** PP

                              TIGR00118 425 akpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvk 496
                                            a+p + vv+++G++sf+mn+qel+t+v+y +pvk+ ilnn+++Gmv+qWqel++ +ryse++ ++ lpdfvk
  lcl|NCBI__GCF_000013085.1:YP_425559.1 439 AHPGALVVDISGEASFMMNMQELATAVQYRLPVKVFILNNRYMGMVRQWQELLHGGRYSESYSEC-LPDFVK 509
                                            ****************************************************************8.****** PP

                              TIGR00118 497 laeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldelv 554
                                            laea+G++g+r ekp++l++ ++e++++++pvl+dv vd +e+v+Pm+++Ga  ++++
  lcl|NCBI__GCF_000013085.1:YP_425559.1 510 LAEAFGAVGLRSEKPADLDDVIAEMIAVDRPVLVDVAVDPSENVFPMIPSGAPHNQML 567
                                            *****************************************************99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (586 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 11.09
//
[ok]

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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