Alignments for a candidate for ilvI in Rhizobium leguminosarum 3841

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Rhizobium leguminosarum 3841

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_003541291.1 RL_RS16715 acetolactate synthase 3 large subunit

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



>NCBI__GCF_000009265.1:WP_003541291.1
          Length = 596

 Score =  619 bits (1597), Expect = 0.0
 Identities = 313/576 (54%), Positives = 413/576 (71%), Gaps = 6/576 (1%)

Query: 12  NSSAAPEMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVH 71
           N +A   M GAEI++ AL + GVE+++GYPGGAVL IYDE+ +Q   +HILVRHEQ A H
Sbjct: 5   NQAAGNRMTGAEIVLKALKDNGVEHIFGYPGGAVLPIYDEIFQQEDVKHILVRHEQGAGH 64

Query: 72  AADGYARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQEC 131
           AA+GYAR+TGKVGV LVTSGPG TNAVT +  A +DSIP+V +TG VPT  IG DAFQEC
Sbjct: 65  AAEGYARSTGKVGVMLVTSGPGATNAVTPLQDALMDSIPLVCLTGQVPTSLIGSDAFQEC 124

Query: 132 DTVGITRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPK 191
           DTVGITRP  KHN+LVKDV +LAA I +AF IA +GRPGPVVVDIPKDV      Y  P 
Sbjct: 125 DTVGITRPCTKHNWLVKDVNELAAVIHEAFRIAQSGRPGPVVVDIPKDVQFATGTYTPPA 184

Query: 192 SIDM-RSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLA--NASDELRQLAALTGH 248
              + +SY P  +G   QI  A+ L+  A RP IY+GGGVV +   AS  LR+L  LT  
Sbjct: 185 DYSIQKSYQPKVQGDLNQIHAAIELMANARRPVIYSGGGVVNSGPEASKLLRELVELTDF 244

Query: 249 PVTNTLMGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFT 308
           P+T+TLMGLGA+P + K ++ MLGMHG+YEANMAM +CDV++ IGARFDDR+ G    F+
Sbjct: 245 PITSTLMGLGAYPASGKNWLKMLGMHGSYEANMAMHDCDVMVCIGARFDDRITGRLNAFS 304

Query: 309 SQARKIIHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQI 368
             ++K IHIDIDPSSI+K V+VDI I G+V  VL++++   +A   KP++  L  WW  I
Sbjct: 305 PNSKK-IHIDIDPSSINKNVRVDIGIRGDVGHVLEDMVRLWRALPKKPEKGRLDDWWTDI 363

Query: 369 EQWRSVDCLKYDRSSEIIKPQYVVEKIWELTKG-DAFICSDVGQHQMWAAQFYKFDEPRR 427
            +WR+ +   Y +S+++I PQY +E+++  TK  D +I ++VGQHQMWAAQF+ F++P R
Sbjct: 364 ARWRARNSFAYTKSNDVIMPQYALERLFAHTKDRDTYITTEVGQHQMWAAQFFGFEQPNR 423

Query: 428 WINSGGLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSL 487
           W+ SGGLGTMG GLP A+G++ A P+  V+ I G+ SIQMCIQE+S  +Q+D P+KI  +
Sbjct: 424 WMTSGGLGTMGYGLPAALGVQIAHPDSLVIDIAGDASIQMCIQEMSAAIQHDAPIKIFIM 483

Query: 488 NNGYLGMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFR 547
           NN Y+GMVRQWQ++ + NR S+SY +A+PDFVKLAEAYG VG+R EK   ++  + E   
Sbjct: 484 NNQYMGMVRQWQQLLHGNRLSNSYTEAMPDFVKLAEAYGAVGLRCEKPDALDDTILEMIE 543

Query: 548 LKDRTVFLDFQTDPTENVWPMVQAGKGISEMLLGAE 583
           ++   +F D +     N +PM+ +GK  +EMLL  E
Sbjct: 544 VRKPVIF-DCRVANLANCFPMIPSGKAHNEMLLPDE 578


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: 947
Number of extensions: 41
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: 596
Length adjustment: 37
Effective length of query: 548
Effective length of database: 559
Effective search space:   306332
Effective search space used:   306332
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_003541291.1 RL_RS16715 (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.859.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.8e-241  787.0   0.0   5.5e-241  786.8   0.0    1.0  1  lcl|NCBI__GCF_000009265.1:WP_003541291.1  RL_RS16715 acetolactate synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009265.1:WP_003541291.1  RL_RS16715 acetolactate synthase 3 large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  786.8   0.0  5.5e-241  5.5e-241       1     555 [.      12     575 ..      12     577 .. 0.97

  Alignments for each domain:
  == domain 1  score: 786.8 bits;  conditional E-value: 5.5e-241
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 
                                               ++gaei++++lk++gve++fGyPGGavlpiyd+++ +++++hilvrheq+a haa+Gyar++GkvGv+l
  lcl|NCBI__GCF_000009265.1:WP_003541291.1  12 MTGAEIVLKALKDNGVEHIFGYPGGAVLPIYDEIFqQEDVKHILVRHEQGAGHAAEGYARSTGKVGVML 80 
                                               79*********************************9999****************************** PP

                                 TIGR00118  69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137
                                               +tsGPGatn+vt++ +a +ds+Plv ltGqv+tsliGsdafqe+d +Git+p+tkh++lvk++++l+++
  lcl|NCBI__GCF_000009265.1:WP_003541291.1  81 VTSGPGATNAVTPLQDALMDSIPLVCLTGQVPTSLIGSDAFQECDTVGITRPCTKHNWLVKDVNELAAV 149
                                               ********************************************************************* PP

                                 TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleveekvel.pgykptvkghklqikkaleliekakkPvl 205
                                               ++eaf ia++GrPGPv+vd+Pkdv+ a+ +++ +++ ++ ++y+p+v+g+ +qi++a+el+++a++Pv+
  lcl|NCBI__GCF_000009265.1:WP_003541291.1 150 IHEAFRIAQSGRPGPVVVDIPKDVQFATGTYTPPADYSIqKSYQPKVQGDLNQIHAAIELMANARRPVI 218
                                               *******************************99988877369*************************** PP

                                 TIGR00118 206 lvGgGviia..easeelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadllia 272
                                               + GgGv+ +  eas+ l+el+e ++ p+t+tl+GlGa+p+  ++ l mlGmhG++ean+a++++d++++
  lcl|NCBI__GCF_000009265.1:WP_003541291.1 219 YSGGGVVNSgpEASKLLRELVELTDFPITSTLMGLGAYPASGKNWLKMLGMHGSYEANMAMHDCDVMVC 287
                                               *******8744699******************************************************* PP

                                 TIGR00118 273 vGarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkek 337
                                               +Garfddr+tg l+ f+p++k ihididP++i+knv+vdi i Gd+ +vle++++  ++     ek   
  lcl|NCBI__GCF_000009265.1:WP_003541291.1 288 IGARFDDRITGRLNAFSPNSKKIHIDIDPSSINKNVRVDIGIRGDVGHVLEDMVRLWRALpkkpEKGRL 356
                                               *****************************************************9988777555544444 PP

                                 TIGR00118 338 e.WlekieewkkeyilkldeeeesikPqkvikelskllkd.eaivttdvGqhqmwaaqfyktkkprkfi 404
                                               + W+  i++w++++ +++ ++++ i Pq+ +++l   +kd ++++tt+vGqhqmwaaqf+ +++p++++
  lcl|NCBI__GCF_000009265.1:WP_003541291.1 357 DdWWTDIARWRARNSFAYTKSNDVIMPQYALERLFAHTKDrDTYITTEVGQHQMWAAQFFGFEQPNRWM 425
                                               46**********************************999989*************************** PP

                                 TIGR00118 405 tsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqW 473
                                               tsgGlGtmG+GlPaalG+++a+p++ v++++Gd+s+qm +qe+s++ + d p+ki i+nn+++Gmv+qW
  lcl|NCBI__GCF_000009265.1:WP_003541291.1 426 TSGGLGTMGYGLPAALGVQIAHPDSLVIDIAGDASIQMCIQEMSAAIQHDAPIKIFIMNNQYMGMVRQW 494
                                               ********************************************************************* PP

                                 TIGR00118 474 qelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlP 542
                                               q+l++ +r s+++ ++ +pdfvklaeayG++g+r ekp+ l++ + e++e+++pv++d +v++ ++++P
  lcl|NCBI__GCF_000009265.1:WP_003541291.1 495 QQLLHGNRLSNSYTEA-MPDFVKLAEAYGAVGLRCEKPDALDDTILEMIEVRKPVIFDCRVANLANCFP 562
                                               ***************5.**************************************************** PP

                                 TIGR00118 543 mvapGagldelve 555
                                               m+++G++ +e++ 
  lcl|NCBI__GCF_000009265.1:WP_003541291.1 563 MIPSGKAHNEMLL 575
                                               **********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (596 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: 00:00:00.03
# Mc/sec: 10.54
//
[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