Alignments for a candidate for ilvI in Sinorhizobium medicae WSM419

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Sinorhizobium medicae WSM419

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate YP_001327676.1 Smed_2008 acetolactate synthase 3 catalytic subunit

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



>NCBI__GCF_000017145.1:YP_001327676.1
          Length = 592

 Score =  625 bits (1613), Expect = 0.0
 Identities = 311/575 (54%), Positives = 417/575 (72%), Gaps = 6/575 (1%)

Query: 13  SSAAPEMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHA 72
           S    +M GAEI++ AL + GVE+++GYPGGAVL IYDE+ +Q   +HILVRHEQ A H 
Sbjct: 2   SGTENQMTGAEIVLQALKDNGVEHIFGYPGGAVLPIYDEIFQQEDIQHILVRHEQGAGHM 61

Query: 73  ADGYARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECD 132
           A+GYAR+TGKVGV LVTSGPG TNAVT +  A +DSIP+V I+G VPT  IG DAFQECD
Sbjct: 62  AEGYARSTGKVGVMLVTSGPGATNAVTPLQDALMDSIPLVCISGQVPTSLIGSDAFQECD 121

Query: 133 TVGITRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKS 192
           TVGITRP  KHN+LV+DV +LA  I +AF +A +GRPGPVVVDIPKD+      Y  P +
Sbjct: 122 TVGITRPCTKHNWLVRDVNELARVIHEAFRVAQSGRPGPVVVDIPKDIQFATGAYTPPSA 181

Query: 193 I-DMRSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLA--NASDELRQLAALTGHP 249
           +   +SY P  +G   +I +AVAL++ A +P IY+GGGV+ +   A+  LR+L  LT  P
Sbjct: 182 VPTQKSYQPKTQGDLKKIEEAVALMKSARQPVIYSGGGVINSGPQAAHFLRELVELTDFP 241

Query: 250 VTNTLMGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTS 309
           +T+TLMGLGA+P + K ++GMLGMHGTYEAN+AM +CDV+I IGARFDDR+ G    F+ 
Sbjct: 242 ITSTLMGLGAYPASGKNWLGMLGMHGTYEANLAMHDCDVMICIGARFDDRITGRLNAFSP 301

Query: 310 QARKIIHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIE 369
            ++K IHIDIDPSSI+K V+VD+PI+G+V  VL++++   +A+     R  L  WW+ I 
Sbjct: 302 NSKK-IHIDIDPSSINKNVRVDVPIIGDVAAVLEDMVRLWRAAAKTVDRTRLEDWWKSIT 360

Query: 370 QWRSVDCLKYDRSSEIIKPQYVVEKIWELTKG-DAFICSDVGQHQMWAAQFYKFDEPRRW 428
           +WR+ + L Y  S+++I PQY +++++ELTK  D +I ++VGQHQMWAAQF+ F+EP RW
Sbjct: 361 KWRARNSLAYTPSADVIMPQYAIQRLYELTKDRDTYITTEVGQHQMWAAQFFGFEEPNRW 420

Query: 429 INSGGLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLN 488
           + SGGLGTMG G P A+G++ A P+  V+ I G+ SIQMCIQE+S  +QY  PVKI  LN
Sbjct: 421 MTSGGLGTMGYGFPAAVGVQVAHPDSLVIDIAGDASIQMCIQEMSCAVQYGLPVKIFILN 480

Query: 489 NGYLGMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRL 548
           N Y+GMVRQWQ++ + NR SHSY +A+PDFVKLAEAYG VG+R EK  +++ A+++    
Sbjct: 481 NQYMGMVRQWQQLLHGNRLSHSYTEAMPDFVKLAEAYGGVGIRCEKPGELDEAIKQMIDT 540

Query: 549 KDRTVFLDFQTDPTENVWPMVQAGKGISEMLLGAE 583
               +F D +     N +PM+ +GK  +EMLL  E
Sbjct: 541 PAPVIF-DCRVANLANCFPMIPSGKAHNEMLLPDE 574


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: 962
Number of extensions: 38
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: 592
Length adjustment: 37
Effective length of query: 548
Effective length of database: 555
Effective search space:   304140
Effective search space used:   304140
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_001327676.1 Smed_2008 (acetolactate synthase 3 catalytic 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.17974.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.9e-245  801.5   0.1   2.2e-245  801.3   0.1    1.0  1  lcl|NCBI__GCF_000017145.1:YP_001327676.1  Smed_2008 acetolactate synthase 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000017145.1:YP_001327676.1  Smed_2008 acetolactate synthase 3 catalytic subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  801.3   0.1  2.2e-245  2.2e-245       1     555 [.       8     571 ..       8     573 .. 0.97

  Alignments for each domain:
  == domain 1  score: 801.3 bits;  conditional E-value: 2.2e-245
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 
                                               ++gaei++++lk++gve++fGyPGGavlpiyd+++ +++++hilvrheq+a h+a+Gyar++GkvGv+l
  lcl|NCBI__GCF_000017145.1:YP_001327676.1   8 MTGAEIVLQALKDNGVEHIFGYPGGAVLPIYDEIFqQEDIQHILVRHEQGAGHMAEGYARSTGKVGVML 76 
                                               79*********************************999******************************* PP

                                 TIGR00118  69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137
                                               +tsGPGatn+vt++ +a +ds+Plv ++Gqv+tsliGsdafqe+d +Git+p+tkh++lv+++++l+++
  lcl|NCBI__GCF_000017145.1:YP_001327676.1  77 VTSGPGATNAVTPLQDALMDSIPLVCISGQVPTSLIGSDAFQECDTVGITRPCTKHNWLVRDVNELARV 145
                                               ********************************************************************* PP

                                 TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleveekv.elpgykptvkghklqikkaleliekakkPvl 205
                                               ++eaf +a++GrPGPv+vd+Pkd++ a+  ++ ++ v + ++y+p+++g+ ++i++a+ l+++a++Pv+
  lcl|NCBI__GCF_000017145.1:YP_001327676.1 146 IHEAFRVAQSGRPGPVVVDIPKDIQFATGAYTPPSAVpTQKSYQPKTQGDLKKIEEAVALMKSARQPVI 214
                                               *****************************999997763679**************************** PP

                                 TIGR00118 206 lvGgGviia..easeelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadllia 272
                                               + GgGvi +  +a + l+el+e ++ p+t+tl+GlGa+p+  ++ lgmlGmhGt+eanla++++d++i+
  lcl|NCBI__GCF_000017145.1:YP_001327676.1 215 YSGGGVINSgpQAAHFLRELVELTDFPITSTLMGLGAYPASGKNWLGMLGMHGTYEANLAMHDCDVMIC 283
                                               *******883357789***************************************************** PP

                                 TIGR00118 273 vGarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkek 337
                                               +Garfddr+tg l+ f+p++k ihididP++i+knv+vd+pi+Gd+  vle++++  ++     +++  
  lcl|NCBI__GCF_000017145.1:YP_001327676.1 284 IGARFDDRITGRLNAFSPNSKKIHIDIDPSSINKNVRVDVPIIGDVAAVLEDMVRLWRAAaktvDRTRL 352
                                               *****************************************************9877665555656666 PP

                                 TIGR00118 338 e.WlekieewkkeyilkldeeeesikPqkvikelskllkd.eaivttdvGqhqmwaaqfyktkkprkfi 404
                                               e W+++i++w++++ l++  + + i Pq+ i++l++l+kd ++++tt+vGqhqmwaaqf+ +++p++++
  lcl|NCBI__GCF_000017145.1:YP_001327676.1 353 EdWWKSITKWRARNSLAYTPSADVIMPQYAIQRLYELTKDrDTYITTEVGQHQMWAAQFFGFEEPNRWM 421
                                               67*************************************999*************************** PP

                                 TIGR00118 405 tsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqW 473
                                               tsgGlGtmG+G+Paa+G++va+p++ v++++Gd+s+qm +qe+s +v+y++pvki ilnn+++Gmv+qW
  lcl|NCBI__GCF_000017145.1:YP_001327676.1 422 TSGGLGTMGYGFPAAVGVQVAHPDSLVIDIAGDASIQMCIQEMSCAVQYGLPVKIFILNNQYMGMVRQW 490
                                               ********************************************************************* PP

                                 TIGR00118 474 qelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlP 542
                                               q+l++ +r s+++ ++ +pdfvklaeayG +gir ekp el+e++k+++ + +pv++d +v++ ++++P
  lcl|NCBI__GCF_000017145.1:YP_001327676.1 491 QQLLHGNRLSHSYTEA-MPDFVKLAEAYGGVGIRCEKPGELDEAIKQMIDTPAPVIFDCRVANLANCFP 558
                                               ***************5.**************************************************** PP

                                 TIGR00118 543 mvapGagldelve 555
                                               m+++G++ +e++ 
  lcl|NCBI__GCF_000017145.1:YP_001327676.1 559 MIPSGKAHNEMLL 571
                                               **********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (592 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: 10.32
//
[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