GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Sinorhizobium meliloti 1021

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate SMc01431 SMc01431 acetolactate synthase 3 catalytic subunit

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



>FitnessBrowser__Smeli:SMc01431
          Length = 592

 Score =  629 bits (1623), Expect = 0.0
 Identities = 314/575 (54%), Positives = 418/575 (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
           T+GITRP  KHN+LV+DV +LA  I +AF +A +GRPGPVVVDIPKDV      Y  P +
Sbjct: 122 TIGITRPCTKHNWLVRDVNELARVIHEAFRVAQSGRPGPVVVDIPKDVQFATGTYTPPSA 181

Query: 193 I-DMRSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLA--NASDELRQLAALTGHP 249
           +   +SY P  +G   +I +AVAL++ A +P IY+GGGV+ +   A+  LR+L  LTG P
Sbjct: 182 VPTQKSYQPKTQGDLKKIEEAVALMKTARQPVIYSGGGVINSGPQAAHFLRELVELTGFP 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+++I   +A+     +  L  WW+ I 
Sbjct: 302 NSKK-IHIDIDPSSINKNVRVDVPIIGDVAAVLEDMIRLWRAAAKTVDQTRLGDWWKSIS 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 PE  V+ I G+ SIQMCIQE+S  +QY  PVKI  LN
Sbjct: 421 MTSGGLGTMGYGFPAAVGVQVAHPESLVIDIAGDASIQMCIQEMSCAVQYGLPVKIFILN 480

Query: 489 NGYLGMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRL 548
           N Y+GMVRQWQ++ + NR SHSY +A+PDFVKLAEAYG VG+R EK  +++ A+R+    
Sbjct: 481 NQYMGMVRQWQQLLHGNRLSHSYTEAMPDFVKLAEAYGGVGIRCEKPGELDDAIRQMIDT 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: 964
Number of extensions: 37
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 SMc01431 SMc01431 (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.1035.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.8e-244  798.2   0.1   2.1e-244  798.0   0.1    1.0  1  lcl|FitnessBrowser__Smeli:SMc01431  SMc01431 acetolactate synthase 3


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc01431  SMc01431 acetolactate synthase 3 catalytic subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  798.0   0.1  2.1e-244  2.1e-244       1     555 [.       8     571 ..       8     573 .. 0.97

  Alignments for each domain:
  == domain 1  score: 798.0 bits;  conditional E-value: 2.1e-244
                           TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGPG 74 
                                         ++gaei++++lk++gve++fGyPGGavlpiyd+++ +++++hilvrheq+a h+a+Gyar++GkvGv+l+tsGPG
  lcl|FitnessBrowser__Smeli:SMc01431   8 MTGAEIVLQALKDNGVEHIFGYPGGAVLPIYDEIFqQEDIQHILVRHEQGAGHMAEGYARSTGKVGVMLVTSGPG 82 
                                         79*********************************999************************************* PP

                           TIGR00118  75 atnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGr 149
                                         atn+vt++ +a +ds+Plv ++Gqv+tsliGsdafqe+d +Git+p+tkh++lv+++++l+++++eaf +a++Gr
  lcl|FitnessBrowser__Smeli:SMc01431  83 ATNAVTPLQDALMDSIPLVCISGQVPTSLIGSDAFQECDTIGITRPCTKHNWLVRDVNELARVIHEAFRVAQSGR 157
                                         *************************************************************************** PP

                           TIGR00118 150 PGPvlvdlPkdvteaeieleveekv.elpgykptvkghklqikkaleliekakkPvllvGgGviia..easeelk 221
                                         PGPv+vd+Pkdv+ a+ +++ ++ v + ++y+p+++g+ ++i++a+ l+++a++Pv++ GgGvi +  +a + l+
  lcl|FitnessBrowser__Smeli:SMc01431 158 PGPVVVDIPKDVQFATGTYTPPSAVpTQKSYQPKTQGDLKKIEEAVALMKTARQPVIYSGGGVINSgpQAAHFLR 232
                                         ******************99997763679***********************************883357789** PP

                           TIGR00118 222 elaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiih 296
                                         el+e +  p+t+tl+GlGa+p+  ++ lgmlGmhGt+eanla++++d++i++Garfddr+tg l+ f+p++k ih
  lcl|FitnessBrowser__Smeli:SMc01431 233 ELVELTGFPITSTLMGLGAYPASGKNWLGMLGMHGTYEANLAMHDCDVMICIGARFDDRITGRLNAFSPNSKKIH 307
                                         *************************************************************************** PP

                           TIGR00118 297 ididPaeigknvkvdipivGdakkvleellkklkee....ekkeke.WlekieewkkeyilkldeeeesikPqkv 366
                                         ididP++i+knv+vd+pi+Gd+  vle++++  ++     +++    W+++i++w++++ l++  + + i Pq+ 
  lcl|FitnessBrowser__Smeli:SMc01431 308 IDIDPSSINKNVRVDVPIIGDVAAVLEDMIRLWRAAaktvDQTRLGdWWKSISKWRARNSLAYTPSADVIMPQYA 382
                                         *****************************998776655553444336**************************** PP

                           TIGR00118 367 ikelskllkd.eaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsf 440
                                         i++l++l+kd ++++tt+vGqhqmwaaqf+ +++p++++tsgGlGtmG+G+Paa+G++va+pe+ v++++Gd+s+
  lcl|FitnessBrowser__Smeli:SMc01431 383 IQRLYELTKDrDTYITTEVGQHQMWAAQFFGFEEPNRWMTSGGLGTMGYGFPAAVGVQVAHPESLVIDIAGDASI 457
                                         *********999*************************************************************** PP

                           TIGR00118 441 qmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeele 515
                                         qm +qe+s +v+y++pvki ilnn+++Gmv+qWq+l++ +r s+++ ++ +pdfvklaeayG +gir ekp el+
  lcl|FitnessBrowser__Smeli:SMc01431 458 QMCIQEMSCAVQYGLPVKIFILNNQYMGMVRQWQQLLHGNRLSHSYTEA-MPDFVKLAEAYGGVGIRCEKPGELD 531
                                         ************************************************5.************************* PP

                           TIGR00118 516 eklkealeskepvlldvevdkeeevlPmvapGagldelve 555
                                         +++++++ + +pv++d +v++ ++++Pm+++G++ +e++ 
  lcl|FitnessBrowser__Smeli:SMc01431 532 DAIRQMIDTPAPVIFDCRVANLANCFPMIPSGKAHNEMLL 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 7.47
//
[ok]

This GapMind analysis is from Apr 09 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:

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:

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:

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:

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