Alignments for a candidate for ilvI in Bradyrhizobium sp. BTAi1

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Bradyrhizobium sp. BTAi1

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_012045965.1 BBTA_RS28470 acetolactate synthase 3 large subunit

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



>NCBI__GCF_000015165.1:WP_012045965.1
          Length = 589

 Score =  645 bits (1664), Expect = 0.0
 Identities = 319/570 (55%), Positives = 424/570 (74%), Gaps = 9/570 (1%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           +M GA ++V AL + GV++++GYPGGAVL IYDE+ +Q++ EHILVRHEQ A HAA+GYA
Sbjct: 10  QMTGAAMIVRALIDHGVQHIFGYPGGAVLPIYDEIFQQSEVEHILVRHEQGAGHAAEGYA 69

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           R+TGK GV LVTSGPG TN VT +A A +DSIP+V ITG VPTH IG DAFQECDTVGIT
Sbjct: 70  RSTGKPGVVLVTSGPGATNMVTPLADAMMDSIPLVCITGQVPTHLIGNDAFQECDTVGIT 129

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMR- 196
           RP  KHN+LV++V DLA  + +AF++A +GRPGPVVVD+PKDV      Y  P+  D+  
Sbjct: 130 RPCTKHNWLVRNVNDLAKVLHEAFYVATSGRPGPVVVDVPKDVQFATGTYHPPRKSDVHV 189

Query: 197 SYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLA--NASDELRQLAALTGHPVTNTL 254
           SY P  KG + QIRKAVALL  A+RP IY+GGGV+ +   AS  LR L  +TG P+T+TL
Sbjct: 190 SYAPRVKGDAMQIRKAVALLASAKRPVIYSGGGVINSGPEASRLLRGLVEVTGFPITSTL 249

Query: 255 MGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKI 314
           MGLGA+P +   ++GMLGMHGTYEANM M +CDV++ +GARFDDR+ G    F+  ++K 
Sbjct: 250 MGLGAYPASGTNWLGMLGMHGTYEANMTMHDCDVMLCVGARFDDRITGRTDAFSPNSKK- 308

Query: 315 IHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSV 374
           IHIDIDPSSI+K ++VD+PI+G+  DVL +++   KA    P  +A   WW+QI  WR+ 
Sbjct: 309 IHIDIDPSSINKNIRVDVPIIGDCGDVLADILQVFKAEAKTPDIKA---WWQQIATWRAR 365

Query: 375 DCLKYDRSSEIIKPQYVVEKIWELTKG-DAFICSDVGQHQMWAAQFYKFDEPRRWINSGG 433
           + L Y  + ++I PQY +++++ELT+G D +I ++VGQHQMWAAQFY F+EP RW+ SGG
Sbjct: 366 NSLAYKPNRDVIMPQYAIQRLFELTRGRDTYITTEVGQHQMWAAQFYGFEEPHRWMTSGG 425

Query: 434 LGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLG 493
           LGTMG GLP A+G++ A P+  V+ I G+ S+QM +QE+ST +QY+ PVKI  LNN Y+G
Sbjct: 426 LGTMGYGLPAAIGVQVAHPDSLVIDIGGDASVQMTMQEMSTAVQYELPVKIFILNNQYMG 485

Query: 494 MVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTV 553
           MVRQWQ++ + NR SHSY +ALPDFVKLAEAYG VG++V K  D++ A++E   +K + V
Sbjct: 486 MVRQWQQLLHGNRLSHSYSEALPDFVKLAEAYGGVGLQVSKPGDLDGAIKEMISVK-KPV 544

Query: 554 FLDFQTDPTENVWPMVQAGKGISEMLLGAE 583
             D +    EN +PM+ +GK  +EM+L AE
Sbjct: 545 LFDCRVAALENCFPMIPSGKAHNEMILPAE 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: 943
Number of extensions: 36
Number of successful extensions: 8
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: 589
Length adjustment: 37
Effective length of query: 548
Effective length of database: 552
Effective search space:   302496
Effective search space used:   302496
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_012045965.1 BBTA_RS28470 (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.26030.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-248  812.1   0.2   1.4e-248  811.9   0.2    1.0  1  lcl|NCBI__GCF_000015165.1:WP_012045965.1  BBTA_RS28470 acetolactate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015165.1:WP_012045965.1  BBTA_RS28470 acetolactate synthase 3 large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  811.9   0.2  1.4e-248  1.4e-248       1     555 [.      11     571 ..      11     573 .. 0.98

  Alignments for each domain:
  == domain 1  score: 811.9 bits;  conditional E-value: 1.4e-248
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 
                                               ++ga ++v++l ++gv+++fGyPGGavlpiyd+++ +se+ehilvrheq+a haa+Gyar++Gk+Gvvl
  lcl|NCBI__GCF_000015165.1:WP_012045965.1  11 MTGAAMIVRALIDHGVQHIFGYPGGAVLPIYDEIFqQSEVEHILVRHEQGAGHAAEGYARSTGKPGVVL 79 
                                               79*********************************99******************************** PP

                                 TIGR00118  69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137
                                               +tsGPGatn+vt++a+a++ds+Plv +tGqv+t+liG+dafqe+d +Git+p+tkh++lv++++dl+++
  lcl|NCBI__GCF_000015165.1:WP_012045965.1  80 VTSGPGATNMVTPLADAMMDSIPLVCITGQVPTHLIGNDAFQECDTVGITRPCTKHNWLVRNVNDLAKV 148
                                               ********************************************************************* PP

                                 TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleveekvelp.gykptvkghklqikkaleliekakkPvl 205
                                               l+eaf++a++GrPGPv+vd+Pkdv+ a+ +++ ++k ++  +y+p+vkg+ +qi+ka+ l+++ak+Pv+
  lcl|NCBI__GCF_000015165.1:WP_012045965.1 149 LHEAFYVATSGRPGPVVVDVPKDVQFATGTYHPPRKSDVHvSYAPRVKGDAMQIRKAVALLASAKRPVI 217
                                               *****************************9999977776439*************************** PP

                                 TIGR00118 206 lvGgGviia..easeelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadllia 272
                                               + GgGvi +  eas+ l+ l+e +  p+t+tl+GlGa+p+   + lgmlGmhGt+ean++++++d++++
  lcl|NCBI__GCF_000015165.1:WP_012045965.1 218 YSGGGVINSgpEASRLLRGLVEVTGFPITSTLMGLGAYPASGTNWLGMLGMHGTYEANMTMHDCDVMLC 286
                                               *******8744699******************************************************* PP

                                 TIGR00118 273 vGarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee.ekkeke.W 339
                                               vGarfddr+tg  + f+p++k ihididP++i+kn++vd+pi+Gd+  vl+++l+  k+e ++ +++ W
  lcl|NCBI__GCF_000015165.1:WP_012045965.1 287 VGARFDDRITGRTDAFSPNSKKIHIDIDPSSINKNIRVDVPIIGDCGDVLADILQVFKAEaKTPDIKaW 355
                                               *******************************************************9998866667778* PP

                                 TIGR00118 340 lekieewkkeyilkldeeeesikPqkvikelskllkd.eaivttdvGqhqmwaaqfyktkkprkfitsg 407
                                               +++i+ w++++ l+++ + + i Pq+ i++l +l+++ ++++tt+vGqhqmwaaqfy +++p++++tsg
  lcl|NCBI__GCF_000015165.1:WP_012045965.1 356 WQQIATWRARNSLAYKPNRDVIMPQYAIQRLFELTRGrDTYITTEVGQHQMWAAQFYGFEEPHRWMTSG 424
                                               ***********************************9989****************************** PP

                                 TIGR00118 408 GlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqel 476
                                               GlGtmG+GlPaa+G++va+p++ v+++ Gd+s+qm++qe+st+v+y++pvki ilnn+++Gmv+qWq+l
  lcl|NCBI__GCF_000015165.1:WP_012045965.1 425 GLGTMGYGLPAAIGVQVAHPDSLVIDIGGDASVQMTMQEMSTAVQYELPVKIFILNNQYMGMVRQWQQL 493
                                               ********************************************************************* PP

                                 TIGR00118 477 fyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmva 545
                                               ++ +r s+++ ++ lpdfvklaeayG +g++++kp +l+ ++ke++++k+pvl+d +v+  e+++Pm++
  lcl|NCBI__GCF_000015165.1:WP_012045965.1 494 LHGNRLSHSYSEA-LPDFVKLAEAYGGVGLQVSKPGDLDGAIKEMISVKKPVLFDCRVAALENCFPMIP 561
                                               ***********95.******************************************************* PP

                                 TIGR00118 546 pGagldelve 555
                                               +G++ +e++ 
  lcl|NCBI__GCF_000015165.1:WP_012045965.1 562 SGKAHNEMIL 571
                                               ********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (589 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: 12.00
//
[ok]

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

Downloads

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

Related tools

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