Alignments for a candidate for ilvI in Azospirillum brasilense Sp245

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Azospirillum brasilense Sp245

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate AZOBR_RS06560 AZOBR_RS06560 acetolactate synthase

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



>FitnessBrowser__azobra:AZOBR_RS06560
          Length = 587

 Score =  633 bits (1633), Expect = 0.0
 Identities = 311/570 (54%), Positives = 411/570 (72%), Gaps = 4/570 (0%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           ++ GA+I++ AL ++GV+ ++GYPGGAVL IYD + +Q   +HILVRHEQAAVHAA+GYA
Sbjct: 5   KLTGAQIVIKALKDQGVDIIFGYPGGAVLPIYDAIFQQNDIKHILVRHEQAAVHAAEGYA 64

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           R+TGKVG  LVTSGPG TNAVTG+  A  DSIP+V ++G VPTH IG DAFQE DT GIT
Sbjct: 65  RSTGKVGCVLVTSGPGATNAVTGLLDALCDSIPLVCLSGQVPTHLIGNDAFQEADTTGIT 124

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
           RP  KHN+LVKDV  LA T+ +AF++A +GRPGPV+VDIPKDV      Y  P  +  ++
Sbjct: 125 RPCTKHNYLVKDVNQLARTMHEAFYVARSGRPGPVLVDIPKDVQFADGTYIPPTEVKHKT 184

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLAN--ASDELRQLAALTGHPVTNTLM 255
           Y P  K    ++ +A+ L+  A+RP  YTGGGVV A   A+  L Q   +TG P+T+TLM
Sbjct: 185 YRPQVKPEIARVEEAIELIATAKRPIFYTGGGVVNAGPIAAKLLTQFVKMTGFPITSTLM 244

Query: 256 GLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKII 315
           GLGAFP +  Q++GMLGMHGTYEAN+AM NCDV+I IGARFDDRV G  + F   ++K I
Sbjct: 245 GLGAFPASDPQWLGMLGMHGTYEANLAMYNCDVMINIGARFDDRVTGKLSEFAPGSKK-I 303

Query: 316 HIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVD 375
           H+DIDPSSI+K V VDIPIVG+   VL+++I   KA   +  + AL +WW Q+E WR+ +
Sbjct: 304 HVDIDPSSINKNVAVDIPIVGDAGAVLEDMIRIWKARQKRADQTALKEWWGQVEGWRARN 363

Query: 376 CLKYDRSSEIIKPQYVVEKIWELTKG-DAFICSDVGQHQMWAAQFYKFDEPRRWINSGGL 434
           CL Y+R+  +IKPQY +E++ E  +G + ++ ++VGQHQMWAAQF  FDEP RW+ SGGL
Sbjct: 364 CLNYNRTEAVIKPQYALERLREALRGKNHYVTTEVGQHQMWAAQFLPFDEPNRWMTSGGL 423

Query: 435 GTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGM 494
           GTMG GLP A+G + A P+  VV ++GE S  M +QE+ T +QY  PVKI  LNN Y+GM
Sbjct: 424 GTMGYGLPAAIGAQLAHPDAIVVDVSGEASFLMNMQEIGTAVQYRAPVKIFILNNKYMGM 483

Query: 495 VRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVF 554
           VRQWQE+ + +RYS+SY +ALPDFVKLAE++G VG+R    ++V+  + +   + DR   
Sbjct: 484 VRQWQELLHGSRYSNSYSEALPDFVKLAESWGCVGLRATTVAEVDEVIEKMLAVTDRPCI 543

Query: 555 LDFQTDPTENVWPMVQAGKGISEMLLGAED 584
           +D   DP EN +PM+  GK  +E+L G ED
Sbjct: 544 IDIAVDPKENCFPMIPGGKAHNEILFGPED 573


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: 946
Number of extensions: 24
Number of successful extensions: 4
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: 587
Length adjustment: 37
Effective length of query: 548
Effective length of database: 550
Effective search space:   301400
Effective search space used:   301400
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 AZOBR_RS06560 AZOBR_RS06560 (acetolactate synthase)
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.15329.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.7e-244  796.9   0.1   5.7e-244  796.6   0.1    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS06560  AZOBR_RS06560 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS06560  AZOBR_RS06560 acetolactate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  796.6   0.1  5.7e-244  5.7e-244       1     554 [.       6     568 ..       6     570 .. 0.97

  Alignments for each domain:
  == domain 1  score: 796.6 bits;  conditional E-value: 5.7e-244
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 
                                               l+ga+i++++lk++gv+++fGyPGGavlpiyda++ +++++hilvrheqaa+haa+Gyar++GkvG+vl
  lcl|FitnessBrowser__azobra:AZOBR_RS06560   6 LTGAQIVIKALKDQGVDIIFGYPGGAVLPIYDAIFqQNDIKHILVRHEQAAVHAAEGYARSTGKVGCVL 74 
                                               68*********************************999******************************* PP

                                 TIGR00118  69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137
                                               +tsGPGatn+vtg+++a  ds+Plv l+Gqv+t+liG+dafqe+d +Git+p+tkh++lvk++++l+++
  lcl|FitnessBrowser__azobra:AZOBR_RS06560  75 VTSGPGATNAVTGLLDALCDSIPLVCLSGQVPTHLIGNDAFQEADTTGITRPCTKHNYLVKDVNQLART 143
                                               ********************************************************************* PP

                                 TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvll 206
                                               ++eaf++a +GrPGPvlvd+Pkdv+ a+ ++  +++v+ ++y+p+vk++ +++++a+eli++ak+P+ +
  lcl|FitnessBrowser__azobra:AZOBR_RS06560 144 MHEAFYVARSGRPGPVLVDIPKDVQFADGTYIPPTEVKHKTYRPQVKPEIARVEEAIELIATAKRPIFY 212
                                               ********************************************************************* PP

                                 TIGR00118 207 vGgGviiae..aseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliav 273
                                                GgGv+ a+  a + l+++++++  p+t+tl+GlGafp+ +p+ lgmlGmhGt+eanla+ ++d++i +
  lcl|FitnessBrowser__azobra:AZOBR_RS06560 213 TGGGVVNAGpiAAKLLTQFVKMTGFPITSTLMGLGAFPASDPQWLGMLGMHGTYEANLAMYNCDVMINI 281
                                               ******998668999****************************************************** PP

                                 TIGR00118 274 GarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke 338
                                               Garfddrvtg+l++fap +k ih+didP++i+knv+vdipivGda  vle++++  k++    +++  +
  lcl|FitnessBrowser__azobra:AZOBR_RS06560 282 GARFDDRVTGKLSEFAPGSKKIHVDIDPSSINKNVAVDIPIVGDAGAVLEDMIRIWKARqkraDQTALK 350
                                               ****************************************************98666554455334444 PP

                                 TIGR00118 339 .WlekieewkkeyilkldeeeesikPqkvikelskllkd.eaivttdvGqhqmwaaqfyktkkprkfit 405
                                                W+ ++e w+++++l+++++e  ikPq+ +++l + l++ + +vtt+vGqhqmwaaqf+++++p++++t
  lcl|FitnessBrowser__azobra:AZOBR_RS06560 351 eWWGQVEGWRARNCLNYNRTEAVIKPQYALERLREALRGkNHYVTTEVGQHQMWAAQFLPFDEPNRWMT 419
                                               5**********************************9998689*************************** PP

                                 TIGR00118 406 sgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWq 474
                                               sgGlGtmG+GlPaa+Ga++a+p++ vv+v+G++sf mn+qe+ t+v+y  pvki ilnn+++Gmv+qWq
  lcl|FitnessBrowser__azobra:AZOBR_RS06560 420 SGGLGTMGYGLPAAIGAQLAHPDAIVVDVSGEASFLMNMQEIGTAVQYRAPVKIFILNNKYMGMVRQWQ 488
                                               ********************************************************************* PP

                                 TIGR00118 475 elfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevlP 542
                                               el++  rys+++ ++ lpdfvklae++G +g+r ++ +e++e ++++l+++ +p ++d+ vd +e+++P
  lcl|FitnessBrowser__azobra:AZOBR_RS06560 489 ELLHGSRYSNSYSEA-LPDFVKLAESWGCVGLRATTVAEVDEVIEKMLAVTdRPCIIDIAVDPKENCFP 556
                                               ************995.*******************************997669**************** PP

                                 TIGR00118 543 mvapGagldelv 554
                                               m++ G++ +e++
  lcl|FitnessBrowser__azobra:AZOBR_RS06560 557 MIPGGKAHNEIL 568
                                               *********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (587 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 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 7.45
//
[ok]

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

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
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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