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.1983.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 11.30
//
[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