GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Phaeobacter inhibens BS107

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate GFF1987 PGA1_c20210 acetolactate synthase isozyme 3 large subunit

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



>FitnessBrowser__Phaeo:GFF1987
          Length = 583

 Score =  598 bits (1543), Expect = e-175
 Identities = 310/570 (54%), Positives = 397/570 (69%), Gaps = 6/570 (1%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           EM GA+++V AL ++GV+ V+GYPGGAVL IYDE+  Q    HILVRHEQ AVHAA+GYA
Sbjct: 4   EMTGAKMVVQALKDQGVDTVFGYPGGAVLPIYDEIFLQNDIRHILVRHEQGAVHAAEGYA 63

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           R+TGK GV LVTSGPG TNAVTG+  A LDSIP+VV+TG VPT  IG DAFQE DTVGIT
Sbjct: 64  RSTGKPGVVLVTSGPGATNAVTGLTDALLDSIPLVVLTGQVPTFMIGSDAFQEADTVGIT 123

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
           RP  KHN+LVKD   LA T+ +AF +A  GRPGPV++DIPKDV      Y+ PK      
Sbjct: 124 RPCTKHNWLVKDTEKLAGTLHEAFHVATAGRPGPVLIDIPKDVQFATGTYQDPKPA-ASH 182

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLA--NASDELRQLAALTGHPVTNTLM 255
           Y P  KG    I + VA ++ A+RP  YTGGGV+ +   AS  LR+L A TG PVT+TLM
Sbjct: 183 YQPPVKGDLEAITELVAAMETAKRPVFYTGGGVINSGPGASQLLRELVAATGIPVTSTLM 242

Query: 256 GLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKII 315
           GLGA+P + K ++GMLGMHG YEANMAM +CD++I IGARFDDR+ G    F+  + K  
Sbjct: 243 GLGAYPASGKNWLGMLGMHGLYEANMAMHDCDLMINIGARFDDRITGRLDAFSPNSTK-A 301

Query: 316 HIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVD 375
           HIDIDPSSI+K ++VDIPIVG++  VL++++   K+   K    A+AKW EQI +WR + 
Sbjct: 302 HIDIDPSSINKVIRVDIPIVGDIGHVLEDVLKVWKSRGRKVDSAAIAKWQEQITEWRDIR 361

Query: 376 CLKYDRSSEIIKPQYVVEKIWELTKG-DAFICSDVGQHQMWAAQFYKFDEPRRWINSGGL 434
           CL Y  S   IKPQY +E++  LTK  + +I ++VGQHQMWAAQ+  F++P RW+ SGGL
Sbjct: 362 CLAYTASESTIKPQYALERLEALTKDRNRYITTEVGQHQMWAAQYLGFEDPNRWMTSGGL 421

Query: 435 GTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGM 494
           GTMG G P ++G++ A P+  V+ + GE S  M +QE+ T +QY  PVK   LNN  LGM
Sbjct: 422 GTMGYGTPASLGVQVAHPDALVINVAGEASWLMNMQEMGTAVQYRLPVKQFILNNERLGM 481

Query: 495 VRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVF 554
           VRQWQE+ +  RYSHS+ +ALPDFVKLAEA+G  G+  +   D++ A+ E     D  V 
Sbjct: 482 VRQWQELLHGERYSHSWSEALPDFVKLAEAFGAKGIICKDPKDLDDAIMEMLDY-DGPVI 540

Query: 555 LDFQTDPTENVWPMVQAGKGISEMLLGAED 584
            D   +  EN +PM+ +GK  +EMLLG  D
Sbjct: 541 FDCLVEKHENCFPMIPSGKAHNEMLLGEAD 570


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: 987
Number of extensions: 40
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: 583
Length adjustment: 36
Effective length of query: 549
Effective length of database: 547
Effective search space:   300303
Effective search space used:   300303
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 GFF1987 PGA1_c20210 (acetolactate synthase isozyme 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.15365.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
     4e-236  770.7   0.0   4.6e-236  770.5   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF1987  PGA1_c20210 acetolactate synthas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF1987  PGA1_c20210 acetolactate synthase isozyme 3 large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  770.5   0.0  4.6e-236  4.6e-236       1     554 [.       5     565 ..       5     568 .. 0.97

  Alignments for each domain:
  == domain 1  score: 770.5 bits;  conditional E-value: 4.6e-236
                          TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGPGa 75 
                                        ++ga+++v++lk++gv+tvfGyPGGavlpiyd+++ +++++hilvrheq+a+haa+Gyar++Gk+Gvvl+tsGPGa
  lcl|FitnessBrowser__Phaeo:GFF1987   5 MTGAKMVVQALKDQGVDTVFGYPGGAVLPIYDEIFlQNDIRHILVRHEQGAVHAAEGYARSTGKPGVVLVTSGPGA 80 
                                        79*********************************99*************************************** PP

                          TIGR00118  76 tnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGrPG 151
                                        tn+vtg+++a lds+PlvvltGqv+t +iGsdafqe+d +Git+p+tkh++lvk++e l+ +l+eaf++a++GrPG
  lcl|FitnessBrowser__Phaeo:GFF1987  81 TNAVTGLTDALLDSIPLVVLTGQVPTFMIGSDAFQEADTVGITRPCTKHNWLVKDTEKLAGTLHEAFHVATAGRPG 156
                                        **************************************************************************** PP

                          TIGR00118 152 PvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviia..easeelkelae 225
                                        Pvl+d+Pkdv+ a+ +++ + k     y+p vkg+   i +++ ++e+ak+Pv + GgGvi +  +as+ l+el+ 
  lcl|FitnessBrowser__Phaeo:GFF1987 157 PVLIDIPKDVQFATGTYQDP-KPAASHYQPPVKGDLEAITELVAAMETAKRPVFYTGGGVINSgpGASQLLRELVA 231
                                        *************9999988.667899**********************************8733699******** PP

                          TIGR00118 226 rlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihididP 301
                                        ++ ipvt+tl+GlGa+p+  ++ lgmlGmhG +ean+a++++dl+i +Garfddr+tg l+ f+p+++  hididP
  lcl|FitnessBrowser__Phaeo:GFF1987 232 ATGIPVTSTLMGLGAYPASGKNWLGMLGMHGLYEANMAMHDCDLMINIGARFDDRITGRLDAFSPNSTKAHIDIDP 307
                                        **************************************************************************** PP

                          TIGR00118 302 aeigknvkvdipivGdakkvleellkklkee.....ekkekeWlekieewkkeyilkldeeeesikPqkvikelsk 372
                                        ++i+k+++vdipivGd  +vle++lk  k++     +    +W e+i+ew++  +l++  +e++ikPq+ +++l  
  lcl|FitnessBrowser__Phaeo:GFF1987 308 SSINKVIRVDIPIVGDIGHVLEDVLKVWKSRgrkvdSAAIAKWQEQITEWRDIRCLAYTASESTIKPQYALERLEA 383
                                        *************************99888776553333445********************************** PP

                          TIGR00118 373 llkd.eaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqel 447
                                        l+kd + ++tt+vGqhqmwaaq++ ++ p++++tsgGlGtmG+G Pa+lG++va+p++ v++v+G++s  mn+qe+
  lcl|FitnessBrowser__Phaeo:GFF1987 384 LTKDrNRYITTEVGQHQMWAAQYLGFEDPNRWMTSGGLGTMGYGTPASLGVQVAHPDALVINVAGEASWLMNMQEM 459
                                        ***9889********************************************************************* PP

                          TIGR00118 448 stiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkeale 523
                                         t+v+y +pvk  ilnne lGmv+qWqel++ erys++  ++ lpdfvklaea+G+kgi  ++p++l++++ e+l 
  lcl|FitnessBrowser__Phaeo:GFF1987 460 GTAVQYRLPVKQFILNNERLGMVRQWQELLHGERYSHSWSEA-LPDFVKLAEAFGAKGIICKDPKDLDDAIMEMLD 534
                                        **************************************9995.********************************* PP

                          TIGR00118 524 skepvlldvevdkeeevlPmvapGagldelv 554
                                         ++pv++d  v+k+e+++Pm+++G++ +e++
  lcl|FitnessBrowser__Phaeo:GFF1987 535 YDGPVIFDCLVEKHENCFPMIPSGKAHNEML 565
                                        *****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (583 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: 11.36
//
[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