Alignments for a candidate for ilvI in Phaeobacter inhibens BS107

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.1060.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: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 7.40
//
[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:

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