Alignments for a candidate for ilvI in Pelobacter propionicus DSM 2379

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Pelobacter propionicus DSM 2379

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_011736417.1 PPRO_RS12635 biosynthetic-type acetolactate synthase large subunit

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



>NCBI__GCF_000015045.1:WP_011736417.1
          Length = 566

 Score =  631 bits (1627), Expect = 0.0
 Identities = 319/567 (56%), Positives = 407/567 (71%), Gaps = 4/567 (0%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           +M GA IL+  L +EGV+ V+GYPGG VL +YDEL    +  HI+ RHEQA  HAADGYA
Sbjct: 2   KMNGARILLECLMKEGVDTVFGYPGGTVLNVYDELFGCKEIRHIMPRHEQAGTHAADGYA 61

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           RATGKVGVA+ TSGPG TN VTGIATAY+DSIPMV+ITG VPT  IG DAFQE D VGIT
Sbjct: 62  RATGKVGVAIATSGPGATNTVTGIATAYMDSIPMVIITGQVPTALIGNDAFQEVDIVGIT 121

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
           R   KHNFLVKDV D+A  IKKAF+IA TGRPGPV+VD+PKDV     ++ YP+S+++RS
Sbjct: 122 RSCTKHNFLVKDVNDIAPIIKKAFYIARTGRPGPVLVDLPKDVQIAKTEFCYPESVELRS 181

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257
           Y P   GH  Q+ KAV++L  + RP +Y GGGV+L+NA+ EL  L+ L   PVT TLMGL
Sbjct: 182 YKPTTGGHPRQVSKAVSMLLASHRPVMYVGGGVILSNAAPELTALSRLLSIPVTTTLMGL 241

Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHI 317
           GAFPG     +GMLGMHG Y ANMAM + D+++A+GARFDDRV G    F   A KIIHI
Sbjct: 242 GAFPGDDVNSLGMLGMHGAYCANMAMTHSDLIVAVGARFDDRVTGKVDTFAPHA-KIIHI 300

Query: 318 DIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKAS--DIKPKREALAKWWEQIEQWRSVD 375
           D+DP+SI K V+VD+PIVG+V+DVL ++I +++ S  D    RE+LA W EQI  W+   
Sbjct: 301 DVDPTSIRKNVRVDLPIVGDVRDVLTKMIKKVEKSEGDQAAYRESLAPWHEQIAGWKEKH 360

Query: 376 CLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLG 435
            + + RSS +IKPQ+V++K+ EL+  DA + +DVGQHQMW AQF+ F  PR  + SGGLG
Sbjct: 361 PVSFTRSSAVIKPQFVIQKLRELSDRDAIVSTDVGQHQMWTAQFFSFTGPRTLLTSGGLG 420

Query: 436 TMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMV 495
           TMG GLP AMG + AFP ++V+ I G+G IQM IQE++T +Q   PVKI  +NN +LGMV
Sbjct: 421 TMGFGLPAAMGAQAAFPGRQVIAICGDGGIQMNIQEMATLVQNRLPVKIVIINNNFLGMV 480

Query: 496 RQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFL 555
           RQWQE+ +D RYS S ++   D++KLA+AYG  G    K S+VE  +R+ F  +   V +
Sbjct: 481 RQWQEMFFDKRYSQSCLELPIDYIKLADAYGAKGFVASKPSEVETVIRQGF-AEPGPVIM 539

Query: 556 DFQTDPTENVWPMVQAGKGISEMLLGA 582
           +F+    E V PMV +G  ++EMLL A
Sbjct: 540 EFRVAREEKVLPMVPSGASLNEMLLNA 566


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: 884
Number of extensions: 32
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: 566
Length adjustment: 36
Effective length of query: 549
Effective length of database: 530
Effective search space:   290970
Effective search space used:   290970
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_011736417.1 PPRO_RS12635 (biosynthetic-type acetolactate synthase 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.967628.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.7e-256  835.5   0.6   1.1e-255  835.3   0.6    1.0  1  NCBI__GCF_000015045.1:WP_011736417.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000015045.1:WP_011736417.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  835.3   0.6  1.1e-255  1.1e-255       1     555 [.       3     564 ..       3     566 .] 0.98

  Alignments for each domain:
  == domain 1  score: 835.3 bits;  conditional E-value: 1.1e-255
                             TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsG 72 
                                           ++ga+il+e l kegv+tvfGyPGG+vl++yd+l+  +e++hi++rheqa +haadGyara+GkvGv++atsG
  NCBI__GCF_000015045.1:WP_011736417.1   3 MNGARILLECLMKEGVDTVFGYPGGTVLNVYDELFgCKEIRHIMPRHEQAGTHAADGYARATGKVGVAIATSG 75 
                                           78*********************************99************************************ PP

                             TIGR00118  73 PGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeia 145
                                           PGatn+vtgiatay+ds+P+v++tGqv+t+liG+dafqe+di+Git+++tkh+flvk+++d++ i+k+af+ia
  NCBI__GCF_000015045.1:WP_011736417.1  76 PGATNTVTGIATAYMDSIPMVIITGQVPTALIGNDAFQEVDIVGITRSCTKHNFLVKDVNDIAPIIKKAFYIA 148
                                           ************************************************************************* PP

                             TIGR00118 146 stGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaease 218
                                            tGrPGPvlvdlPkdv+ a++e+ ++e+vel++ykpt+ gh++q+ ka+ ++ ++++Pv++vGgGvi ++a  
  NCBI__GCF_000015045.1:WP_011736417.1 149 RTGRPGPVLVDLPKDVQIAKTEFCYPESVELRSYKPTTGGHPRQVSKAVSMLLASHRPVMYVGGGVILSNAAP 221
                                           ************************************************************************* PP

                             TIGR00118 219 elkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfape 291
                                           el+ l+  l ipvtttl+GlGafp d+ ++lgmlGmhG++ an+a++++dl++avGarfddrvtg++++fap+
  NCBI__GCF_000015045.1:WP_011736417.1 222 ELTALSRLLSIPVTTTLMGLGAFPGDDVNSLGMLGMHGAYCANMAMTHSDLIVAVGARFDDRVTGKVDTFAPH 294
                                           ************************************************************************* PP

                             TIGR00118 292 akiihididPaeigknvkvdipivGdakkvleellkklkee......ekkeke.Wlekieewkkeyilkldee 357
                                           akiihid+dP++i knv+vd+pivGd++ vl++++kk+++        +++   W e+i+ wk+++++++ ++
  NCBI__GCF_000015045.1:WP_011736417.1 295 AKIIHIDVDPTSIRKNVRVDLPIVGDVRDVLTKMIKKVEKSegdqaaYRESLApWHEQIAGWKEKHPVSFTRS 367
                                           **************************************9997877653444457******************* PP

                             TIGR00118 358 eesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeet 430
                                           +  ikPq vi++l +l + +aiv+tdvGqhqmw+aqf++++ pr+ +tsgGlGtmGfGlPaa+Ga+ a p  +
  NCBI__GCF_000015045.1:WP_011736417.1 368 SAVIKPQFVIQKLRELSDRDAIVSTDVGQHQMWTAQFFSFTGPRTLLTSGGLGTMGFGLPAAMGAQAAFPGRQ 440
                                           ************************************************************************* PP

                             TIGR00118 431 vvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGv 503
                                           v+a++Gdg++qmn+qe++t+v+  +pvkivi+nn++lGmv+qWqe+f+++rys+++l+    d++kla+ayG+
  NCBI__GCF_000015045.1:WP_011736417.1 441 VIAICGDGGIQMNIQEMATLVQNRLPVKIVIINNNFLGMVRQWQEMFFDKRYSQSCLEL-PIDYIKLADAYGA 512
                                           **********************************************************6.88*********** PP

                             TIGR00118 504 kgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldelve 555
                                           kg   +kp+e+e  +++ +++ +pv+++++v++ee+vlPmv++Ga+l+e++ 
  NCBI__GCF_000015045.1:WP_011736417.1 513 KGFVASKPSEVETVIRQGFAEPGPVIMEFRVAREEKVLPMVPSGASLNEMLL 564
                                           **************************************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (566 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 19.50
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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