Alignments for a candidate for ilvI in Thiomicrorhabdus chilensis DSM 12352

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Thiomicrorhabdus chilensis DSM 12352

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_028486983.1 B076_RS0108815 acetolactate synthase 3 large subunit

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



>NCBI__GCF_000483485.1:WP_028486983.1
          Length = 567

 Score =  763 bits (1970), Expect = 0.0
 Identities = 377/566 (66%), Positives = 448/566 (79%), Gaps = 4/566 (0%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTK-FEHILVRHEQAAVHAADGY 76
           EM GA+ILV+ L +EGVE++WGYPGGAVL IYD L    K   HILVRHEQAAVHAADGY
Sbjct: 2   EMTGAQILVNYLEDEGVEHIWGYPGGAVLPIYDALDTDAKKLSHILVRHEQAAVHAADGY 61

Query: 77  ARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGI 136
           AR+TGK GV LVTSGPG TNAVTGIATAY+DSIPMV ITG VPT  IG DAFQE DTVGI
Sbjct: 62  ARSTGKPGVVLVTSGPGATNAVTGIATAYMDSIPMVCITGQVPTALIGLDAFQEIDTVGI 121

Query: 137 TRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMR 196
           TRPIVKHNFLVK V +LA+T+KKAF++A TGRPGPVV+DIPKD+      Y YP+ ++MR
Sbjct: 122 TRPIVKHNFLVKSVDELASTLKKAFYLATTGRPGPVVIDIPKDIQNAKSTYVYPQEVEMR 181

Query: 197 SYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMG 256
           SY PV KGHSGQI+KAV ++  A+RP +YTGGGV+L +AS+EL +L    G P+T TLMG
Sbjct: 182 SYLPVTKGHSGQIKKAVEMMLSAKRPILYTGGGVILGDASEELIKLTHKLGFPITQTLMG 241

Query: 257 LGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIH 316
           LGAFP + KQ VGMLGMHGTYEAN++M + DV+IAIGARFDDRV GN   F   A KI+H
Sbjct: 242 LGAFPASDKQSVGMLGMHGTYEANLSMHHSDVIIAIGARFDDRVTGNLEKFCPDA-KIVH 300

Query: 317 IDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDC 376
           +DIDP+SISK V VDIPIVG VK VL E+ A +  +  K   EALA+WW+QIEQWR+  C
Sbjct: 301 VDIDPASISKNVIVDIPIVGPVKQVLTEMNAILDKTKQKVDEEALAEWWQQIEQWRATKC 360

Query: 377 LKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGT 436
           L+YD +   IKPQ  +E +WE+T GDA++ SDVGQHQM+AAQ+Y FD+PRRWINSGGLGT
Sbjct: 361 LRYDTAGSKIKPQAAMEAVWEVTNGDAYVASDVGQHQMFAAQYYPFDKPRRWINSGGLGT 420

Query: 437 MGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVR 496
           MG GLP AMG + AFP+  V+ +TGEGSIQM IQELSTCLQY  PVK+  LNNG+LGMVR
Sbjct: 421 MGFGLPAAMGAQMAFPDATVICVTGEGSIQMNIQELSTCLQYGLPVKVVCLNNGFLGMVR 480

Query: 497 QWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAF--RLKDRTVF 554
           QWQE  Y+ RYS SYM++LPDFVKLAE+YGHVGMR+E    ++  L EAF  + KDR VF
Sbjct: 481 QWQEFFYERRYSMSYMESLPDFVKLAESYGHVGMRIEDPKTMKAQLEEAFSDKNKDRFVF 540

Query: 555 LDFQTDPTENVWPMVQAGKGISEMLL 580
           +D  TD  ENV+PM+ AG G++EM+L
Sbjct: 541 IDIITDQQENVYPMIPAGAGLNEMIL 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: 1018
Number of extensions: 39
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: 567
Length adjustment: 36
Effective length of query: 549
Effective length of database: 531
Effective search space:   291519
Effective search space used:   291519
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_028486983.1 B076_RS0108815 (acetolactate synthase 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.17589.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.8e-270  883.5   2.6   3.1e-270  883.3   2.6    1.0  1  lcl|NCBI__GCF_000483485.1:WP_028486983.1  B076_RS0108815 acetolactate synt


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000483485.1:WP_028486983.1  B076_RS0108815 acetolactate synthase 3 large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  883.3   2.6  3.1e-270  3.1e-270       1     555 [.       3     566 ..       3     567 .] 0.97

  Alignments for each domain:
  == domain 1  score: 883.3 bits;  conditional E-value: 3.1e-270
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly..dselehilvrheqaaahaadGyarasGkvGvv 67 
                                               ++ga+ilv+ l++egve+++GyPGGavlpiydal   +++l+hilvrheqaa+haadGyar++Gk+Gvv
  lcl|NCBI__GCF_000483485.1:WP_028486983.1   3 MTGAQILVNYLEDEGVEHIWGYPGGAVLPIYDALDtdAKKLSHILVRHEQAAVHAADGYARSTGKPGVV 71 
                                               79********************************987889***************************** PP

                                 TIGR00118  68 latsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpe 136
                                               l+tsGPGatn+vtgiatay+ds+P+v +tGqv+t+liG dafqeid +Git+p++kh+flvk++++l++
  lcl|NCBI__GCF_000483485.1:WP_028486983.1  72 LVTSGPGATNAVTGIATAYMDSIPMVCITGQVPTALIGLDAFQEIDTVGITRPIVKHNFLVKSVDELAS 140
                                               ********************************************************************* PP

                                 TIGR00118 137 ilkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvl 205
                                               +lk+af++a+tGrPGPv++d+Pkd+++a+ ++ ++++ve+++y p +kgh  qikka+e++ +ak+P+l
  lcl|NCBI__GCF_000483485.1:WP_028486983.1 141 TLKKAFYLATTGRPGPVVIDIPKDIQNAKSTYVYPQEVEMRSYLPVTKGHSGQIKKAVEMMLSAKRPIL 209
                                               ********************************************************************* PP

                                 TIGR00118 206 lvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavG 274
                                               + GgGvi ++aseel +l+++l  p+t+tl+GlGafp+ +++++gmlGmhGt+eanl+++++d++ia+G
  lcl|NCBI__GCF_000483485.1:WP_028486983.1 210 YTGGGVILGDASEELIKLTHKLGFPITQTLMGLGAFPASDKQSVGMLGMHGTYEANLSMHHSDVIIAIG 278
                                               ********************************************************************* PP

                                 TIGR00118 275 arfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee.....ekkeke 338
                                               arfddrvtgnl+kf+p+aki+h+didPa+i+knv vdipivG +k+vl+e+ + l ++     e+   e
  lcl|NCBI__GCF_000483485.1:WP_028486983.1 279 ARFDDRVTGNLEKFCPDAKIVHVDIDPASISKNVIVDIPIVGPVKQVLTEMNAILDKTkqkvdEEALAE 347
                                               **************************************************9877666544353333446 PP

                                 TIGR00118 339 WlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsg 407
                                               W+++ie+w+++++l++d+  ++ikPq+ +++++++++++a+v++dvGqhqm+aaq+y+++kpr++i+sg
  lcl|NCBI__GCF_000483485.1:WP_028486983.1 348 WWQQIEQWRATKCLRYDTAGSKIKPQAAMEAVWEVTNGDAYVASDVGQHQMFAAQYYPFDKPRRWINSG 416
                                               ********************************************************************* PP

                                 TIGR00118 408 GlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqel 476
                                               GlGtmGfGlPaa+Ga++a p++tv++vtG+gs+qmn+qelst+ +y++pvk+v+lnn +lGmv+qWqe+
  lcl|NCBI__GCF_000483485.1:WP_028486983.1 417 GLGTMGFGLPAAMGAQMAFPDATVICVTGEGSIQMNIQELSTCLQYGLPVKVVCLNNGFLGMVRQWQEF 485
                                               ********************************************************************* PP

                                 TIGR00118 477 fyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk...epvlldvevdkeeevlP 542
                                               fye+rys ++++s lpdfvklae+yG++g+rie+p+ ++++l+ea++ k   + v++d+  d++e+v+P
  lcl|NCBI__GCF_000483485.1:WP_028486983.1 486 FYERRYSMSYMES-LPDFVKLAESYGHVGMRIEDPKTMKAQLEEAFSDKnkdRFVFIDIITDQQENVYP 553
                                               ************5.*******************************998756689*************** PP

                                 TIGR00118 543 mvapGagldelve 555
                                               m++ Gagl+e++ 
  lcl|NCBI__GCF_000483485.1:WP_028486983.1 554 MIPAGAGLNEMIL 566
                                               ***********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (567 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: 11.04
//
[ok]

This GapMind analysis is from Apr 10 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