Alignments for a candidate for ilvI in Thioalkalivibrio thiocyanodenitrificans ARhD 1

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Thioalkalivibrio thiocyanodenitrificans ARhD 1

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_018232002.1 THITHI_RS0105115 acetolactate synthase 3 large subunit

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



>NCBI__GCF_000378965.1:WP_018232002.1
          Length = 564

 Score =  806 bits (2081), Expect = 0.0
 Identities = 385/563 (68%), Positives = 456/563 (80%), Gaps = 1/563 (0%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           E+ GAEI V  L EEGV+ ++GYPGGAVL+IYD L+KQ K  HILVRHEQ A+HAA+GYA
Sbjct: 2   ELTGAEIFVRCLQEEGVDLIFGYPGGAVLHIYDALYKQDKVAHILVRHEQGAIHAAEGYA 61

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           ++T K GVALVTSGPG TNA+TGIA AY+DS+P+VV TG VPTH IG DAFQE DTVGIT
Sbjct: 62  KSTDKPGVALVTSGPGATNAITGIADAYMDSVPLVVFTGQVPTHLIGNDAFQEVDTVGIT 121

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
           RP VKHNFLVKDV+DLA T+KKAF++A TGRPGPVVVDIPKDV+   C+Y YPK+I MRS
Sbjct: 122 RPCVKHNFLVKDVKDLATTLKKAFYVATTGRPGPVVVDIPKDVTAAKCEYSYPKTIRMRS 181

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257
           YNP  KGH+GQIRKA+ L+  A +P IY GGGV+L  A+  L     L G+P+TNTLMGL
Sbjct: 182 YNPTVKGHTGQIRKAIDLILEARQPIIYAGGGVILGRAAKSLTDFTRLLGYPITNTLMGL 241

Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHI 317
           G +P T K  VGMLGMHGTYEANMAM + D++IAIGARFDDRV GN   F   A KI+H+
Sbjct: 242 GGYPATDKLSVGMLGMHGTYEANMAMHHADLVIAIGARFDDRVTGNIEKFCPYA-KIVHV 300

Query: 318 DIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDCL 377
           D+DP+SISK VKVD+PIVG V  VL+ +I +IKA   KP   AL  WW+QI +WR++DCL
Sbjct: 301 DVDPASISKNVKVDVPIVGQVDTVLKAMIKEIKADPRKPDAAALKAWWKQIGEWRAMDCL 360

Query: 378 KYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGTM 437
           KYDR+SE+IKPQYV+E +W+LTKGDAF+ SDVGQHQMWAAQFYKFD+P RWINSGGLGTM
Sbjct: 361 KYDRNSELIKPQYVLETLWKLTKGDAFVTSDVGQHQMWAAQFYKFDKPNRWINSGGLGTM 420

Query: 438 GVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVRQ 497
           G GLP AMG++ A P+  V  +TGE SIQMCIQELSTCLQY  P+K+ +LNN Y+GMVRQ
Sbjct: 421 GFGLPAAMGVQLAHPKATVACVTGEASIQMCIQELSTCLQYQLPIKVVNLNNRYMGMVRQ 480

Query: 498 WQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFLDF 557
           WQE  Y  RY+ SYMDALPDFV LAEAYGHVGMR+EK +DVE AL+EA +LKDR VF+DF
Sbjct: 481 WQEFFYQGRYAMSYMDALPDFVVLAEAYGHVGMRIEKPADVEGALKEALKLKDRLVFMDF 540

Query: 558 QTDPTENVWPMVQAGKGISEMLL 580
            TD +ENV+PM+ AG G +EM+L
Sbjct: 541 ITDQSENVYPMIPAGAGQNEMIL 563


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: 1025
Number of extensions: 32
Number of successful extensions: 2
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: 564
Length adjustment: 36
Effective length of query: 549
Effective length of database: 528
Effective search space:   289872
Effective search space used:   289872
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_018232002.1 THITHI_RS0105115 (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.21659.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.4e-267  871.8   1.5   1.1e-266  871.6   1.5    1.0  1  lcl|NCBI__GCF_000378965.1:WP_018232002.1  THITHI_RS0105115 acetolactate sy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000378965.1:WP_018232002.1  THITHI_RS0105115 acetolactate synthase 3 large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  871.6   1.5  1.1e-266  1.1e-266       1     555 [.       3     563 ..       3     564 .] 0.98

  Alignments for each domain:
  == domain 1  score: 871.6 bits;  conditional E-value: 1.1e-266
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 
                                               l+gaei+v+ l++egv+ +fGyPGGavl+iydaly ++++ hilvrheq+a+haa+Gya+++ k+Gv+l
  lcl|NCBI__GCF_000378965.1:WP_018232002.1   3 LTGAEIFVRCLQEEGVDLIFGYPGGAVLHIYDALYkQDKVAHILVRHEQGAIHAAEGYAKSTDKPGVAL 71 
                                               68*********************************999******************************* PP

                                 TIGR00118  69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137
                                               +tsGPGatn++tgia+ay+dsvPlvv+tGqv+t+liG+dafqe+d +Git+p++kh+flvk+++dl+++
  lcl|NCBI__GCF_000378965.1:WP_018232002.1  72 VTSGPGATNAITGIADAYMDSVPLVVFTGQVPTHLIGNDAFQEVDTVGITRPCVKHNFLVKDVKDLATT 140
                                               ********************************************************************* PP

                                 TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvll 206
                                               lk+af++a+tGrPGPv+vd+Pkdvt+a++e+++++++ +++y+ptvkgh+ qi+ka++li +a++P+++
  lcl|NCBI__GCF_000378965.1:WP_018232002.1 141 LKKAFYVATTGRPGPVVVDIPKDVTAAKCEYSYPKTIRMRSYNPTVKGHTGQIRKAIDLILEARQPIIY 209
                                               ********************************************************************* PP

                                 TIGR00118 207 vGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGa 275
                                               +GgGvi + a + l++++  l  p+t tl+GlG++p++++l++gmlGmhGt+ean+a+++adl+ia+Ga
  lcl|NCBI__GCF_000378965.1:WP_018232002.1 210 AGGGVILGRAAKSLTDFTRLLGYPITNTLMGLGGYPATDKLSVGMLGMHGTYEANMAMHHADLVIAIGA 278
                                               ********************************************************************* PP

                                 TIGR00118 276 rfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke.W 339
                                               rfddrvtgn++kf+p aki+h+d+dPa+i+knvkvd+pivG++ +vl+ ++k++k+     +    + W
  lcl|NCBI__GCF_000378965.1:WP_018232002.1 279 RFDDRVTGNIEKFCPYAKIVHVDVDPASISKNVKVDVPIVGQVDTVLKAMIKEIKADprkpDAAALKaW 347
                                               ******************************************************99876654444557* PP

                                 TIGR00118 340 lekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgG 408
                                               +++i ew++  +lk+d+++e ikPq+v+++l+kl+k++a+vt+dvGqhqmwaaqfyk++kp+++i+sgG
  lcl|NCBI__GCF_000378965.1:WP_018232002.1 348 WKQIGEWRAMDCLKYDRNSELIKPQYVLETLWKLTKGDAFVTSDVGQHQMWAAQFYKFDKPNRWINSGG 416
                                               ********************************************************************* PP

                                 TIGR00118 409 lGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelf 477
                                               lGtmGfGlPaa+G+++a+p++tv +vtG++s+qm +qelst+ +y++p+k+v+lnn+++Gmv+qWqe+f
  lcl|NCBI__GCF_000378965.1:WP_018232002.1 417 LGTMGFGLPAAMGVQLAHPKATVACVTGEASIQMCIQELSTCLQYQLPIKVVNLNNRYMGMVRQWQEFF 485
                                               ********************************************************************* PP

                                 TIGR00118 478 yeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevlPmva 545
                                               y++ry+ +++ + lpdfv laeayG++g+riekp+++e +lkeal+ k ++v++d+  d++e+v+Pm++
  lcl|NCBI__GCF_000378965.1:WP_018232002.1 486 YQGRYAMSYMDA-LPDFVVLAEAYGHVGMRIEKPADVEGALKEALKLKdRLVFMDFITDQSENVYPMIP 553
                                               ***********5.********************************988699****************** PP

                                 TIGR00118 546 pGagldelve 555
                                                Gag +e++ 
  lcl|NCBI__GCF_000378965.1:WP_018232002.1 554 AGAGQNEMIL 563
                                               ********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (564 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: 0.03u 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 7.26
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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Protein sequences (fasta format)
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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