Alignments for a candidate for ilvI in Thermocrinis albus DSM 14484

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Thermocrinis albus DSM 14484

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_012992620.1 THAL_RS08055 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_000025605.1:WP_012992620.1
          Length = 584

 Score =  621 bits (1601), Expect = 0.0
 Identities = 311/565 (55%), Positives = 397/565 (70%), Gaps = 6/565 (1%)

Query: 21  GAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYARAT 80
           GA+I++  L EEGVE ++G+PGGA++ +YD L++     HIL RHEQ A H A+GYA+AT
Sbjct: 5   GADIVIEVLKEEGVEVIFGHPGGAIMEVYDALYRDGGIRHILARHEQGAGHMAEGYAKAT 64

Query: 81  GKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGITRPI 140
           GKVGVA+ TSGPG TN VT IA AY+DS+P+V ITG VPTH IG DAFQE D VGITRPI
Sbjct: 65  GKVGVAMATSGPGATNLVTAIADAYMDSVPVVFITGQVPTHLIGNDAFQEVDIVGITRPI 124

Query: 141 VKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS--- 197
            KHNFLVK + DL   +++AF+IA TGRPGPV+VDIPKD+++       P   +++    
Sbjct: 125 TKHNFLVKRIEDLPLILRQAFYIARTGRPGPVLVDIPKDITQKLSDVGIPTLEEVKESLP 184

Query: 198 -YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMG 256
            Y P  +G+  QI+KAV L+  A+RP +Y GGG V + A  EL +LA +   PVT T MG
Sbjct: 185 GYKPHVEGNPQQIKKAVKLIMEAKRPVLYVGGGAVQSEAQKELVELAEMMKIPVTTTNMG 244

Query: 257 LGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIH 316
            GAFP      + MLGMHGTY ANMA+ +CD+LIA+GARFDDRV G    F  +A KIIH
Sbjct: 245 KGAFPENHPLALHMLGMHGTYYANMAVYHCDLLIAVGARFDDRVTGKVEEFAPRA-KIIH 303

Query: 317 IDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPK-REALAKWWEQIEQWRSVD 375
           IDIDP+SISK + VD+PIVG+VK VL++++  ++    +    E   KW EQIE+W+ + 
Sbjct: 304 IDIDPASISKNIVVDVPIVGDVKVVLRKILEDLRKEGARILFPEERQKWLEQIEKWKKLH 363

Query: 376 CLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLG 435
            L Y +S ++IKPQ+V+E+I+E T+GDA IC+ VGQHQMWAA FY++  PR++INSGGLG
Sbjct: 364 PLTYKKSDKVIKPQFVIEQIYEATRGDAIICTGVGQHQMWAAMFYRYSYPRQFINSGGLG 423

Query: 436 TMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMV 495
           TMG G P  +G K   P+KEV  I G+GS  M +QEL T +QY  PVK+  +NN YLGMV
Sbjct: 424 TMGFGFPAGIGAKIGRPDKEVFVIDGDGSFMMTMQELVTAVQYKVPVKVAIINNSYLGMV 483

Query: 496 RQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFL 555
           RQWQE+ Y+ RYS   +   PDFVKLAEA G VG R EK SDV   + EA R+ DR V +
Sbjct: 484 RQWQELFYEKRYSEVDLSVQPDFVKLAEACGAVGFRAEKPSDVREIIEEALRIDDRPVIM 543

Query: 556 DFQTDPTENVWPMVQAGKGISEMLL 580
           DF  D  ENV PMV AGK   +M+L
Sbjct: 544 DFHVDREENVLPMVPAGKSYRDMIL 568


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: 940
Number of extensions: 35
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: 584
Length adjustment: 37
Effective length of query: 548
Effective length of database: 547
Effective search space:   299756
Effective search space used:   299756
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_012992620.1 THAL_RS08055 (acetolactate synthase, large subunit, biosynthetic type)
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.17273.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     1e-265  868.4   2.1   1.2e-265  868.2   2.1    1.0  1  lcl|NCBI__GCF_000025605.1:WP_012992620.1  THAL_RS08055 acetolactate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025605.1:WP_012992620.1  THAL_RS08055 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  868.2   2.1  1.2e-265  1.2e-265       2     555 ..       4     568 ..       3     570 .. 0.97

  Alignments for each domain:
  == domain 1  score: 868.2 bits;  conditional E-value: 1.2e-265
                                 TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               kga+i++e lk+egve++fG+PGGa++++ydaly d++++hil+rheq+a h+a+Gya+a+GkvGv++a
  lcl|NCBI__GCF_000025605.1:WP_012992620.1   4 KGADIVIEVLKEEGVEVIFGHPGGAIMEVYDALYrDGGIRHILARHEQGAGHMAEGYAKATGKVGVAMA 72 
                                               79********************************999******************************** PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPGatnlvt+ia+ay+dsvP+v +tGqv+t+liG+dafqe+di+Git+p+tkh+flvk+ edlp il
  lcl|NCBI__GCF_000025605.1:WP_012992620.1  73 TSGPGATNLVTAIADAYMDSVPVVFITGQVPTHLIGNDAFQEVDIVGITRPITKHNFLVKRIEDLPLIL 141
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleve....ekvelpgykptvkghklqikkaleliekakkP 203
                                               ++af+ia tGrPGPvlvd+Pkd+t++  ++ ++     k +lpgykp+v+g+++qikka++li++ak+P
  lcl|NCBI__GCF_000025605.1:WP_012992620.1 142 RQAFYIARTGRPGPVLVDIPKDITQKLSDVGIPtleeVKESLPGYKPHVEGNPQQIKKAVKLIMEAKRP 210
                                               ************************99888776656445568**************************** PP

                                 TIGR00118 204 vllvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadllia 272
                                               vl+vGgG++++ea++el+elae++kipvttt +G+Gafpe+hplal mlGmhGt++an+av ++dllia
  lcl|NCBI__GCF_000025605.1:WP_012992620.1 211 VLYVGGGAVQSEAQKELVELAEMMKIPVTTTNMGKGAFPENHPLALHMLGMHGTYYANMAVYHCDLLIA 279
                                               ********************************************************************* PP

                                 TIGR00118 273 vGarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee......ekk 335
                                               vGarfddrvtg++++fap+akiihididPa+i+kn+ vd+pivGd+k vl+++l+ l++e       ++
  lcl|NCBI__GCF_000025605.1:WP_012992620.1 280 VGARFDDRVTGKVEEFAPRAKIIHIDIDPASISKNIVVDVPIVGDVKVVLRKILEDLRKEgarilfPEE 348
                                               **********************************************************99999986455 PP

                                 TIGR00118 336 ekeWlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfi 404
                                                ++Wle+ie+wkk ++l+++++++ ikPq vi+++++ ++++ai+ t+vGqhqmwaa fy++++pr+fi
  lcl|NCBI__GCF_000025605.1:WP_012992620.1 349 RQKWLEQIEKWKKLHPLTYKKSDKVIKPQFVIEQIYEATRGDAIICTGVGQHQMWAAMFYRYSYPRQFI 417
                                               556****************************************************************** PP

                                 TIGR00118 405 tsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqW 473
                                               +sgGlGtmGfG+Pa +Gak++ p+++v  ++Gdgsf+m++qel t+v+y++pvk+ i+nn++lGmv+qW
  lcl|NCBI__GCF_000025605.1:WP_012992620.1 418 NSGGLGTMGFGFPAGIGAKIGRPDKEVFVIDGDGSFMMTMQELVTAVQYKVPVKVAIINNSYLGMVRQW 486
                                               ********************************************************************* PP

                                 TIGR00118 474 qelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevl 541
                                               qelfye+ryse+ l+  +pdfvklaea G++g r ekp+++ e ++eal+ + +pv++d++vd+ee+vl
  lcl|NCBI__GCF_000025605.1:WP_012992620.1 487 QELFYEKRYSEVDLSV-QPDFVKLAEACGAVGFRAEKPSDVREIIEEALRIDdRPVIMDFHVDREENVL 554
                                               ***************6.*********************************9879*************** PP

                                 TIGR00118 542 PmvapGagldelve 555
                                               Pmv+ G++  +++ 
  lcl|NCBI__GCF_000025605.1:WP_012992620.1 555 PMVPAGKSYRDMIL 568
                                               **********9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (584 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 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 8.52
//
[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