Alignments for a candidate for ilvI in Desulfotalea psychrophila LSv54

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Desulfotalea psychrophila LSv54

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_011190010.1 DP_RS14050 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_000025945.1:WP_011190010.1
          Length = 612

 Score =  611 bits (1575), Expect = e-179
 Identities = 314/566 (55%), Positives = 392/566 (69%), Gaps = 5/566 (0%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           ++ G+  +V  L EEGV+ ++GYPGGAV+ +YD L   T  EH+LVRHEQ AVHAAD +A
Sbjct: 48  KITGSRAIVQCLKEEGVQTIFGYPGGAVIDLYDALMDSTDIEHVLVRHEQGAVHAADAFA 107

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           R TG+VGVAL+TSGPG TN VTGIATAYLDSIP+VV+TG VP   IG DAFQE D VGIT
Sbjct: 108 RVTGEVGVALLTSGPGATNGVTGIATAYLDSIPLVVLTGQVPRALIGNDAFQEVDIVGIT 167

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
           RP  KHN+LV    DL   +++AF +A TGRPGPV+VD+PKD+      Y     I + S
Sbjct: 168 RPCTKHNYLVSKPEDLVPVLREAFHVAKTGRPGPVLVDLPKDILATLIDYPQIAPIKLDS 227

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257
           Y P  K H GQI KA  LL  A++P +Y GGGV+L+N+  EL  LA     PVT TLMGL
Sbjct: 228 YQPNYKPHQGQITKACKLLMQAKKPVLYVGGGVILSNSHKELSALAEKLQIPVTMTLMGL 287

Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHI 317
           GAFPG+    +GMLGMHG+Y ANMA+   D+LIA+GARFDDRV G    F S+A KIIH+
Sbjct: 288 GAFPGSHDLSMGMLGMHGSYTANMAVAESDLLIAVGARFDDRVTGKLEDFASKA-KIIHV 346

Query: 318 DIDPSSISKRVKVDIPIVGN---VKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSV 374
           DIDP+SISK VKVD+PIV +       + + + +    +I  +R+A   W + +  W   
Sbjct: 347 DIDPTSISKNVKVDVPIVADCLAALTAINDWLEKCPEEEIAERRDAHKPWIDTVHNWTKE 406

Query: 375 DCLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGL 434
             ++Y+ +   IKPQ+VVE I  LTKG+A I ++VGQ+QMWAAQFYKF+ PR ++ SGGL
Sbjct: 407 HPMRYNSNGSEIKPQFVVETIDRLTKGEAIITTEVGQNQMWAAQFYKFNHPRHFVTSGGL 466

Query: 435 GTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGM 494
           GTMG GLP A+G + AFP+K V+ I G+GSIQM IQEL+T  Q +  VKI  LNNGYLGM
Sbjct: 467 GTMGFGLPAAIGAQMAFPDKIVIDIAGDGSIQMNIQELATARQNNCNVKIVILNNGYLGM 526

Query: 495 VRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVF 554
           VRQWQE+ YD RY+ + MD  PDFVKLAEAYG VG+R  K  +VE  L E     D  V 
Sbjct: 527 VRQWQELFYDKRYASTVMDVAPDFVKLAEAYGAVGLRATKKEEVESVLAEGL-ATDNVVI 585

Query: 555 LDFQTDPTENVWPMVQAGKGISEMLL 580
           ++F   P E V+PMV AGK  +EMLL
Sbjct: 586 MEFLVAPEEGVYPMVPAGKANTEMLL 611


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: 979
Number of extensions: 37
Number of successful extensions: 5
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: 612
Length adjustment: 37
Effective length of query: 548
Effective length of database: 575
Effective search space:   315100
Effective search space used:   315100
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_011190010.1 DP_RS14050 (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.14768.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.1e-258  843.0   2.0   5.8e-258  842.8   2.0    1.0  1  lcl|NCBI__GCF_000025945.1:WP_011190010.1  DP_RS14050 acetolactate synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025945.1:WP_011190010.1  DP_RS14050 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  842.8   2.0  5.8e-258  5.8e-258       2     554 ..      50     610 ..      49     612 .] 0.97

  Alignments for each domain:
  == domain 1  score: 842.8 bits;  conditional E-value: 5.8e-258
                                 TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               +g++++v+ lk+egv+t+fGyPGGav+++ydal  + ++eh+lvrheq+a+haad +ar++G+vGv+l 
  lcl|NCBI__GCF_000025945.1:WP_011190010.1  50 TGSRAIVQCLKEEGVQTIFGYPGGAVIDLYDALMdSTDIEHVLVRHEQGAVHAADAFARVTGEVGVALL 118
                                               7999******************************7889******************************* PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPGatn vtgiataylds+PlvvltGqv+++liG+dafqe+di+Git+p+tkh++lv+k+edl  +l
  lcl|NCBI__GCF_000025945.1:WP_011190010.1 119 TSGPGATNGVTGIATAYLDSIPLVVLTGQVPRALIGNDAFQEVDIVGITRPCTKHNYLVSKPEDLVPVL 187
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207
                                               +eaf++a+tGrPGPvlvdlPkd+ ++ i++++ + ++l +y+p+ k+h+ qi ka +l+++akkPvl+v
  lcl|NCBI__GCF_000025945.1:WP_011190010.1 188 REAFHVAKTGRPGPVLVDLPKDILATLIDYPQIAPIKLDSYQPNYKPHQGQITKACKLLMQAKKPVLYV 256
                                               ********************************************************************* PP

                                 TIGR00118 208 GgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGar 276
                                               GgGvi +++++el  lae+l+ipvt+tl+GlGafp  h l++gmlGmhG+++an+av e+dlliavGar
  lcl|NCBI__GCF_000025945.1:WP_011190010.1 257 GGGVILSNSHKELSALAEKLQIPVTMTLMGLGAFPGSHDLSMGMLGMHGSYTANMAVAESDLLIAVGAR 325
                                               ********************************************************************* PP

                                 TIGR00118 277 fddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee......ekkeke. 338
                                               fddrvtg+l+ fa++akiih+didP++i+knvkvd+piv d+   l+ + + l++       e+++ + 
  lcl|NCBI__GCF_000025945.1:WP_011190010.1 326 FDDRVTGKLEDFASKAKIIHVDIDPTSISKNVKVDVPIVADCLAALTAINDWLEKCpeeeiaERRDAHk 394
                                               *****************************************9888877665555544447875554444 PP

                                 TIGR00118 339 .WlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfits 406
                                                W++ +++w ke++++++++ ++ikPq v++++ +l+k+eai+tt+vGq+qmwaaqfyk+++pr+f+ts
  lcl|NCBI__GCF_000025945.1:WP_011190010.1 395 pWIDTVHNWTKEHPMRYNSNGSEIKPQFVVETIDRLTKGEAIITTEVGQNQMWAAQFYKFNHPRHFVTS 463
                                               8******************************************************************** PP

                                 TIGR00118 407 gGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqe 475
                                               gGlGtmGfGlPaa+Ga++a p++ v++++Gdgs+qmn+qel+t+++ + +vkivilnn +lGmv+qWqe
  lcl|NCBI__GCF_000025945.1:WP_011190010.1 464 GGLGTMGFGLPAAIGAQMAFPDKIVIDIAGDGSIQMNIQELATARQNNCNVKIVILNNGYLGMVRQWQE 532
                                               ********************************************************************* PP

                                 TIGR00118 476 lfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmv 544
                                               lfy++ry++t +    pdfvklaeayG++g+r +k+ee+e+ l+e l++++ v++++ v+ ee v+Pmv
  lcl|NCBI__GCF_000025945.1:WP_011190010.1 533 LFYDKRYASTVMDV-APDFVKLAEAYGAVGLRATKKEEVESVLAEGLATDNVVIMEFLVAPEEGVYPMV 600
                                               *************6.****************************************************** PP

                                 TIGR00118 545 apGagldelv 554
                                               + G++++e++
  lcl|NCBI__GCF_000025945.1:WP_011190010.1 601 PAGKANTEML 610
                                               ********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (612 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: 12.23
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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