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_041278049.1 DP_RS14050 biosynthetic-type acetolactate synthase large subunit

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



>NCBI__GCF_000025945.1:WP_041278049.1
          Length = 567

 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: 3   KITGSRAIVQCLKEEGVQTIFGYPGGAVIDLYDALMDSTDIEHVLVRHEQGAVHAADAFA 62

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           R TG+VGVAL+TSGPG TN VTGIATAYLDSIP+VV+TG VP   IG DAFQE D VGIT
Sbjct: 63  RVTGEVGVALLTSGPGATNGVTGIATAYLDSIPLVVLTGQVPRALIGNDAFQEVDIVGIT 122

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
           RP  KHN+LV    DL   +++AF +A TGRPGPV+VD+PKD+      Y     I + S
Sbjct: 123 RPCTKHNYLVSKPEDLVPVLREAFHVAKTGRPGPVLVDLPKDILATLIDYPQIAPIKLDS 182

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257
           Y P  K H GQI KA  LL  A++P +Y GGGV+L+N+  EL  LA     PVT TLMGL
Sbjct: 183 YQPNYKPHQGQITKACKLLMQAKKPVLYVGGGVILSNSHKELSALAEKLQIPVTMTLMGL 242

Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHI 317
           GAFPG+    +GMLGMHG+Y ANMA+   D+LIA+GARFDDRV G    F S+A KIIH+
Sbjct: 243 GAFPGSHDLSMGMLGMHGSYTANMAVAESDLLIAVGARFDDRVTGKLEDFASKA-KIIHV 301

Query: 318 DIDPSSISKRVKVDIPIVGN---VKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSV 374
           DIDP+SISK VKVD+PIV +       + + + +    +I  +R+A   W + +  W   
Sbjct: 302 DIDPTSISKNVKVDVPIVADCLAALTAINDWLEKCPEEEIAERRDAHKPWIDTVHNWTKE 361

Query: 375 DCLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGL 434
             ++Y+ +   IKPQ+VVE I  LTKG+A I ++VGQ+QMWAAQFYKF+ PR ++ SGGL
Sbjct: 362 HPMRYNSNGSEIKPQFVVETIDRLTKGEAIITTEVGQNQMWAAQFYKFNHPRHFVTSGGL 421

Query: 435 GTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGM 494
           GTMG GLP A+G + AFP+K V+ I G+GSIQM IQEL+T  Q +  VKI  LNNGYLGM
Sbjct: 422 GTMGFGLPAAIGAQMAFPDKIVIDIAGDGSIQMNIQELATARQNNCNVKIVILNNGYLGM 481

Query: 495 VRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVF 554
           VRQWQE+ YD RY+ + MD  PDFVKLAEAYG VG+R  K  +VE  L E     D  V 
Sbjct: 482 VRQWQELFYDKRYASTVMDVAPDFVKLAEAYGAVGLRATKKEEVESVLAEGL-ATDNVVI 540

Query: 555 LDFQTDPTENVWPMVQAGKGISEMLL 580
           ++F   P E V+PMV AGK  +EMLL
Sbjct: 541 MEFLVAPEEGVYPMVPAGKANTEMLL 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: 923
Number of extensions: 35
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: 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_041278049.1 DP_RS14050 (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.2126652.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.8e-258  843.4   2.0   4.3e-258  843.2   2.0    1.0  1  NCBI__GCF_000025945.1:WP_041278049.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000025945.1:WP_041278049.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  843.2   2.0  4.3e-258  4.3e-258       2     554 ..       5     565 ..       4     567 .] 0.97

  Alignments for each domain:
  == domain 1  score: 843.2 bits;  conditional E-value: 4.3e-258
                             TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGP 73 
                                           +g++++v+ lk+egv+t+fGyPGGav+++ydal  + ++eh+lvrheq+a+haad +ar++G+vGv+l tsGP
  NCBI__GCF_000025945.1:WP_041278049.1   5 TGSRAIVQCLKEEGVQTIFGYPGGAVIDLYDALMdSTDIEHVLVRHEQGAVHAADAFARVTGEVGVALLTSGP 77 
                                           7999******************************7889*********************************** PP

                             TIGR00118  74 GatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeias 146
                                           Gatn vtgiataylds+PlvvltGqv+++liG+dafqe+di+Git+p+tkh++lv+k+edl  +l+eaf++a+
  NCBI__GCF_000025945.1:WP_041278049.1  78 GATNGVTGIATAYLDSIPLVVLTGQVPRALIGNDAFQEVDIVGITRPCTKHNYLVSKPEDLVPVLREAFHVAK 150
                                           ************************************************************************* PP

                             TIGR00118 147 tGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeasee 219
                                           tGrPGPvlvdlPkd+ ++ i++++ + ++l +y+p+ k+h+ qi ka +l+++akkPvl+vGgGvi +++++e
  NCBI__GCF_000025945.1:WP_041278049.1 151 TGRPGPVLVDLPKDILATLIDYPQIAPIKLDSYQPNYKPHQGQITKACKLLMQAKKPVLYVGGGVILSNSHKE 223
                                           ************************************************************************* PP

                             TIGR00118 220 lkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapea 292
                                           l  lae+l+ipvt+tl+GlGafp  h l++gmlGmhG+++an+av e+dlliavGarfddrvtg+l+ fa++a
  NCBI__GCF_000025945.1:WP_041278049.1 224 LSALAEKLQIPVTMTLMGLGAFPGSHDLSMGMLGMHGSYTANMAVAESDLLIAVGARFDDRVTGKLEDFASKA 296
                                           ************************************************************************* PP

                             TIGR00118 293 kiihididPaeigknvkvdipivGdakkvleellkklkee......ekkeke..Wlekieewkkeyilkldee 357
                                           kiih+didP++i+knvkvd+piv d+   l+ + + l++       e+++ +  W++ +++w ke++++++++
  NCBI__GCF_000025945.1:WP_041278049.1 297 KIIHVDIDPTSISKNVKVDVPIVADCLAALTAINDWLEKCpeeeiaERRDAHkpWIDTVHNWTKEHPMRYNSN 369
                                           *************************98888776655555444478755544448******************* PP

                             TIGR00118 358 eesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeet 430
                                            ++ikPq v++++ +l+k+eai+tt+vGq+qmwaaqfyk+++pr+f+tsgGlGtmGfGlPaa+Ga++a p++ 
  NCBI__GCF_000025945.1:WP_041278049.1 370 GSEIKPQFVVETIDRLTKGEAIITTEVGQNQMWAAQFYKFNHPRHFVTSGGLGTMGFGLPAAIGAQMAFPDKI 442
                                           ************************************************************************* PP

                             TIGR00118 431 vvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGv 503
                                           v++++Gdgs+qmn+qel+t+++ + +vkivilnn +lGmv+qWqelfy++ry++t +    pdfvklaeayG+
  NCBI__GCF_000025945.1:WP_041278049.1 443 VIDIAGDGSIQMNIQELATARQNNCNVKIVILNNGYLGMVRQWQELFYDKRYASTVMDV-APDFVKLAEAYGA 514
                                           **********************************************************6.************* PP

                             TIGR00118 504 kgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldelv 554
                                           +g+r +k+ee+e+ l+e l++++ v++++ v+ ee v+Pmv+ G++++e++
  NCBI__GCF_000025945.1:WP_041278049.1 515 VGLRATKKEEVESVLAEGLATDNVVIMEFLVAPEEGVYPMVPAGKANTEML 565
                                           *************************************************98 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 29.48
//
[ok]

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