Alignments for a candidate for ilvI in Desulfobacter vibrioformis DSM 8776

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Desulfobacter vibrioformis DSM 8776

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_035240748.1 Q366_RS15945 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_000745975.1:WP_035240748.1
          Length = 563

 Score =  568 bits (1464), Expect = e-166
 Identities = 288/563 (51%), Positives = 384/563 (68%), Gaps = 2/563 (0%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           ++ GA+IL+H +  +GV+ ++GYPGGA + I+DE+ K     H+LVRHEQ AVH AD YA
Sbjct: 2   KLTGAQILIHMIKAQGVDTIFGYPGGATIDIHDEILKHDDLRHVLVRHEQGAVHMADAYA 61

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           R     GVALVTSGPG TNAVTG+A+A+ DSIP+VV TG VPT  IG DAFQE D VGIT
Sbjct: 62  RTHKTTGVALVTSGPGATNAVTGLASAHCDSIPIVVFTGQVPTGLIGNDAFQEVDIVGIT 121

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
           RP  KHN+LVKD   LA  I++AFFIA +GRPGPV+VD+PKDV +    ++ P  + M +
Sbjct: 122 RPCTKHNYLVKDPSKLAEIIQEAFFIAGSGRPGPVLVDLPKDVVQAIIDFQMPGPVKMNT 181

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257
           Y P  K +  Q+  AV +++ A RP ++ GGGV+L+ AS E  ++A     PVT +LMGL
Sbjct: 182 YKPNYKPNKKQMTTAVKMIKEARRPVMFAGGGVILSGASQEFTRIAKFANLPVTASLMGL 241

Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHI 317
           GAFPG+   ++GMLGMHGTY ANM++ + D++ A G RFDDRV GN   F   A K+I I
Sbjct: 242 GAFPGSDANWLGMLGMHGTYRANMSIGHSDLIFAAGVRFDDRVTGNLEKFAPDA-KVIQI 300

Query: 318 DIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDCL 377
           DIDP+SI K V+VD PIVG+ K  L ++   ++    +   +    W  +I +W+ +  L
Sbjct: 301 DIDPTSIHKNVEVDCPIVGDCKMALADIAGLMEKEAPENFMKDREAWLNRINEWKQLTPL 360

Query: 378 KYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGTM 437
           KYD+S + IKPQYVVEK++E+TKG+A + ++VGQ+QMWAAQ+Y F++P  +I SGGLG M
Sbjct: 361 KYDQSFDTIKPQYVVEKLYEITKGNAIVTTEVGQNQMWAAQYYHFEKPNHFITSGGLGVM 420

Query: 438 GVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVRQ 497
           G GLP A+G K   P+K VV + G+GSIQM  QEL T +     VKI  LNN YLGMVRQ
Sbjct: 421 GFGLPAAIGAKAGAPDKLVVCVAGDGSIQMNSQELMTAVAEKLDVKIVILNNRYLGMVRQ 480

Query: 498 WQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFLDF 557
           WQE+ Y+  Y+ + M+A PDFVKLA+AYG  G R +  + V   L         TV ++F
Sbjct: 481 WQELFYNKVYADTNMEAQPDFVKLADAYGATGFRCDDPAKVTQTLEMGLNTPG-TVIMEF 539

Query: 558 QTDPTENVWPMVQAGKGISEMLL 580
             +  E+V+PMV AG  I++MLL
Sbjct: 540 IVEREESVYPMVPAGGAITDMLL 562


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: 900
Number of extensions: 29
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: 563
Length adjustment: 36
Effective length of query: 549
Effective length of database: 527
Effective search space:   289323
Effective search space used:   289323
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_035240748.1 Q366_RS15945 (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.22450.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.8e-244  798.3   4.0     2e-244  798.1   4.0    1.0  1  lcl|NCBI__GCF_000745975.1:WP_035240748.1  Q366_RS15945 acetolactate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000745975.1:WP_035240748.1  Q366_RS15945 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  798.1   4.0    2e-244    2e-244       1     554 [.       3     561 ..       3     563 .] 0.98

  Alignments for each domain:
  == domain 1  score: 798.1 bits;  conditional E-value: 2e-244
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 
                                               l+ga+il++++k++gv+t+fGyPGGa ++i+d++  +++l+h+lvrheq+a+h+ad yar+   +Gv+l
  lcl|NCBI__GCF_000745975.1:WP_035240748.1   3 LTGAQILIHMIKAQGVDTIFGYPGGATIDIHDEILkHDDLRHVLVRHEQGAVHMADAYARTHKTTGVAL 71 
                                               68*******************************99899******************************* PP

                                 TIGR00118  69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137
                                               +tsGPGatn+vtg+a+a+ ds+P+vv+tGqv+t liG+dafqe+di+Git+p+tkh++lvk+++ l+ei
  lcl|NCBI__GCF_000745975.1:WP_035240748.1  72 VTSGPGATNAVTGLASAHCDSIPIVVFTGQVPTGLIGNDAFQEVDIVGITRPCTKHNYLVKDPSKLAEI 140
                                               ********************************************************************* PP

                                 TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvll 206
                                               ++eaf ia +GrPGPvlvdlPkdv++a i+++++  v++ +ykp+ k++k+q+  a+++i++a++Pv++
  lcl|NCBI__GCF_000745975.1:WP_035240748.1 141 IQEAFFIAGSGRPGPVLVDLPKDVVQAIIDFQMPGPVKMNTYKPNYKPNKKQMTTAVKMIKEARRPVMF 209
                                               ********************************************************************* PP

                                 TIGR00118 207 vGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGa 275
                                               +GgGvi ++as+e++++a+ +++pvt++l+GlGafp  + + lgmlGmhGt+ an+++ ++dl++a G+
  lcl|NCBI__GCF_000745975.1:WP_035240748.1 210 AGGGVILSGASQEFTRIAKFANLPVTASLMGLGAFPGSDANWLGMLGMHGTYRANMSIGHSDLIFAAGV 278
                                               ********************************************************************* PP

                                 TIGR00118 276 rfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke.W 339
                                               rfddrvtgnl+kfap+ak+i ididP++i knv+vd pivGd+k  l+++   +++e      k++e W
  lcl|NCBI__GCF_000745975.1:WP_035240748.1 279 RFDDRVTGNLEKFAPDAKVIQIDIDPTSIHKNVEVDCPIVGDCKMALADIAGLMEKEapenFMKDREaW 347
                                               ************************************************99888888766663455556* PP

                                 TIGR00118 340 lekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgG 408
                                               l++i+ewk+ ++lk+d++ ++ikPq+v+++l++++k++aivtt+vGq+qmwaaq+y+++kp++fitsgG
  lcl|NCBI__GCF_000745975.1:WP_035240748.1 348 LNRINEWKQLTPLKYDQSFDTIKPQYVVEKLYEITKGNAIVTTEVGQNQMWAAQYYHFEKPNHFITSGG 416
                                               ********************************************************************* PP

                                 TIGR00118 409 lGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelf 477
                                               lG mGfGlPaa+Gak + p++ vv+v+Gdgs+qmn qel t+v  +++vkivilnn++lGmv+qWqelf
  lcl|NCBI__GCF_000745975.1:WP_035240748.1 417 LGVMGFGLPAAIGAKAGAPDKLVVCVAGDGSIQMNSQELMTAVAEKLDVKIVILNNRYLGMVRQWQELF 485
                                               ********************************************************************* PP

                                 TIGR00118 478 yeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvap 546
                                               y++ y++t++++ +pdfvkla+ayG++g r  +p+++ + l+  l++ + v++++ v++ee+v+Pmv+ 
  lcl|NCBI__GCF_000745975.1:WP_035240748.1 486 YNKVYADTNMEA-QPDFVKLADAYGATGFRCDDPAKVTQTLEMGLNTPGTVIMEFIVEREESVYPMVPA 553
                                               ***********5.******************************************************** PP

                                 TIGR00118 547 Gagldelv 554
                                               G+++++++
  lcl|NCBI__GCF_000745975.1:WP_035240748.1 554 GGAITDML 561
                                               *****997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (563 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: 12.68
//
[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