Alignments for a candidate for ilvI in Sulfuritalea hydrogenivorans DSM 22779

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Sulfuritalea hydrogenivorans DSM 22779

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_041099921.1 SUTH_RS13455 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_000828635.1:WP_041099921.1
          Length = 569

 Score =  828 bits (2139), Expect = 0.0
 Identities = 399/567 (70%), Positives = 479/567 (84%), Gaps = 1/567 (0%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           ++ GAEI++  L EE VEYV+GYPGG+VL+IYDEL KQ KF+H+LVRHEQAAVHAAD Y+
Sbjct: 2   QLTGAEIVIRCLQEEKVEYVFGYPGGSVLFIYDELFKQDKFKHVLVRHEQAAVHAADAYS 61

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           R++ K+GV +VTSGPGVTNAVTGIATA++DS+PMV+I+G VPT  IGQDAFQECDTVGIT
Sbjct: 62  RSSNKIGVCMVTSGPGVTNAVTGIATAHMDSVPMVIISGQVPTAYIGQDAFQECDTVGIT 121

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
           RP VKHNFLVKDVRDLA T+KKAF+IA TGRPGPV+VDIPKD++   C+++YPK+I MRS
Sbjct: 122 RPCVKHNFLVKDVRDLAITLKKAFYIAKTGRPGPVLVDIPKDITNQKCEFDYPKTIAMRS 181

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257
           YNPV KGHSGQI+KAV +L  A+RP IY GGGV+L++A+++L +LA   G+PVTNTLMGL
Sbjct: 182 YNPVVKGHSGQIKKAVQMLLEAKRPMIYAGGGVILSDAAEKLAKLARTLGYPVTNTLMGL 241

Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHI 317
           G +P T KQ +GMLGMHGTYEANMAMQNCDVLIA+GARFDDRVIGNP HF    RKIIHI
Sbjct: 242 GGYPATDKQSLGMLGMHGTYEANMAMQNCDVLIAVGARFDDRVIGNPVHFAEIPRKIIHI 301

Query: 318 DIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDCL 377
           DIDPSSISKRVKVD+PIVGN+ DVL EL   ++AS   P  +ALA WW+QI++WR    L
Sbjct: 302 DIDPSSISKRVKVDVPIVGNLPDVLDELQKLLEASAGVPDSKALAVWWKQIDEWRGKKSL 361

Query: 378 KYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGTM 437
           KY +  E+I PQYVVEK++E+T G+AFI SDVGQHQMWAAQ+YKFD+PRRWINSGGLGTM
Sbjct: 362 KYKQGKEVIMPQYVVEKLYEVTGGEAFITSDVGQHQMWAAQYYKFDKPRRWINSGGLGTM 421

Query: 438 GVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVRQ 497
           GVGLPYAMG++ A P+  V  +TGE SIQM IQELST  Q+  P+KI +LNN YLGMVRQ
Sbjct: 422 GVGLPYAMGVRFANPKATVACVTGEASIQMNIQELSTAKQFRLPIKIINLNNRYLGMVRQ 481

Query: 498 WQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAF-RLKDRTVFLD 556
           WQ++ + NRYS SY+DALPDFVKLAE+YGHVGM++E+ +DVEPALREAF + K+  VF+D
Sbjct: 482 WQQMFHGNRYSESYVDALPDFVKLAESYGHVGMKIERPADVEPALREAFTKHKNDLVFMD 541

Query: 557 FQTDPTENVWPMVQAGKGISEMLLGAE 583
           F TD T NV+PMV AGKG+SEM+L  E
Sbjct: 542 FLTDQTANVYPMVAAGKGLSEMILAEE 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: 1012
Number of extensions: 28
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: 569
Length adjustment: 36
Effective length of query: 549
Effective length of database: 533
Effective search space:   292617
Effective search space used:   292617
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_041099921.1 SUTH_RS13455 (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.7317.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.5e-254  830.0   1.4   5.2e-254  829.7   1.4    1.0  1  lcl|NCBI__GCF_000828635.1:WP_041099921.1  SUTH_RS13455 acetolactate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000828635.1:WP_041099921.1  SUTH_RS13455 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  829.7   1.4  5.2e-254  5.2e-254       1     555 [.       3     565 ..       3     567 .. 0.98

  Alignments for each domain:
  == domain 1  score: 829.7 bits;  conditional E-value: 5.2e-254
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 
                                               l+gaei+++ l++e+ve+vfGyPGG+vl iyd+l+ +++++h+lvrheqaa+haad y+r+s k+Gv++
  lcl|NCBI__GCF_000828635.1:WP_041099921.1   3 LTGAEIVIRCLQEEKVEYVFGYPGGSVLFIYDELFkQDKFKHVLVRHEQAAVHAADAYSRSSNKIGVCM 71 
                                               68*********************************999******************************* PP

                                 TIGR00118  69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137
                                               +tsGPG tn+vtgiata++dsvP+v+++Gqv+t+ iG+dafqe+d +Git+p++kh+flvk+++dl+ +
  lcl|NCBI__GCF_000828635.1:WP_041099921.1  72 VTSGPGVTNAVTGIATAHMDSVPMVIISGQVPTAYIGQDAFQECDTVGITRPCVKHNFLVKDVRDLAIT 140
                                               ********************************************************************* PP

                                 TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvll 206
                                               lk+af+ia+tGrPGPvlvd+Pkd+t++++e+++++++ +++y+p vkgh  qikka++++ +ak+P+++
  lcl|NCBI__GCF_000828635.1:WP_041099921.1 141 LKKAFYIAKTGRPGPVLVDIPKDITNQKCEFDYPKTIAMRSYNPVVKGHSGQIKKAVQMLLEAKRPMIY 209
                                               ********************************************************************* PP

                                 TIGR00118 207 vGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGa 275
                                               +GgGvi ++a e+l +la +l  pvt tl+GlG++p++++++lgmlGmhGt+ean+a++++d+liavGa
  lcl|NCBI__GCF_000828635.1:WP_041099921.1 210 AGGGVILSDAAEKLAKLARTLGYPVTNTLMGLGGYPATDKQSLGMLGMHGTYEANMAMQNCDVLIAVGA 278
                                               ********************************************************************* PP

                                 TIGR00118 276 rfddrvtgnlakfape.akiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke. 338
                                               rfddrv gn  +fa+   kiihididP++i+k vkvd+pivG+   vl+el k l++     ++k    
  lcl|NCBI__GCF_000828635.1:WP_041099921.1 279 RFDDRVIGNPVHFAEIpRKIIHIDIDPSSISKRVKVDVPIVGNLPDVLDELQKLLEASagvpDSKALAv 347
                                               **************86257******************************99999998888875555557 PP

                                 TIGR00118 339 WlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsg 407
                                               W+++i+ew+ ++ lk+++ +e i Pq+v+++l++++ +ea++t+dvGqhqmwaaq+yk++kpr++i+sg
  lcl|NCBI__GCF_000828635.1:WP_041099921.1 348 WWKQIDEWRGKKSLKYKQGKEVIMPQYVVEKLYEVTGGEAFITSDVGQHQMWAAQYYKFDKPRRWINSG 416
                                               ********************************************************************* PP

                                 TIGR00118 408 GlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqel 476
                                               GlGtmG GlP a+G++ a+p++tv +vtG++s+qmn+qelst++++ +p+ki++lnn++lGmv+qWq++
  lcl|NCBI__GCF_000828635.1:WP_041099921.1 417 GLGTMGVGLPYAMGVRFANPKATVACVTGEASIQMNIQELSTAKQFRLPIKIINLNNRYLGMVRQWQQM 485
                                               ********************************************************************* PP

                                 TIGR00118 477 fyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk..epvlldvevdkeeevlPm 543
                                               f+ +ryse+++ + lpdfvklae+yG++g++ie+p+++e +l+ea++++  ++v++d+  d++++v+Pm
  lcl|NCBI__GCF_000828635.1:WP_041099921.1 486 FHGNRYSESYVDA-LPDFVKLAESYGHVGMKIERPADVEPALREAFTKHknDLVFMDFLTDQTANVYPM 553
                                               ************5.*******************************98764589**************** PP

                                 TIGR00118 544 vapGagldelve 555
                                               va G+gl+e++ 
  lcl|NCBI__GCF_000828635.1:WP_041099921.1 554 VAAGKGLSEMIL 565
                                               **********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (569 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 0.01s 00:00:00.04 Elapsed: 00:00:00.02
# Mc/sec: 11.51
//
[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