Alignments for a candidate for ilvI in Nitratifractor salsuginis DSM 16511

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Nitratifractor salsuginis DSM 16511

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_013553443.1 NITSA_RS02435 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_000186245.1:WP_013553443.1
          Length = 564

 Score =  582 bits (1500), Expect = e-170
 Identities = 297/567 (52%), Positives = 388/567 (68%), Gaps = 5/567 (0%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           +M GA+++  A+  EGV+ V+GYPGGA++ +YDE++KQ  F+HIL RHEQAAVHAADGYA
Sbjct: 2   KMSGAQMVCEAIIAEGVKTVFGYPGGAIMNVYDEIYKQNAFKHILTRHEQAAVHAADGYA 61

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           RATG+VGVA+VTSGPG TNAVTG+ATAY+DS+P+VVI+G VP   IG D FQE D VGI+
Sbjct: 62  RATGEVGVAMVTSGPGFTNAVTGLATAYMDSVPLVVISGQVPLSLIGTDGFQEVDAVGIS 121

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
           RP  KHN+LV+ + DL   +K+AF+IA +GRPGPV+VDIPKD++    ++ YP  +++ +
Sbjct: 122 RPCTKHNYLVRSIEDLPRILKEAFYIARSGRPGPVLVDIPKDITGEMGEFIYPDHVNLPT 181

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257
           Y P  KG+  QI+KAV  +  A++P +Y GGG VL+NA  E+R+ A LT  P   TLM  
Sbjct: 182 YKPRYKGNDRQIKKAVEAIVKAKKPLLYIGGGTVLSNAYQEVREFAELTQIPTVETLMAR 241

Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHI 317
           G     +   VGMLGMHG+Y ANMAM   D++I++GARFDDRV G  + F   A  IIH+
Sbjct: 242 GVMGAKNPLLVGMLGMHGSYAANMAMSETDLIISLGARFDDRVTGKLSEFARYA-DIIHV 300

Query: 318 DIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDCL 377
           DIDP++I K V VD PIVG+VK V+ +++  I+   + P R  +  W + + ++  +  L
Sbjct: 301 DIDPANIGKLVDVDYPIVGDVKTVVNKMLEMIR-EKVDPDRYQV--WRDILARYDELHPL 357

Query: 378 KYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGTM 437
            Y  S E+IKPQ+VVE++ EL   DA I SDVGQHQMW AQFY FD PR+WINSGGLGTM
Sbjct: 358 SYTDSDEVIKPQWVVERVGELVGSDAIITSDVGQHQMWTAQFYPFDRPRQWINSGGLGTM 417

Query: 438 GVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVRQ 497
           G G P A+G K   PEK V+  TG+GSI M +QEL T  +Y  PV    LNN +LGMVRQ
Sbjct: 418 GYGFPAAIGAKVGVPEKTVINFTGDGSILMNVQELVTAAEYGVPVINIILNNHFLGMVRQ 477

Query: 498 WQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFLDF 557
           WQ   YD RYS + +   PD+ KLAEA G  G  V   ++ + ALR A     +  F++ 
Sbjct: 478 WQTFFYDKRYSETDLSYQPDWKKLAEACGGAGYDVTTKAEFDEALRSAME-GGKVTFINV 536

Query: 558 QTDPTENVWPMVQAGKGISEMLLGAED 584
             D  ENV PMV AG  +  MLL  +D
Sbjct: 537 AVDRFENVLPMVPAGGALYNMLLEHKD 563


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: 971
Number of extensions: 37
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: 564
Length adjustment: 36
Effective length of query: 549
Effective length of database: 528
Effective search space:   289872
Effective search space used:   289872
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_013553443.1 NITSA_RS02435 (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.10336.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-248  811.8   0.7   1.7e-248  811.6   0.7    1.0  1  lcl|NCBI__GCF_000186245.1:WP_013553443.1  NITSA_RS02435 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000186245.1:WP_013553443.1  NITSA_RS02435 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  811.6   0.7  1.7e-248  1.7e-248       1     555 [.       3     559 ..       3     561 .. 0.99

  Alignments for each domain:
  == domain 1  score: 811.6 bits;  conditional E-value: 1.7e-248
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 
                                               ++ga+++ e++ +egv+tvfGyPGGa++++yd++y ++ ++hil+rheqaa+haadGyara+G+vGv++
  lcl|NCBI__GCF_000186245.1:WP_013553443.1   3 MSGAQMVCEAIIAEGVKTVFGYPGGAIMNVYDEIYkQNAFKHILTRHEQAAVHAADGYARATGEVGVAM 71 
                                               79*********************************8899****************************** PP

                                 TIGR00118  69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137
                                               +tsGPG tn+vtg+atay+dsvPlvv++Gqv+ sliG+d fqe+d +Gi++p+tkh++lv++ edlp+i
  lcl|NCBI__GCF_000186245.1:WP_013553443.1  72 VTSGPGFTNAVTGLATAYMDSVPLVVISGQVPLSLIGTDGFQEVDAVGISRPCTKHNYLVRSIEDLPRI 140
                                               ********************************************************************* PP

                                 TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvll 206
                                               lkeaf+ia +GrPGPvlvd+Pkd+t +  e+ ++++v+lp+ykp+ kg+ +qikka+e+i kakkP+l+
  lcl|NCBI__GCF_000186245.1:WP_013553443.1 141 LKEAFYIARSGRPGPVLVDIPKDITGEMGEFIYPDHVNLPTYKPRYKGNDRQIKKAVEAIVKAKKPLLY 209
                                               ********************************************************************* PP

                                 TIGR00118 207 vGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGa 275
                                               +GgG + ++a +e++e+ae ++ip + tl+  G + +++pl +gmlGmhG+++an+a+se+dl+i++Ga
  lcl|NCBI__GCF_000186245.1:WP_013553443.1 210 IGGGTVLSNAYQEVREFAELTQIPTVETLMARGVMGAKNPLLVGMLGMHGSYAANMAMSETDLIISLGA 278
                                               ********************************************************************* PP

                                 TIGR00118 276 rfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee.ekkeke.Wlek 342
                                               rfddrvtg+l++fa+ a iih+didPa+igk v vd pivGd+k+v++++l+ ++e+ + +  + W + 
  lcl|NCBI__GCF_000186245.1:WP_013553443.1 279 RFDDRVTGKLSEFARYADIIHVDIDPANIGKLVDVDYPIVGDVKTVVNKMLEMIREKvDPDRYQvWRDI 347
                                               ******************************************************99965555567**** PP

                                 TIGR00118 343 ieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGt 411
                                               ++++ + ++l++  ++e ikPq v++++ +l+  +ai+t+dvGqhqmw+aqfy++++pr++i+sgGlGt
  lcl|NCBI__GCF_000186245.1:WP_013553443.1 348 LARYDELHPLSYTDSDEVIKPQWVVERVGELVGSDAIITSDVGQHQMWTAQFYPFDRPRQWINSGGLGT 416
                                               ********************************************************************* PP

                                 TIGR00118 412 mGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyee 480
                                               mG+G+Paa+Gakv++pe+tv++ tGdgs+ mn+qel t++ey++pv+ +ilnn++lGmv+qWq +fy++
  lcl|NCBI__GCF_000186245.1:WP_013553443.1 417 MGYGFPAAIGAKVGVPEKTVINFTGDGSILMNVQELVTAAEYGVPVINIILNNHFLGMVRQWQTFFYDK 485
                                               ********************************************************************* PP

                                 TIGR00118 481 rysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGag 549
                                               ryset l+  +pd++klaea G  g  +++++e +e+l+ a+e  +  +++v vd+ e+vlPmv+ G++
  lcl|NCBI__GCF_000186245.1:WP_013553443.1 486 RYSETDLSY-QPDWKKLAEACGGAGYDVTTKAEFDEALRSAMEGGKVTFINVAVDRFENVLPMVPAGGA 553
                                               ********6.*********************************************************** PP

                                 TIGR00118 550 ldelve 555
                                               l +++ 
  lcl|NCBI__GCF_000186245.1:WP_013553443.1 554 LYNMLL 559
                                               **9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (564 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: 11.58
//
[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