Alignments for a candidate for ilvI in Methylosarcina fibrata AML-C10

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Methylosarcina fibrata AML-C10

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_020564706.1 A3OW_RS0117295 acetolactate synthase 3 large subunit

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



>NCBI__GCF_000372865.1:WP_020564706.1
          Length = 578

 Score =  788 bits (2036), Expect = 0.0
 Identities = 380/565 (67%), Positives = 457/565 (80%), Gaps = 3/565 (0%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           E+ GA+ILV +L +EGVEY++GYPGGAVL++YD L +Q   +HILVRHEQ A HAADGYA
Sbjct: 2   ELSGAQILVQSLKDEGVEYIFGYPGGAVLHLYDALFQQEAIKHILVRHEQGATHAADGYA 61

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           RATGK GV LVTSGPG TNA+TGIATAY+DSIP+VVI+G V    IG DAFQE D +GI+
Sbjct: 62  RATGKPGVVLVTSGPGATNAITGIATAYMDSIPLVVISGQVSLPVIGSDAFQEVDMIGIS 121

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACK--YEYPKSIDM 195
           RP VKHNFLVKDV  LA TIKKAF++A +GRPGPVVVD+PKD++    K  Y+YPK I +
Sbjct: 122 RPCVKHNFLVKDVTKLAETIKKAFYVATSGRPGPVVVDVPKDITDPNIKVPYKYPKKISL 181

Query: 196 RSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLM 255
           RSYNPV  GH GQI+KAV LL  AERP IY+GGGV+L  AS EL +   L  +PVTNTLM
Sbjct: 182 RSYNPVVLGHKGQIKKAVDLLLSAERPIIYSGGGVILGEASRELTEFGRLLEYPVTNTLM 241

Query: 256 GLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKII 315
           GLG +PGT +QFVGMLGMHGTYEANMAM   D++IA+GARFDDRV G    F   AR II
Sbjct: 242 GLGGYPGTDRQFVGMLGMHGTYEANMAMHESDLIIAVGARFDDRVTGKLDKFCPYAR-II 300

Query: 316 HIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVD 375
           HID+DP+SISK VKVDIPIVG VK VL+++I  I+ S  KP ++AL  WW +I QW+SV+
Sbjct: 301 HIDVDPASISKTVKVDIPIVGEVKPVLEQMIELIRESKKKPNKKALEAWWSRINQWKSVN 360

Query: 376 CLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLG 435
           CL YDR S +IKPQYV+E+++++TKG+A++ SDVGQHQMWAAQ+Y+FD+PR WINSGGLG
Sbjct: 361 CLDYDRESRLIKPQYVIEQLYDVTKGEAYVTSDVGQHQMWAAQYYRFDKPRHWINSGGLG 420

Query: 436 TMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMV 495
           TMG GLP A+G+K AFPE +V  +TGE SIQMCIQELST LQY+T VKI +LNN Y+GMV
Sbjct: 421 TMGFGLPAAIGVKLAFPEADVACVTGEASIQMCIQELSTALQYNTAVKIVNLNNRYMGMV 480

Query: 496 RQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFL 555
           RQWQE  Y++RYSHSYMD +PDFVKLAEAYGHVGMR++K  DV  AL +AF LKDRTVF+
Sbjct: 481 RQWQEFSYESRYSHSYMDTIPDFVKLAEAYGHVGMRIDKPEDVRGALEQAFALKDRTVFI 540

Query: 556 DFQTDPTENVWPMVQAGKGISEMLL 580
           D  TD TENV+PM++AGK  ++M L
Sbjct: 541 DIMTDRTENVYPMIEAGKAHNDMKL 565


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: 1059
Number of extensions: 36
Number of successful extensions: 3
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: 578
Length adjustment: 36
Effective length of query: 549
Effective length of database: 542
Effective search space:   297558
Effective search space used:   297558
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_020564706.1 A3OW_RS0117295 (acetolactate synthase 3 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.1356712.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.5e-269  880.3   0.3   2.9e-269  880.1   0.3    1.0  1  NCBI__GCF_000372865.1:WP_020564706.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000372865.1:WP_020564706.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  880.1   0.3  2.9e-269  2.9e-269       1     553 [.       3     563 ..       3     567 .. 0.98

  Alignments for each domain:
  == domain 1  score: 880.1 bits;  conditional E-value: 2.9e-269
                             TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsG 72 
                                           l+ga+ilv+slk+egve++fGyPGGavl++ydal+ ++ ++hilvrheq+a+haadGyara+Gk+Gvvl+tsG
  NCBI__GCF_000372865.1:WP_020564706.1   3 LSGAQILVQSLKDEGVEYIFGYPGGAVLHLYDALFqQEAIKHILVRHEQGATHAADGYARATGKPGVVLVTSG 75 
                                           68*********************************8889********************************** PP

                             TIGR00118  73 PGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeia 145
                                           PGatn++tgiatay+ds+Plvv++Gqv+  +iGsdafqe+d++Gi++p++kh+flvk++  l+e++k+af++a
  NCBI__GCF_000372865.1:WP_020564706.1  76 PGATNAITGIATAYMDSIPLVVISGQVSLPVIGSDAFQEVDMIGISRPCVKHNFLVKDVTKLAETIKKAFYVA 148
                                           ************************************************************************* PP

                             TIGR00118 146 stGrPGPvlvdlPkdvteaeieleve..ekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaea 216
                                           ++GrPGPv+vd+Pkd+t+++i+++++  +k++l++y+p v ghk qikka++l+ +a++P+++ GgGvi +ea
  NCBI__GCF_000372865.1:WP_020564706.1 149 TSGRPGPVVVDVPKDITDPNIKVPYKypKKISLRSYNPVVLGHKGQIKKAVDLLLSAERPIIYSGGGVILGEA 221
                                           **********************998888********************************************* PP

                             TIGR00118 217 seelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfa 289
                                           s+el+e+   l+ pvt tl+GlG++p ++++++gmlGmhGt+ean+a++e+dl+iavGarfddrvtg+l+kf+
  NCBI__GCF_000372865.1:WP_020564706.1 222 SRELTEFGRLLEYPVTNTLMGLGGYPGTDRQFVGMLGMHGTYEANMAMHESDLIIAVGARFDDRVTGKLDKFC 294
                                           ************************************************************************* PP

                             TIGR00118 290 peakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke.Wlekieewkkeyilkldee 357
                                           p a+iihid+dPa+i+k+vkvdipivG++k vle++++ ++e     +kk  e W+++i++wk+ ++l +d+e
  NCBI__GCF_000372865.1:WP_020564706.1 295 PYARIIHIDVDPASISKTVKVDIPIVGEVKPVLEQMIELIRESkkkpNKKALEaWWSRINQWKSVNCLDYDRE 367
                                           **************************************9988766665566668******************* PP

                             TIGR00118 358 eesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeet 430
                                           +  ikPq+vi++l+ ++k+ea+vt+dvGqhqmwaaq+y+++kpr++i+sgGlGtmGfGlPaa+G+k+a pe++
  NCBI__GCF_000372865.1:WP_020564706.1 368 SRLIKPQYVIEQLYDVTKGEAYVTSDVGQHQMWAAQYYRFDKPRHWINSGGLGTMGFGLPAAIGVKLAFPEAD 440
                                           ************************************************************************* PP

                             TIGR00118 431 vvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGv 503
                                           v +vtG++s+qm +qelst+ +y++ vkiv+lnn+++Gmv+qWqe+ ye rys++++ +  pdfvklaeayG+
  NCBI__GCF_000372865.1:WP_020564706.1 441 VACVTGEASIQMCIQELSTALQYNTAVKIVNLNNRYMGMVRQWQEFSYESRYSHSYMDT-IPDFVKLAEAYGH 512
                                           **********************************************************5.************* PP

                             TIGR00118 504 kgiriekpeeleeklkealesk.epvlldvevdkeeevlPmvapGagldel 553
                                           +g+ri kpe++  +l++a++ k + v++d+  d++e+v+Pm+  G++ +++
  NCBI__GCF_000372865.1:WP_020564706.1 513 VGMRIDKPEDVRGALEQAFALKdRTVFIDIMTDRTENVYPMIEAGKAHNDM 563
                                           ******************9987699**********************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (578 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: 26.52
//
[ok]

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

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

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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