Alignments for a candidate for ilvI in Methylomicrobium alcaliphilum 20Z

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Methylomicrobium alcaliphilum 20Z

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_046061644.1 MEALZ_RS16195 acetolactate synthase 3 large subunit

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



>NCBI__GCF_000968535.2:WP_046061644.1
          Length = 578

 Score =  798 bits (2061), Expect = 0.0
 Identities = 388/565 (68%), Positives = 462/565 (81%), Gaps = 3/565 (0%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           E+ GA+ILV +L +EGVEY++GYPGGAVL+IYD + +Q   +HILVRHEQ A HAAD YA
Sbjct: 2   ELNGAQILVQSLKDEGVEYIFGYPGGAVLHIYDAIFQQDDVKHILVRHEQGATHAADAYA 61

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           RATGK GV LVTSGPG TNAVTGIATAY+DSIPMVVI+G VP+  IG DAFQE D VGI+
Sbjct: 62  RATGKAGVVLVTSGPGATNAVTGIATAYMDSIPMVVISGQVPSPVIGSDAFQEVDMVGIS 121

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACK--YEYPKSIDM 195
           RP VKHNFLVKDV  LA TIKKAF++A+TGRPGPVVVD+PKD++    K  Y+YP+ + M
Sbjct: 122 RPCVKHNFLVKDVTKLAETIKKAFYVASTGRPGPVVVDVPKDITDPNIKVPYKYPRKVIM 181

Query: 196 RSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLM 255
           RSYNP  +GH GQI+KAV LL  A+RP IY+GGGV+L  AS EL +L    G+P+TNTLM
Sbjct: 182 RSYNPAIEGHKGQIKKAVELLLSAQRPMIYSGGGVILGEASRELIELTRTLGYPITNTLM 241

Query: 256 GLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKII 315
           GLGA+P T KQF+GMLGMHGTYEANM M   DV++A+GARFDDRV G  A F   A KII
Sbjct: 242 GLGAYPATDKQFIGMLGMHGTYEANMGMHESDVILAVGARFDDRVTGKLAEFCPYA-KII 300

Query: 316 HIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVD 375
           HID+DP+SISK VKVDIPIVG VK VL ++I QIK S  +P ++ALA WWEQI++WRSV 
Sbjct: 301 HIDVDPASISKTVKVDIPIVGQVKPVLTQMIEQIKESKKQPSKKALAAWWEQIDKWRSVQ 360

Query: 376 CLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLG 435
           CL+YDR S +IKPQYV+E+++E+TKGDA+I SDVGQHQM+AAQ+Y FD+PRRWINSGGLG
Sbjct: 361 CLEYDRESPLIKPQYVIEQLYEVTKGDAYITSDVGQHQMYAAQYYHFDKPRRWINSGGLG 420

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

Query: 496 RQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFL 555
           RQWQE  Y++RYS+SYMD LPDFVKLAEAYGHVGM VE  +D+  AL EAF +KDRTVF+
Sbjct: 481 RQWQEFSYESRYSNSYMDTLPDFVKLAEAYGHVGMLVENKADLRSALEEAFAMKDRTVFM 540

Query: 556 DFQTDPTENVWPMVQAGKGISEMLL 580
           D  TD TENV+PM+++GKG  +M L
Sbjct: 541 DIITDRTENVYPMIESGKGHHDMKL 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: 1053
Number of extensions: 34
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_046061644.1 MEALZ_RS16195 (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.25243.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     6e-267  872.5   2.6   7.4e-267  872.2   2.6    1.0  1  lcl|NCBI__GCF_000968535.2:WP_046061644.1  MEALZ_RS16195 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000968535.2:WP_046061644.1  MEALZ_RS16195 acetolactate synthase 3 large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  872.2   2.6  7.4e-267  7.4e-267       1     553 [.       3     563 ..       3     566 .. 0.98

  Alignments for each domain:
  == domain 1  score: 872.2 bits;  conditional E-value: 7.4e-267
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 
                                               l+ga+ilv+slk+egve++fGyPGGavl+iyda++ +++++hilvrheq+a+haad yara+Gk+Gvvl
  lcl|NCBI__GCF_000968535.2:WP_046061644.1   3 LNGAQILVQSLKDEGVEYIFGYPGGAVLHIYDAIFqQDDVKHILVRHEQGATHAADAYARATGKAGVVL 71 
                                               579********************************999******************************* PP

                                 TIGR00118  69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137
                                               +tsGPGatn+vtgiatay+ds+P+vv++Gqv++ +iGsdafqe+d++Gi++p++kh+flvk++  l+e+
  lcl|NCBI__GCF_000968535.2:WP_046061644.1  72 VTSGPGATNAVTGIATAYMDSIPMVVISGQVPSPVIGSDAFQEVDMVGISRPCVKHNFLVKDVTKLAET 140
                                               ********************************************************************* PP

                                 TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleve..ekvelpgykptvkghklqikkaleliekakkPv 204
                                               +k+af++astGrPGPv+vd+Pkd+t+++i+++++  +kv +++y+p ++ghk qikka+el+ +a++P+
  lcl|NCBI__GCF_000968535.2:WP_046061644.1 141 IKKAFYVASTGRPGPVVVDVPKDITDPNIKVPYKypRKVIMRSYNPAIEGHKGQIKKAVELLLSAQRPM 209
                                               ******************************998888********************************* PP

                                 TIGR00118 205 llvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliav 273
                                               ++ GgGvi +eas+el el+ +l  p+t tl+GlGa+p+++++++gmlGmhGt+ean+ ++e+d+++av
  lcl|NCBI__GCF_000968535.2:WP_046061644.1 210 IYSGGGVILGEASRELIELTRTLGYPITNTLMGLGAYPATDKQFIGMLGMHGTYEANMGMHESDVILAV 278
                                               ********************************************************************* PP

                                 TIGR00118 274 GarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke 338
                                               Garfddrvtg+la+f+p akiihid+dPa+i+k+vkvdipivG++k vl+++++++ke     +kk   
  lcl|NCBI__GCF_000968535.2:WP_046061644.1 279 GARFDDRVTGKLAEFCPYAKIIHIDVDPASISKTVKVDIPIVGQVKPVLTQMIEQIKESkkqpSKKALA 347
                                               *******************************************************99886665445555 PP

                                 TIGR00118 339 .WlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfits 406
                                                W+e+i++w++ ++l++d+e+  ikPq+vi++l++++k++a++t+dvGqhqm+aaq+y+++kpr++i+s
  lcl|NCBI__GCF_000968535.2:WP_046061644.1 348 aWWEQIDKWRSVQCLEYDRESPLIKPQYVIEQLYEVTKGDAYITSDVGQHQMYAAQYYHFDKPRRWINS 416
                                               7******************************************************************** PP

                                 TIGR00118 407 gGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqe 475
                                               gGlGtmGfGlPaa+G+k+a pe++v +vtG++s+qm +qelst+ +y++pvki++lnn+++Gmv+qWqe
  lcl|NCBI__GCF_000968535.2:WP_046061644.1 417 GGLGTMGFGLPAAIGVKLAFPEADVACVTGEASIQMCIQELSTALQYKTPVKIINLNNRYMGMVRQWQE 485
                                               ********************************************************************* PP

                                 TIGR00118 476 lfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevlPm 543
                                               + ye rys++++ + lpdfvklaeayG++g+ +e++++l ++l+ea+++k + v++d+  d++e+v+Pm
  lcl|NCBI__GCF_000968535.2:WP_046061644.1 486 FSYESRYSNSYMDT-LPDFVKLAEAYGHVGMLVENKADLRSALEEAFAMKdRTVFMDIITDRTENVYPM 553
                                               *************5.*******************************9988689**************** PP

                                 TIGR00118 544 vapGagldel 553
                                               + +G+g +++
  lcl|NCBI__GCF_000968535.2:WP_046061644.1 554 IESGKGHHDM 563
                                               ******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: 0.01u 0.02s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 11.64
//
[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