Alignments for a candidate for ilvI in Magnetospirillum magneticum AMB-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Magnetospirillum magneticum AMB-1

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_011385867.1 AMB_RS17740 acetolactate synthase 3 large subunit

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



>NCBI__GCF_000009985.1:WP_011385867.1
          Length = 588

 Score =  644 bits (1660), Expect = 0.0
 Identities = 321/569 (56%), Positives = 416/569 (73%), Gaps = 6/569 (1%)

Query: 19  MIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYAR 78
           + GAEIL+ AL ++GVE ++GYPGGAVL IYDEL KQ +  H+LVRHEQAAVHAA+GYAR
Sbjct: 7   LTGAEILLKALVDQGVEVIFGYPGGAVLPIYDELFKQNRLRHVLVRHEQAAVHAAEGYAR 66

Query: 79  ATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGITR 138
           +TGKVG  LVTSGPG TNAVTG+A A  DS+P+V +TG VPTH IG DAFQE D  GITR
Sbjct: 67  STGKVGCVLVTSGPGATNAVTGLADAQCDSVPLVCLTGQVPTHLIGNDAFQEADITGITR 126

Query: 139 PIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRSY 198
           P  KHN+LVKDV DLA T+ +AF +A +GRPGPV+VD+PKDV +   +Y+ P  +  + Y
Sbjct: 127 PCTKHNYLVKDVADLARTVHEAFHVARSGRPGPVLVDLPKDVVQAKGEYQPPSKLKSK-Y 185

Query: 199 NPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLAN--ASDELRQLAALTGHPVTNTLMG 256
            P  KG    I KA+ ++  A++P  Y GGGVV +   A   L Q   +TG+P T TLMG
Sbjct: 186 KPQVKGDLKAIEKAIEMIAHAKKPIFYVGGGVVNSGPAACQLLTQFVRMTGYPCTLTLMG 245

Query: 257 LGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIH 316
           LGAFPG+   F+GMLGMHGT EANMAM +CD++I IGARFDDRV G    F+ +++K IH
Sbjct: 246 LGAFPGSDPLFLGMLGMHGTVEANMAMHDCDLMINIGARFDDRVTGKLDGFSPKSKK-IH 304

Query: 317 IDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDC 376
           +DIDPSSI+K V VD+PIVG+   VL+++I   KA   +   +AL  WW +I+QWR  DC
Sbjct: 305 VDIDPSSINKNVAVDLPIVGDCAHVLEDMIKVWKAKQSRVDDKALKAWWAKIDQWRGADC 364

Query: 377 LKYDRSSEIIKPQYVVEKIWELTK-GDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLG 435
           L ++ S++IIKPQY +++++E+T+  + + C++VGQHQMWAAQ  KFD P  W+ SGGLG
Sbjct: 365 LSFENSNKIIKPQYAIQRLYEMTRHRNPYFCTEVGQHQMWAAQHLKFDLPLHWLTSGGLG 424

Query: 436 TMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMV 495
           TMG GLP AMG++ A PE  V+ I GE SIQM IQE++T +Q+  PVKI  LNN YLGMV
Sbjct: 425 TMGYGLPSAMGVQMAHPEALVINIAGEASIQMNIQEMATLVQHRLPVKIVILNNQYLGMV 484

Query: 496 RQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFL 555
           RQWQE+ +  RYS S+M   PDFVKLAEA+G VG+R +K  +V+ A++E   + DR V L
Sbjct: 485 RQWQELIHGGRYSESHMIHHPDFVKLAEAFGAVGLRADKPGEVDGAIKEMIAV-DRPVIL 543

Query: 556 DFQTDPTENVWPMVQAGKGISEMLLGAED 584
           + +TD +ENV+PM+  G   +EM+LG ED
Sbjct: 544 ELRTDASENVFPMIMPGMAHNEMVLGPED 572


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: 962
Number of extensions: 30
Number of successful extensions: 6
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: 588
Length adjustment: 37
Effective length of query: 548
Effective length of database: 551
Effective search space:   301948
Effective search space used:   301948
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_011385867.1 AMB_RS17740 (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.11657.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.4e-246  804.5   0.3   2.7e-246  804.3   0.3    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011385867.1  AMB_RS17740 acetolactate synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011385867.1  AMB_RS17740 acetolactate synthase 3 large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  804.3   0.3  2.7e-246  2.7e-246       1     554 [.       7     567 ..       7     570 .. 0.97

  Alignments for each domain:
  == domain 1  score: 804.3 bits;  conditional E-value: 2.7e-246
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 
                                               l+gaeil+++l ++gve++fGyPGGavlpiyd+l+ ++ l+h+lvrheqaa+haa+Gyar++GkvG+vl
  lcl|NCBI__GCF_000009985.1:WP_011385867.1   7 LTGAEILLKALVDQGVEVIFGYPGGAVLPIYDELFkQNRLRHVLVRHEQAAVHAAEGYARSTGKVGCVL 75 
                                               68*********************************8999****************************** PP

                                 TIGR00118  69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137
                                               +tsGPGatn+vtg+a+a  dsvPlv ltGqv+t+liG+dafqe+di+Git+p+tkh++lvk+++dl+++
  lcl|NCBI__GCF_000009985.1:WP_011385867.1  76 VTSGPGATNAVTGLADAQCDSVPLVCLTGQVPTHLIGNDAFQEADITGITRPCTKHNYLVKDVADLART 144
                                               ********************************************************************* PP

                                 TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvll 206
                                               ++eaf++a +GrPGPvlvdlPkdv++a+ e++ ++k++   ykp+vkg+ + i+ka+e+i++akkP+ +
  lcl|NCBI__GCF_000009985.1:WP_011385867.1 145 VHEAFHVARSGRPGPVLVDLPKDVVQAKGEYQPPSKLK-SKYKPQVKGDLKAIEKAIEMIAHAKKPIFY 212
                                               *********************************98877.56**************************** PP

                                 TIGR00118 207 vGgGviiae..aseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliav 273
                                               vGgGv+ ++  a + l++++ ++  p t tl+GlGafp  +pl+lgmlGmhGt ean+a++++dl+i +
  lcl|NCBI__GCF_000009985.1:WP_011385867.1 213 VGGGVVNSGpaACQLLTQFVRMTGYPCTLTLMGLGAFPGSDPLFLGMLGMHGTVEANMAMHDCDLMINI 281
                                               ******88643678999**************************************************** PP

                                 TIGR00118 274 GarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke 338
                                               Garfddrvtg+l+ f+p++k ih+didP++i+knv+vd+pivGd+ +vle+++k  k++    ++k  +
  lcl|NCBI__GCF_000009985.1:WP_011385867.1 282 GARFDDRVTGKLDGFSPKSKKIHVDIDPSSINKNVAVDLPIVGDCAHVLEDMIKVWKAKqsrvDDKALK 350
                                               *****************************************************9877765566555556 PP

                                 TIGR00118 339 .WlekieewkkeyilkldeeeesikPqkvikelskllkd.eaivttdvGqhqmwaaqfyktkkprkfit 405
                                                W++ki++w+   +l+++++++ ikPq+ i++l++++++ + +  t+vGqhqmwaaq++k++ p +++t
  lcl|NCBI__GCF_000009985.1:WP_011385867.1 351 aWWAKIDQWRGADCLSFENSNKIIKPQYAIQRLYEMTRHrNPYFCTEVGQHQMWAAQHLKFDLPLHWLT 419
                                               7***********************************998689*************************** PP

                                 TIGR00118 406 sgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWq 474
                                               sgGlGtmG+GlP+a+G+++a+pe+ v++++G++s+qmn+qe++t+v+  +pvkivilnn++lGmv+qWq
  lcl|NCBI__GCF_000009985.1:WP_011385867.1 420 SGGLGTMGYGLPSAMGVQMAHPEALVINIAGEASIQMNIQEMATLVQHRLPVKIVILNNQYLGMVRQWQ 488
                                               ********************************************************************* PP

                                 TIGR00118 475 elfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPm 543
                                               el++ +ryse+++ + +pdfvklaea+G++g+r  kp e++ ++ke++++++pv+l+++ d +e+v+Pm
  lcl|NCBI__GCF_000009985.1:WP_011385867.1 489 ELIHGGRYSESHMIH-HPDFVKLAEAFGAVGLRADKPGEVDGAIKEMIAVDRPVILELRTDASENVFPM 556
                                               **************5.***************************************************** PP

                                 TIGR00118 544 vapGagldelv 554
                                               ++pG++ +e+v
  lcl|NCBI__GCF_000009985.1:WP_011385867.1 557 IMPGMAHNEMV 567
                                               **********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (588 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: 00:00:00.03
# Mc/sec: 10.20
//
[ok]

This GapMind analysis is from Apr 09 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