Alignments for a candidate for ilvI in Acidimicrobium ferrooxidans DSM 10331

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Acidimicrobium ferrooxidans DSM 10331

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_015798948.1 AFER_RS08020 acetolactate synthase large subunit

Query= BRENDA::P9WG41
         (618 letters)



>NCBI__GCF_000023265.1:WP_015798948.1
          Length = 569

 Score =  680 bits (1754), Expect = 0.0
 Identities = 338/565 (59%), Positives = 424/565 (75%), Gaps = 9/565 (1%)

Query: 37  QLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVRHEQGAGHAASGYA 96
           +LTGAQA++R+LE  GVDV+FG+PGGA+LPVYDPL DS  +RHVLVRHEQGAGH A GYA
Sbjct: 2   RLTGAQALVRALEMEGVDVVFGLPGGAILPVYDPLLDSP-IRHVLVRHEQGAGHMAEGYA 60

Query: 97  HVTGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADISGIT 156
             +GR GV + TSGP ATN+VT +ADA +DS+P+V ITGQV  G IG+DAFQE D +GIT
Sbjct: 61  QASGRPGVAIVTSGPAATNIVTAVADAAIDSVPMVVITGQVPTGAIGSDAFQEVDTTGIT 120

Query: 157 MPITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFSWPPRMELPG 216
           M +TKHN+LV    DIPRV+AEAFH+A +GRPG VL+D+PKDV  G+  + WP R++LPG
Sbjct: 121 MSVTKHNWLVTDPADIPRVVAEAFHVATTGRPGPVLIDLPKDVSTGELEWYWPRRLDLPG 180

Query: 217 YKPNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVTTLMAR 276
           Y+P TK H + + +AA LI AAR+PV+Y GGG++R  A  +LR LAE TGIPVVTTL+AR
Sbjct: 181 YQPVTKGHPKMIEQAAALITAARRPVIYAGGGLVRAGAERELRALAERTGIPVVTTLLAR 240

Query: 277 GAFPDSHRQNLGMPGMHGTVAAVAALQRSDLLIALGTRFDDRVTGKLDSFAPEAKVIHAD 336
           G  PD H   LGMPGMHGT AAV A+QR+DLLI LG RFDDRVTG++ +FAPEAKVIH D
Sbjct: 241 GIIPDDHPLALGMPGMHGTYAAVMAMQRADLLITLGARFDDRVTGRVSAFAPEAKVIHVD 300

Query: 337 IDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPGTIEMADWWAYLNGVRKTYPLSY 396
           +DPAE+GK R ADVPIVGD++ V+ EL+  L         ++  W A +   ++ YPLSY
Sbjct: 301 VDPAELGKVRRADVPIVGDLRNVLPELLRRLPAE----PADLGAWRATIAEWQQRYPLSY 356

Query: 397 GPQSDGSLS-PEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFIRYEKPRSWLNSGGLGTM 455
            P   GS + P++V+E+L  +   D + VAGVGQHQMWA+QF  +  PR W+NSGGLGTM
Sbjct: 357 VPSEPGSATKPQFVVERLRALTPDDTILVAGVGQHQMWASQFWTFRAPRQWINSGGLGTM 416

Query: 456 GFAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATCAVEGIPVKVALINNGNLGMVRQ 515
           GFA+PAA+GAK A P   VWAIDGDG FQMT QE+ T + E IP+KVA++NNG LGMVRQ
Sbjct: 417 GFAVPAAVGAKAARPRQMVWAIDGDGSFQMTAQEIVTASAERIPIKVAILNNGYLGMVRQ 476

Query: 516 WQSLFYAERYSQTDLATHSHRIPDFVKLAEALGCVGLRCEREEDVVDVINQARAINDCPV 575
           WQ +FY ERYS+  L   S  +PD+V+ AEA+G VG+R +  E+V   I +A  ++D PV
Sbjct: 477 WQEMFYDERYSEVYL---SPDLPDYVRWAEAMGAVGMRVDAPEEVDAAIEKANEVDDRPV 533

Query: 576 VIDFIVGADAQVWPMVAAGTSNDEI 600
           VIDF V    +V+PMV AG SND+I
Sbjct: 534 VIDFRVDTFEKVYPMVPAGASNDDI 558


Lambda     K      H
   0.319    0.136    0.414 

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: 1147
Number of extensions: 48
Number of successful extensions: 5
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: 618
Length of database: 569
Length adjustment: 37
Effective length of query: 581
Effective length of database: 532
Effective search space:   309092
Effective search space used:   309092
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_015798948.1 AFER_RS08020 (acetolactate synthase 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.2148895.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.1e-242  792.4   0.0   1.2e-242  792.2   0.0    1.0  1  NCBI__GCF_000023265.1:WP_015798948.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000023265.1:WP_015798948.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  792.2   0.0  1.2e-242  1.2e-242       1     554 [.       3     559 ..       3     562 .. 0.99

  Alignments for each domain:
  == domain 1  score: 792.2 bits;  conditional E-value: 1.2e-242
                             TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvlatsGP 73 
                                           l+ga++lv++l++egv++vfG PGGa+lp+yd l ds ++h+lvrheq+a h+a+Gya+asG++Gv+++tsGP
  NCBI__GCF_000023265.1:WP_015798948.1   3 LTGAQALVRALEMEGVDVVFGLPGGAILPVYDPLLDSPIRHVLVRHEQGAGHMAEGYAQASGRPGVAIVTSGP 75 
                                           68*********************************************************************** PP

                             TIGR00118  74 GatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeias 146
                                            atn+vt++a+a +dsvP+vv+tGqv+t +iGsdafqe+d +Git++vtkh++lv++++d+p+++ eaf++a+
  NCBI__GCF_000023265.1:WP_015798948.1  76 AATNIVTAVADAAIDSVPMVVITGQVPTGAIGSDAFQEVDTTGITMSVTKHNWLVTDPADIPRVVAEAFHVAT 148
                                           ************************************************************************* PP

                             TIGR00118 147 tGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeasee 219
                                           tGrPGPvl+dlPkdv++ e+e   +++++lpgy+p +kgh++ i++a+ li++a++Pv+++GgG++ a+a++e
  NCBI__GCF_000023265.1:WP_015798948.1 149 TGRPGPVLIDLPKDVSTGELEWYWPRRLDLPGYQPVTKGHPKMIEQAAALITAARRPVIYAGGGLVRAGAERE 221
                                           ************************************************************************* PP

                             TIGR00118 220 lkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapea 292
                                           l+ laer+ ipv+ttll  G +p+dhplalgm GmhGt++a +a++ adlli++Garfddrvtg ++ fapea
  NCBI__GCF_000023265.1:WP_015798948.1 222 LRALAERTGIPVVTTLLARGIIPDDHPLALGMPGMHGTYAAVMAMQRADLLITLGARFDDRVTGRVSAFAPEA 294
                                           ************************************************************************* PP

                             TIGR00118 293 kiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekieewkkeyilk.ldeeees.ikP 363
                                           k+ih+d+dPae+gk++++d+pivGd ++vl ell++l +e  +   W + i+ew+++y+l+ + +e +s  kP
  NCBI__GCF_000023265.1:WP_015798948.1 295 KVIHVDVDPAELGKVRRADVPIVGDLRNVLPELLRRLPAEPADLGAWRATIAEWQQRYPLSyVPSEPGSaTKP 367
                                           *************************************999888888**************97777776669** PP

                             TIGR00118 364 qkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtG 436
                                           q v+++l  l++d++i+ ++vGqhqmwa+qf+++++pr++i+sgGlGtmGf +Paa+Gak a p + v a++G
  NCBI__GCF_000023265.1:WP_015798948.1 368 QFVVERLRALTPDDTILVAGVGQHQMWASQFWTFRAPRQWINSGGLGTMGFAVPAAVGAKAARPRQMVWAIDG 440
                                           ************************************************************************* PP

                             TIGR00118 437 dgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgirie 509
                                           dgsfqm+ qe+ t++   ip+k+ ilnn +lGmv+qWqe+fy+eryse++l+ +lpd+v+ aea+G++g+r+ 
  NCBI__GCF_000023265.1:WP_015798948.1 441 DGSFQMTAQEIVTASAERIPIKVAILNNGYLGMVRQWQEMFYDERYSEVYLSPDLPDYVRWAEAMGAVGMRVD 513
                                           ************************************************************************* PP

                             TIGR00118 510 kpeeleeklkealesk.epvlldvevdkeeevlPmvapGagldelv 554
                                            pee+++++++a e++ +pv++d++vd+ e+v+Pmv+ Ga++d++v
  NCBI__GCF_000023265.1:WP_015798948.1 514 APEEVDAAIEKANEVDdRPVVIDFRVDTFEKVYPMVPAGASNDDIV 559
                                           *************99879*************************998 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 33.28
//
[ok]

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

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Steps (tab-delimited)
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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