Alignments for a candidate for ilvI in Leptospirillum ferrooxidans C2-3

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Leptospirillum ferrooxidans C2-3

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_014450635.1 LFE_RS12760 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_000284315.1:WP_014450635.1
          Length = 583

 Score =  627 bits (1616), Expect = 0.0
 Identities = 312/571 (54%), Positives = 404/571 (70%), Gaps = 7/571 (1%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           +M GAE+L+ +L  E V++++GYPGG VL I+D L K    + +L RHEQ AVHAA+GYA
Sbjct: 2   KMSGAEMLLESLKRENVQHIFGYPGGVVLPIFDALFKDPSLQVVLTRHEQGAVHAAEGYA 61

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           R+T KVGV LVTSGPG TN VTG+A A +DSIP+VVITG VPT  IG DAFQE D VGI+
Sbjct: 62  RSTNKVGVVLVTSGPGATNTVTGLADANMDSIPIVVITGQVPTKMIGNDAFQEADIVGIS 121

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
           R   KHNFLV+ ++DL   IK+AF+IA TGRPGPV+VD+PKDV  +   + YP S+ +RS
Sbjct: 122 RSCTKHNFLVRKIQDLPRIIKEAFYIARTGRPGPVLVDLPKDVIVDRADFIYPDSVSIRS 181

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257
           YNP  +G+  QIRKA   +  A+RP +Y GGG++ ++A+ EL  L  LT  P T TLMGL
Sbjct: 182 YNPTMQGNRWQIRKAAQAISKAKRPVLYAGGGIISSDATKELLDLVTLTNIPTTLTLMGL 241

Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHI 317
           GA  GT  +F+GMLGMHGTY ANMA+ +CD+LIA+G RFDDRV G  + F+  + K+IHI
Sbjct: 242 GALSGTHPRFMGMLGMHGTYAANMAIHHCDLLIAVGVRFDDRVTGKISEFSPHS-KVIHI 300

Query: 318 DIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKP----KREALAKWWEQIEQWRS 373
           DIDP+SI K   VDIPIVG+ K +L++LI +IK  + KP    K + +  W EQ+E+W  
Sbjct: 301 DIDPTSIRKNFHVDIPIVGDAKHILKDLIEEIKELN-KPEPPSKEKLIDPWIEQVEEWEK 359

Query: 374 VDCLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGG 433
              L Y+  +E+IKPQYV+EK+++ T+GD  + +DVGQHQMW AQF+KF +P  W+ SGG
Sbjct: 360 EHPLTYEHDTEVIKPQYVIEKVYQFTQGDCIVSTDVGQHQMWTAQFFKFIKPNTWLTSGG 419

Query: 434 LGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLG 493
           LGTMG G P A+G +KA P+K V+ ITGEGS  M IQEL+T    D PVKI  LNN YLG
Sbjct: 420 LGTMGYGFPAAIGAQKAHPDKRVIAITGEGSFMMNIQELATVASLDIPVKIVILNNKYLG 479

Query: 494 MVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTV 553
           MVRQWQE  Y  RYS S++   PDFVKLAEA+G VG++  +  +VE  + + F  +   V
Sbjct: 480 MVRQWQEFFYGGRYSSSFIGQSPDFVKLAEAFGIVGLKASRHDEVENIILDGFSRRG-PV 538

Query: 554 FLDFQTDPTENVWPMVQAGKGISEMLLGAED 584
            ++F  DP ENV+PMV AG    EM+  A +
Sbjct: 539 LMEFHVDPEENVFPMVPAGGSNIEMIFEAPE 569


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: 918
Number of extensions: 36
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: 583
Length adjustment: 36
Effective length of query: 549
Effective length of database: 547
Effective search space:   300303
Effective search space used:   300303
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_014450635.1 LFE_RS12760 (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.13186.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.8e-261  854.4   0.2   2.1e-261  854.2   0.2    1.0  1  lcl|NCBI__GCF_000284315.1:WP_014450635.1  LFE_RS12760 acetolactate synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000284315.1:WP_014450635.1  LFE_RS12760 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  854.2   0.2  2.1e-261  2.1e-261       1     554 [.       3     564 ..       3     567 .. 0.98

  Alignments for each domain:
  == domain 1  score: 854.2 bits;  conditional E-value: 2.1e-261
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 
                                               ++gae+l+eslk+e+v+++fGyPGG vlpi+dal+ d  l+ +l+rheq+a+haa+Gyar++ kvGvvl
  lcl|NCBI__GCF_000284315.1:WP_014450635.1   3 MSGAEMLLESLKRENVQHIFGYPGGVVLPIFDALFkDPSLQVVLTRHEQGAVHAAEGYARSTNKVGVVL 71 
                                               79*********************************8889****************************** PP

                                 TIGR00118  69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137
                                               +tsGPGatn+vtg+a+a +ds+P+vv+tGqv+t++iG+dafqe+di+Gi++++tkh+flv+k +dlp+i
  lcl|NCBI__GCF_000284315.1:WP_014450635.1  72 VTSGPGATNTVTGLADANMDSIPIVVITGQVPTKMIGNDAFQEADIVGISRSCTKHNFLVRKIQDLPRI 140
                                               ********************************************************************* PP

                                 TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvll 206
                                               +keaf+ia tGrPGPvlvdlPkdv     ++ ++++v++++y+pt++g++ qi+ka+++i+kak+Pvl+
  lcl|NCBI__GCF_000284315.1:WP_014450635.1 141 IKEAFYIARTGRPGPVLVDLPKDVIVDRADFIYPDSVSIRSYNPTMQGNRWQIRKAAQAISKAKRPVLY 209
                                               ********************************************************************* PP

                                 TIGR00118 207 vGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGa 275
                                               +GgG+i ++a++el +l+  ++ip t tl+GlGa+  +hp+++gmlGmhGt++an+a++++dlliavG+
  lcl|NCBI__GCF_000284315.1:WP_014450635.1 210 AGGGIISSDATKELLDLVTLTNIPTTLTLMGLGALSGTHPRFMGMLGMHGTYAANMAIHHCDLLIAVGV 278
                                               ********************************************************************* PP

                                 TIGR00118 276 rfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee.......ekkek 337
                                               rfddrvtg++++f+p++k+ihididP++i kn +vdipivGdak++l++l++++ke        ++k +
  lcl|NCBI__GCF_000284315.1:WP_014450635.1 279 RFDDRVTGKISEFSPHSKVIHIDIDPTSIRKNFHVDIPIVGDAKHILKDLIEEIKELnkpeppsKEKLI 347
                                               ******************************************************998888886434444 PP

                                 TIGR00118 338 e.WlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfit 405
                                               + W+e++eew ke++l+++++ e ikPq+vi++++++++++ iv+tdvGqhqmw+aqf+k+ kp++++t
  lcl|NCBI__GCF_000284315.1:WP_014450635.1 348 DpWIEQVEEWEKEHPLTYEHDTEVIKPQYVIEKVYQFTQGDCIVSTDVGQHQMWTAQFFKFIKPNTWLT 416
                                               58******************************************************************* PP

                                 TIGR00118 406 sgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWq 474
                                               sgGlGtmG+G+Paa+Ga+ a+p++ v+a+tG+gsf+mn+qel+t++ +dipvkivilnn++lGmv+qWq
  lcl|NCBI__GCF_000284315.1:WP_014450635.1 417 SGGLGTMGYGFPAAIGAQKAHPDKRVIAITGEGSFMMNIQELATVASLDIPVKIVILNNKYLGMVRQWQ 485
                                               ********************************************************************* PP

                                 TIGR00118 475 elfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPm 543
                                               e+fy +rys++ +++ +pdfvklaea+G++g++ ++++e+e+ + + ++ ++pvl++++vd ee+v+Pm
  lcl|NCBI__GCF_000284315.1:WP_014450635.1 486 EFFYGGRYSSSFIGQ-SPDFVKLAEAFGIVGLKASRHDEVENIILDGFSRRGPVLMEFHVDPEENVFPM 553
                                               **************6.***************************************************** PP

                                 TIGR00118 544 vapGagldelv 554
                                               v+ G+++ e++
  lcl|NCBI__GCF_000284315.1:WP_014450635.1 554 VPAGGSNIEMI 564
                                               *******9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (583 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 10.20
//
[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