Alignments for a candidate for ilvI in Herbaspirillum autotrophicum IAM 14942

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Herbaspirillum autotrophicum IAM 14942

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_050462618.1 AKL27_RS09690 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_001189915.1:WP_050462618.1
          Length = 572

 Score =  878 bits (2268), Expect = 0.0
 Identities = 421/571 (73%), Positives = 493/571 (86%)

Query: 15  AAPEMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAAD 74
           ++  + GAEILV  LAEEGVE+V+GYPGGAVLYIYD + KQ KF+HILVRHEQAA+HAAD
Sbjct: 2   SSEHITGAEILVRCLAEEGVEHVFGYPGGAVLYIYDAIFKQEKFQHILVRHEQAAIHAAD 61

Query: 75  GYARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTV 134
            Y+R++ KVGVALVTSGPGVTNA+TG+ATAY+DSIPM+VI+G VP+ AIGQDAFQECDTV
Sbjct: 62  AYSRSSEKVGVALVTSGPGVTNAITGLATAYMDSIPMIVISGQVPSTAIGQDAFQECDTV 121

Query: 135 GITRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSID 194
           GITRP VKHNFLVKDV+DLAAT+KKAF+IA TGRPGPV+VDIPKD+S + C YEYPK+++
Sbjct: 122 GITRPCVKHNFLVKDVKDLAATMKKAFYIATTGRPGPVLVDIPKDISMHTCAYEYPKTVE 181

Query: 195 MRSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTL 254
           MRSY PV+KGHSGQIRKA+ LL  AERP IYTGGGV+LANAS EL +L    G P TNTL
Sbjct: 182 MRSYKPVDKGHSGQIRKALQLLLTAERPMIYTGGGVILANASPELNKLVDRLGFPCTNTL 241

Query: 255 MGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKI 314
           MGLGA+  +S +FVGM GMHGTYEANMAMQ+ DV+IAIGARFDDRVIGNP HF S ARKI
Sbjct: 242 MGLGAYKSSSDKFVGMPGMHGTYEANMAMQHSDVMIAIGARFDDRVIGNPKHFASNARKI 301

Query: 315 IHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSV 374
           IHIDIDPSSISKRVKVDIPIVGNVKDVLQEL+AQ+ A++ +P   ALA WW+QI +WR  
Sbjct: 302 IHIDIDPSSISKRVKVDIPIVGNVKDVLQELLAQLDAAETRPNAAALANWWKQINKWRER 361

Query: 375 DCLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGL 434
           DCLK+  S ++IKPQ VV+K+WE+TKGDAFI SDVGQHQMWAAQ+Y FD+PRRWINSGGL
Sbjct: 362 DCLKFALSDDVIKPQAVVQKVWEVTKGDAFITSDVGQHQMWAAQYYGFDKPRRWINSGGL 421

Query: 435 GTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGM 494
           GTMGVGLPYAMG++KA P+  V  ITGE SIQMCIQEL+TC QY    KI  LNN +LGM
Sbjct: 422 GTMGVGLPYAMGVQKANPDATVACITGEASIQMCIQELATCKQYHLTPKIILLNNRFLGM 481

Query: 495 VRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVF 554
           VRQWQ+I+Y +RYS SYMD+LPDF KL E++GHVGM++EK  DV+ AL+EAF +KDR VF
Sbjct: 482 VRQWQQIDYGSRYSESYMDSLPDFTKLVESFGHVGMKIEKPGDVDGALKEAFGMKDRLVF 541

Query: 555 LDFQTDPTENVWPMVQAGKGISEMLLGAEDL 585
           ++F TD TENVWPMV+AGKG++EMLLG+EDL
Sbjct: 542 MNFITDQTENVWPMVKAGKGLTEMLLGSEDL 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: 1029
Number of extensions: 35
Number of successful extensions: 1
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: 572
Length adjustment: 36
Effective length of query: 549
Effective length of database: 536
Effective search space:   294264
Effective search space used:   294264
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_050462618.1 AKL27_RS09690 (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.2455.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-251  821.0   0.9   2.8e-251  820.7   0.9    1.0  1  lcl|NCBI__GCF_001189915.1:WP_050462618.1  AKL27_RS09690 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001189915.1:WP_050462618.1  AKL27_RS09690 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  820.7   0.9  2.8e-251  2.8e-251       2     554 ..       7     566 ..       6     569 .. 0.98

  Alignments for each domain:
  == domain 1  score: 820.7 bits;  conditional E-value: 2.8e-251
                                 TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               +gaeilv+ l +egve+vfGyPGGavl iyda++ +++++hilvrheqaa+haad y+r+s kvGv+l+
  lcl|NCBI__GCF_001189915.1:WP_050462618.1   7 TGAEILVRCLAEEGVEHVFGYPGGAVLYIYDAIFkQEKFQHILVRHEQAAIHAADAYSRSSEKVGVALV 75 
                                               89********************************9999******************************* PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPG tn++tg+atay+ds+P++v++Gqv++++iG+dafqe+d +Git+p++kh+flvk+++dl++++
  lcl|NCBI__GCF_001189915.1:WP_050462618.1  76 TSGPGVTNAITGLATAYMDSIPMIVISGQVPSTAIGQDAFQECDTVGITRPCVKHNFLVKDVKDLAATM 144
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207
                                               k+af+ia+tGrPGPvlvd+Pkd++ +++ +e++++ve+++ykp  kgh  qi+kal+l+ +a++P+++ 
  lcl|NCBI__GCF_001189915.1:WP_050462618.1 145 KKAFYIATTGRPGPVLVDIPKDISMHTCAYEYPKTVEMRSYKPVDKGHSGQIRKALQLLLTAERPMIYT 213
                                               ********************************************************************* PP

                                 TIGR00118 208 GgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGar 276
                                               GgGvi a+as el++l++rl  p t tl+GlGa+++   +++gm GmhGt+ean+a++++d++ia+Gar
  lcl|NCBI__GCF_001189915.1:WP_050462618.1 214 GGGVILANASPELNKLVDRLGFPCTNTLMGLGAYKSSSDKFVGMPGMHGTYEANMAMQHSDVMIAIGAR 282
                                               ********************************************************************* PP

                                 TIGR00118 277 fddrvtgnlakfapeak.iihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke.W 339
                                               fddrv gn ++fa++a+ iihididP++i+k vkvdipivG++k vl+ell++l +     +      W
  lcl|NCBI__GCF_001189915.1:WP_050462618.1 283 FDDRVIGNPKHFASNARkIIHIDIDPSSISKRVKVDIPIVGNVKDVLQELLAQLDAAetrpNAAALAnW 351
                                               ****************66***********************************998855553333335* PP

                                 TIGR00118 340 lekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgG 408
                                               +++i++w+++ +lk+  +++ ikPq+v++++++++k++a++t+dvGqhqmwaaq+y ++kpr++i+sgG
  lcl|NCBI__GCF_001189915.1:WP_050462618.1 352 WKQINKWRERDCLKFALSDDVIKPQAVVQKVWEVTKGDAFITSDVGQHQMWAAQYYGFDKPRRWINSGG 420
                                               ********************************************************************* PP

                                 TIGR00118 409 lGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelf 477
                                               lGtmG GlP a+G++ a+p++tv ++tG++s+qm +qel+t+++y++  ki++lnn++lGmv+qWq++ 
  lcl|NCBI__GCF_001189915.1:WP_050462618.1 421 LGTMGVGLPYAMGVQKANPDATVACITGEASIQMCIQELATCKQYHLTPKIILLNNRFLGMVRQWQQID 489
                                               ********************************************************************* PP

                                 TIGR00118 478 yeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevlPmva 545
                                               y  ryse+++ s lpdf+kl e++G++g++iekp +++ +lkea+ +k ++v++++  d++e+v+Pmv 
  lcl|NCBI__GCF_001189915.1:WP_050462618.1 490 YGSRYSESYMDS-LPDFTKLVESFGHVGMKIEKPGDVDGALKEAFGMKdRLVFMNFITDQTENVWPMVK 557
                                               ***********5.********************************887699****************** PP

                                 TIGR00118 546 pGagldelv 554
                                                G+gl+e++
  lcl|NCBI__GCF_001189915.1:WP_050462618.1 558 AGKGLTEML 566
                                               *******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (572 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: 9.92
//
[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