Alignments for a candidate for ilvI in Trichormus variabilis ATCC 29413

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Trichormus variabilis ATCC 29413

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_011319511.1 AVA_RS13955 biosynthetic-type acetolactate synthase large subunit

Query= BRENDA::P9WG41
         (618 letters)



>NCBI__GCF_000204075.1:WP_011319511.1
          Length = 632

 Score =  549 bits (1415), Expect = e-160
 Identities = 304/596 (51%), Positives = 391/596 (65%), Gaps = 16/596 (2%)

Query: 14  PEPHSAANEPKHPAA--RPKHVAL-QQLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDP 70
           P P S +   KH  +   P  V   Q++TG  A++ SL   GV+ IFG PGGA+LP+YD 
Sbjct: 6   PSPTSPSQTEKHTQSVNSPSVVVTPQRVTGGFALLDSLLRHGVEYIFGYPGGAILPIYDD 65

Query: 71  LFDSK---KLRHVLVRHEQGAGHAASGYAHVTGRVGVCMATSGPGATNLVTPLADAQMDS 127
           L+  +    L+H+LVRHEQGA HAA GYA  TG+VGVC  TSGPGATNLVT +A A MDS
Sbjct: 66  LYKVEATGSLKHILVRHEQGAAHAADGYARATGKVGVCFGTSGPGATNLVTGIATAYMDS 125

Query: 128 IPVVAITGQVGRGLIGTDAFQEADISGITMPITKHNFLVRSGDDIPRVLAEAFHIAASGR 187
           IP+V +TGQV R +IGTDAFQE DI GIT+PI KH+++VR   D+ R++AEAFHIA++GR
Sbjct: 126 IPMVIVTGQVPRKMIGTDAFQETDIYGITLPIVKHSYVVRDPQDMARIVAEAFHIASTGR 185

Query: 188 PGAVLVDIPKDVLQGQCTF--SWPPRMELPGYKPNTKPHSRQVREAAKLIAAARKPVLYV 245
           PG VL+D+PKDV   Q  +    P  ++L GY+P  K + RQ+  A +LI  +R+P+LYV
Sbjct: 186 PGPVLIDVPKDVAFEQFDYVPVEPGSIKLRGYRPTVKGNPRQINAAIELIRESRRPLLYV 245

Query: 246 GGGVIRGEATEQLRELAELTGIPVVTTLMARGAFPDSHRQNLGMPGMHGTVAAVAALQRS 305
           GGG I   A  +++ELAEL  IPV TTLM  GAF + H  +LGM GMHGT  A  A+   
Sbjct: 246 GGGAIASGAHAEIQELAELFNIPVTTTLMGIGAFDEHHPLSLGMLGMHGTAYANFAVTDC 305

Query: 306 DLLIALGTRFDDRVTGKLDSFAPEAKVIHADIDPAEIGKNRHADVPIVGDVKAVITELIA 365
           DLLI +G RFDDRVTGKLD FA  AKVIH DIDPAE+GKNR  +VPIVGDV+ V+ +L+ 
Sbjct: 306 DLLICVGARFDDRVTGKLDEFASRAKVIHIDIDPAEVGKNRIPEVPIVGDVRKVLLDLLR 365

Query: 366 MLRHHHIPGT-IEMADWWAYLNGVRKTYPLSYGPQSDGSLSPEYVIEKLGEIAGPDAVFV 424
             +      T  +  +W   +N  R+ YPL   PQ   S+ P+ VI ++G  A P A + 
Sbjct: 366 RCKQTGAKNTPNQNQEWLNLINRWREDYPLVI-PQHPDSIPPQEVIVEVGSQA-PHAFYT 423

Query: 425 AGVGQHQMWAAQFIRYEKPRSWLNSGGLGTMGFAIPAAMGAKIALPGTEVWAIDGDGCFQ 484
             VGQHQMWAAQF++   PR W++S GLGTMGF +PAA+GAK+A P  +V  I GD  FQ
Sbjct: 424 TDVGQHQMWAAQFLK-NGPRRWISSAGLGTMGFGLPAAIGAKVAFPDEQVICISGDASFQ 482

Query: 485 MTNQELATCAVEGIPVKVALINNGNLGMVRQWQSLFYAERYSQTDLATHSHRIPDFVKLA 544
           M  QEL T +  GI VK  ++NNG  GMVRQWQ  F+ ERYS +++      +PD   LA
Sbjct: 483 MCLQELGTASQYGINVKTVILNNGWQGMVRQWQQAFHGERYSCSNMEV---GMPDVELLA 539

Query: 545 EALGCVGLRCEREEDVVDVINQARAINDCPVVIDFIVGADAQVWPMVAAGTSNDEI 600
           +A G  G+   + E + D I Q  A  D PV++D  V  D   +PMVA G SN ++
Sbjct: 540 KAYGIKGIVVTQREQLKDAIAQMLAY-DGPVILDVRVTKDENCYPMVAPGKSNAQM 594


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: 1155
Number of extensions: 61
Number of successful extensions: 7
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: 632
Length adjustment: 37
Effective length of query: 581
Effective length of database: 595
Effective search space:   345695
Effective search space used:   345695
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: 54 (25.4 bits)

Align candidate WP_011319511.1 AVA_RS13955 (biosynthetic-type 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.24208.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-264  864.7   0.1   1.6e-264  864.4   0.1    1.0  1  lcl|NCBI__GCF_000204075.1:WP_011319511.1  AVA_RS13955 biosynthetic-type ac


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000204075.1:WP_011319511.1  AVA_RS13955 biosynthetic-type acetolactate synthase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  864.4   0.1  1.6e-264  1.6e-264       2     555 ..      34     596 ..      33     598 .. 0.98

  Alignments for each domain:
  == domain 1  score: 864.4 bits;  conditional E-value: 1.6e-264
                                 TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly....dselehilvrheqaaahaadGyarasGkvGv 66 
                                               +g+ +l++sl ++gve++fGyPGGa+lpiyd ly    ++ l+hilvrheq+aahaadGyara+GkvGv
  lcl|NCBI__GCF_000204075.1:WP_011319511.1  34 TGGFALLDSLLRHGVEYIFGYPGGAILPIYDDLYkveaTGSLKHILVRHEQGAAHAADGYARATGKVGV 102
                                               68899*****************************9887789**************************** PP

                                 TIGR00118  67 vlatsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlp 135
                                               +++tsGPGatnlvtgiatay+ds+P+v++tGqv++++iG+dafqe di Gitlp++khs++v++++d++
  lcl|NCBI__GCF_000204075.1:WP_011319511.1 103 CFGTSGPGATNLVTGIATAYMDSIPMVIVTGQVPRKMIGTDAFQETDIYGITLPIVKHSYVVRDPQDMA 171
                                               ********************************************************************* PP

                                 TIGR00118 136 eilkeafeiastGrPGPvlvdlPkdvteaeieleve..ekvelpgykptvkghklqikkaleliekakk 202
                                               +i+ eaf+iastGrPGPvl+d+Pkdv+ +++++      +++l+gy+ptvkg+++qi++a+eli+++++
  lcl|NCBI__GCF_000204075.1:WP_011319511.1 172 RIVAEAFHIASTGRPGPVLIDVPKDVAFEQFDYVPVepGSIKLRGYRPTVKGNPRQINAAIELIRESRR 240
                                               *******************************998765799***************************** PP

                                 TIGR00118 203 PvllvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlli 271
                                               P+l+vGgG+i+++a++e++elae ++ipvtttl+G+Gaf+e+hpl+lgmlGmhGt++an+av+++dlli
  lcl|NCBI__GCF_000204075.1:WP_011319511.1 241 PLLYVGGGAIASGAHAEIQELAELFNIPVTTTLMGIGAFDEHHPLSLGMLGMHGTAYANFAVTDCDLLI 309
                                               ********************************************************************* PP

                                 TIGR00118 272 avGarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee.....ekk 335
                                               +vGarfddrvtg+l++fa++ak+ihididPae+gkn+  ++pivGd++kvl +ll++ k++      ++
  lcl|NCBI__GCF_000204075.1:WP_011319511.1 310 CVGARFDDRVTGKLDEFASRAKVIHIDIDPAEVGKNRIPEVPIVGDVRKVLLDLLRRCKQTgakntPNQ 378
                                               *********************************************************999888775555 PP

                                 TIGR00118 336 ekeWlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfi 404
                                               ++eWl+ i++w+++y+l + ++ +si Pq+vi e+  +++ +a++ttdvGqhqmwaaqf+k+  pr++i
  lcl|NCBI__GCF_000204075.1:WP_011319511.1 379 NQEWLNLINRWREDYPLVIPQHPDSIPPQEVIVEVGSQAP-HAFYTTDVGQHQMWAAQFLKNG-PRRWI 445
                                               666************************************9.7*******************98.***** PP

                                 TIGR00118 405 tsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqW 473
                                               +s+GlGtmGfGlPaa+Gakva p+e+v++++Gd+sfqm lqel t+++y+i+vk+vilnn ++Gmv+qW
  lcl|NCBI__GCF_000204075.1:WP_011319511.1 446 SSAGLGTMGFGLPAAIGAKVAFPDEQVICISGDASFQMCLQELGTASQYGINVKTVILNNGWQGMVRQW 514
                                               ********************************************************************* PP

                                 TIGR00118 474 qelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlP 542
                                               q+ f+ erys ++++ ++pd++ la+ayG+kgi ++++e+l+++++++l+ ++pv+ldv+v k+e+++P
  lcl|NCBI__GCF_000204075.1:WP_011319511.1 515 QQAFHGERYSCSNMEVGMPDVELLAKAYGIKGIVVTQREQLKDAIAQMLAYDGPVILDVRVTKDENCYP 583
                                               ********************************************************************* PP

                                 TIGR00118 543 mvapGagldelve 555
                                               mvapG++++++++
  lcl|NCBI__GCF_000204075.1:WP_011319511.1 584 MVAPGKSNAQMIG 596
                                               ***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (632 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: 10.75
//
[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