Alignments for a candidate for leuB in Trichormus variabilis ATCC 29413

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuB in Trichormus variabilis ATCC 29413

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate WP_011319729.1 AVA_RS15110 3-isopropylmalate dehydrogenase

Query= BRENDA::Q00412
         (355 letters)



>NCBI__GCF_000204075.1:WP_011319729.1
          Length = 362

 Score =  548 bits (1413), Expect = e-161
 Identities = 277/352 (78%), Positives = 306/352 (86%)

Query: 1   MTQNYRITLLSGDGIGPEIMAVAVDVLKAVGKQLDLNFEFKEALMGGVAIDATGEPLPEE 60
           MTQNYRITLL GDGIGPEIMAVAVDVLK VG+Q D+ F+F+EAL+GG AIDATGEPLP  
Sbjct: 1   MTQNYRITLLPGDGIGPEIMAVAVDVLKVVGQQFDIQFDFQEALIGGAAIDATGEPLPSA 60

Query: 61  SLQACRDSDAVLLAAIGGYKWDNLPRPERPETGLLALRAGLGLFANRARLLFCPHVLDAS 120
           +L  CR SDAVLLAAIGGYKWD+LP  +RPE GLL LRAGL LFAN       P ++DAS
Sbjct: 61  TLDTCRQSDAVLLAAIGGYKWDSLPPHQRPEGGLLGLRAGLELFANLRPAQILPQLIDAS 120

Query: 121 SLKREVVEGVDIMVVRELTGGIYFGQPKGIFETETGKNEGSNTMAYGESEIDRIGRVGFE 180
           +LKREVVEGVDIMVVRELTGGIYFG+P+GIF TETG+  G NTM Y ESEIDRIGR+ FE
Sbjct: 121 TLKREVVEGVDIMVVRELTGGIYFGKPRGIFTTETGEKRGVNTMVYTESEIDRIGRIAFE 180

Query: 181 TAKKRQGRLCSVDKANVLDVSQLWRDRIMALAADYPEVELSHLYVDNAAMQLVRWPKQFD 240
           TA+KR+G+LCSVDKANVLDVSQLWRDRI  L+ +YP+VELSHLYVDNAAMQLVR PKQFD
Sbjct: 181 TARKRRGKLCSVDKANVLDVSQLWRDRITKLSQEYPDVELSHLYVDNAAMQLVRAPKQFD 240

Query: 241 TIVTGNLFGDILSDAAAMLTGSIGMLPSASLGASGPGVFEPVHGSAPDIAGQDKANPLAQ 300
           TIVTGNLFGDILSDAAAMLTGSIGMLPSASLGASGPGVFEPVHGSAPDIAG DKANPLAQ
Sbjct: 241 TIVTGNLFGDILSDAAAMLTGSIGMLPSASLGASGPGVFEPVHGSAPDIAGLDKANPLAQ 300

Query: 301 VLSAAMMLRYGLDEPAASDPVEKAVLKVLDWGYPTGDIMSEGMKAVGCRKWG 352
           VLSAAMMLRY L++P A+D +E+AVL+VL+ G  TGDIMS GM  +GCR  G
Sbjct: 301 VLSAAMMLRYALNQPQAADKIEQAVLQVLEQGDRTGDIMSVGMNLLGCRAMG 352


Lambda     K      H
   0.318    0.137    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: 525
Number of extensions: 18
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: 355
Length of database: 362
Length adjustment: 29
Effective length of query: 326
Effective length of database: 333
Effective search space:   108558
Effective search space used:   108558
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate WP_011319729.1 AVA_RS15110 (3-isopropylmalate dehydrogenase)
to HMM TIGR00169 (leuB: 3-isopropylmalate dehydrogenase (EC 1.1.1.85))

# 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/TIGR00169.hmm
# target sequence database:        /tmp/gapView.285588.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00169  [M=349]
Accession:   TIGR00169
Description: leuB: 3-isopropylmalate dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     1e-164  533.6   0.0   1.2e-164  533.4   0.0    1.0  1  NCBI__GCF_000204075.1:WP_011319729.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000204075.1:WP_011319729.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  533.4   0.0  1.2e-164  1.2e-164       1     348 [.       6     354 ..       6     355 .. 0.99

  Alignments for each domain:
  == domain 1  score: 533.4 bits;  conditional E-value: 1.2e-164
                             TIGR00169   1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGG 73 
                                           +i++LpGDgiGpe++a a++vLk+v ++f+++++f+ealiGGaaidatgePlp +tl++c+++davLl+a+GG
  NCBI__GCF_000204075.1:WP_011319729.1   6 RITLLPGDGIGPEIMAVAVDVLKVVGQQFDIQFDFQEALIGGAAIDATGEPLPSATLDTCRQSDAVLLAAIGG 78 
                                           699********************************************************************** PP

                             TIGR00169  74 pkWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYfGepkere 146
                                           +kWd+lp+++rPe gLL lr  l+lfanLrPa++ ++L+++s+lk+e+v+gvD++vvreLtgGiYfG+p++++
  NCBI__GCF_000204075.1:WP_011319729.1  79 YKWDSLPPHQRPEGGLLGLRAGLELFANLRPAQILPQLIDASTLKREVVEGVDIMVVRELTGGIYFGKPRGIF 151
                                           ************************************************************************* PP

                             TIGR00169 147 eaee.ekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPdvelehly 218
                                            +e+ ek++++t++Yt++ei+ri r+afe+arkrr k++svDkanvL++s+lWr++++++ +eyPdvel+hly
  NCBI__GCF_000204075.1:WP_011319729.1 152 TTETgEKRGVNTMVYTESEIDRIGRIAFETARKRRGKLCSVDKANVLDVSQLWRDRITKLSQEYPDVELSHLY 224
                                           *9999******************************************************************** PP

                             TIGR00169 219 iDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvhgsapdiagkgianp 291
                                           +DnaamqLv++P+q+d++vt+nlfGDilsD a+++tGs+G+LPsasl+ +g ++fepvhgsapdiag + anp
  NCBI__GCF_000204075.1:WP_011319729.1 225 VDNAAMQLVRAPKQFDTIVTGNLFGDILSDAAAMLTGSIGMLPSASLGASGPGVFEPVHGSAPDIAGLDKANP 297
                                           ************************************************************************* PP

                             TIGR00169 292 iaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstkeveee 348
                                           +a++lsaa++lry+ln+++aa++ie+av +vle+g rt d++s + +  ++++++++
  NCBI__GCF_000204075.1:WP_011319729.1 298 LAQVLSAAMMLRYALNQPQAADKIEQAVLQVLEQGDRTGDIMSVGMNLLGCRAMGDS 354
                                           ********************************************9999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (362 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 19.49
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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 2024 update 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 original 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