Alignments for a candidate for leuB in Malonomonas rubra DSM 5091

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuB in Malonomonas rubra DSM 5091

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate WP_072905195.1 BUB13_RS02510 3-isopropylmalate dehydrogenase

Query= BRENDA::D2YZL2
         (364 letters)



>NCBI__GCF_900142125.1:WP_072905195.1
          Length = 362

 Score =  452 bits (1162), Expect = e-132
 Identities = 220/355 (61%), Positives = 282/355 (79%)

Query: 2   SYQIAVLAGDGIGPEVMAEARKVLAAVEKRFDLSIEYSEYDVGGAAIDNHGCPLPEATLK 61
           +Y++AVL GDGIGPEVMAEA KVL A+EK++D+S E +  +VGGA IDN G  LP++T++
Sbjct: 4   TYKVAVLPGDGIGPEVMAEALKVLDAIEKKYDVSFERTTANVGGAGIDNEGKALPDSTVE 63

Query: 62  GCEAADAVLFGSVGGPKWEHLPPNDQPERGALLPLRGHFELFCNMRPAKLHPGLEHMSPL 121
            C+A+DA+LFGSVGGPKWE LPP++QPERGALLPLR  F LFCN+RPA + P L   S L
Sbjct: 64  ICKASDAILFGSVGGPKWESLPPDEQPERGALLPLRKIFGLFCNLRPAIIFPALTGASSL 123

Query: 122 RSDISEKGFDILCVRELTGGIYFGKPKGRQGEGENEEAFDTMRYSRKEIRRIAKIAFESA 181
           + ++ E GFD+L VRELTGGIYF +PKG +GEG     FDTM+YS  E+ RI  +AFE+A
Sbjct: 124 KEEVIEGGFDLLVVRELTGGIYFAEPKGIEGEGAARTGFDTMKYSDAEVERITHVAFEAA 183

Query: 182 QGRRKKVTSVDKANVLACSVLWREVVEEVAKDYPDVELEHIYIDNATMQLLRRPNEFDVM 241
           + R KKV S+DKANVL+ SVLWREVVE VAK+YPDVEL H+Y+DNA MQL++ P +FDVM
Sbjct: 184 RKRGKKVCSIDKANVLSTSVLWREVVERVAKEYPDVELSHMYVDNAAMQLVKWPKQFDVM 243

Query: 242 LCSNLFGDIVSDEIAMLTGSMGLLASISMNSQGFGMYEPAGGSAPDIAGQGIANPVAQIL 301
           LC N+FGDI+SDE AMLTGS+G+L S S+    FGMYEP+GGSAPDIAGQGIANP+AQIL
Sbjct: 244 LCGNMFGDIISDEAAMLTGSLGMLPSASLAEGSFGMYEPSGGSAPDIAGQGIANPIAQIL 303

Query: 302 SAALLLRHSLKLEDAALAIEAAVSKALSDGYLTCELLPASERSQAKSTSQMGDYI 356
           SA+++LR+S  + +AA AI+AAV K L+DGY T ++   +   +  +T+++GD I
Sbjct: 304 SASMMLRYSFGMIEAADAIDAAVEKTLNDGYRTGDIYQGTASEKKVNTAEIGDAI 358


Lambda     K      H
   0.317    0.135    0.390 

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: 480
Number of extensions: 15
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: 364
Length of database: 362
Length adjustment: 29
Effective length of query: 335
Effective length of database: 333
Effective search space:   111555
Effective search space used:   111555
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_072905195.1 BUB13_RS02510 (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.25644.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.7e-161  523.0   0.0   1.9e-161  522.8   0.0    1.0  1  lcl|NCBI__GCF_900142125.1:WP_072905195.1  BUB13_RS02510 3-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900142125.1:WP_072905195.1  BUB13_RS02510 3-isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  522.8   0.0  1.9e-161  1.9e-161       1     347 [.       6     356 ..       6     358 .. 0.97

  Alignments for each domain:
  == domain 1  score: 522.8 bits;  conditional E-value: 1.9e-161
                                 TIGR00169   1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlg 69 
                                               k+avLpGDgiGpev+aealkvL+a+e+++++++e  +a++GGa id+ g+ lp+ t++ ck++da+L+g
  lcl|NCBI__GCF_900142125.1:WP_072905195.1   6 KVAVLPGDGIGPEVMAEALKVLDAIEKKYDVSFERTTANVGGAGIDNEGKALPDSTVEICKASDAILFG 74 
                                               79******************************************************************* PP

                                 TIGR00169  70 avGGpkWdnlprdvrPek.gLLklrkeldlfanLrPaklfksLeklsplkeeiv.kgvDlvvvreLtgG 136
                                               +vGGpkW++lp+d +Pe+ +LL+lrk ++lf+nLrPa +f++L+ +s+lkee++  g+Dl+vvreLtgG
  lcl|NCBI__GCF_900142125.1:WP_072905195.1  75 SVGGPKWESLPPDEQPERgALLPLRKIFGLFCNLRPAIIFPALTGASSLKEEVIeGGFDLLVVRELTGG 143
                                               ******************88**********************************558************ PP

                                 TIGR00169 137 iYfGepkereeaeeekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveei 205
                                               iYf epk++e+++  ++++dt+kY+  e+eri++vafe+arkr kkv+s+DkanvL +s lWr++ve +
  lcl|NCBI__GCF_900142125.1:WP_072905195.1 144 IYFAEPKGIEGEGAARTGFDTMKYSDAEVERITHVAFEAARKRGKKVCSIDKANVLSTSVLWREVVERV 212
                                               ********************************************************************* PP

                                 TIGR00169 206 akeyPdvelehlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfe 274
                                               akeyPdvel+h+y+DnaamqLvk P+q+dv++++n+fGDi+sDea+++tGslG+LPsasl++  ++++e
  lcl|NCBI__GCF_900142125.1:WP_072905195.1 213 AKEYPDVELSHMYVDNAAMQLVKWPKQFDVMLCGNMFGDIISDEAAMLTGSLGMLPSASLAEGSFGMYE 281
                                               ********************************************************************* PP

                                 TIGR00169 275 pvhgsapdiagkgianpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseat..tavs 341
                                               p +gsapdiag+gianpia+ilsa+++lrys+++ eaa+ai+aav+k+l++g+rt d+++ ++  ++v 
  lcl|NCBI__GCF_900142125.1:WP_072905195.1 282 PSGGSAPDIAGQGIANPIAQILSASMMLRYSFGMIEAADAIDAAVEKTLNDGYRTGDIYQGTAseKKVN 350
                                               **********************************************************98654115667 PP

                                 TIGR00169 342 tkevee 347
                                               t+e+++
  lcl|NCBI__GCF_900142125.1:WP_072905195.1 351 TAEIGD 356
                                               777766 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: 00:00:00.01
# Mc/sec: 10.26
//
[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