Alignments for a candidate for leuB in Epibacterium ulvae U95

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuB in Epibacterium ulvae U95

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate WP_090219905.1 CV091_RS15535 3-isopropylmalate dehydrogenase

Query= BRENDA::P24404
         (370 letters)



>NCBI__GCF_002796795.1:WP_090219905.1
          Length = 367

 Score =  434 bits (1117), Expect = e-126
 Identities = 227/364 (62%), Positives = 278/364 (76%), Gaps = 4/364 (1%)

Query: 5   SLFLLPGDGIGPEAMTEVRKLIEYMNSAHNAGFTVSEGLVGGSAYDAHGVAISDADMEKA 64
           S+ +LPGDGIGPE MTEVRK+I +     +  F VSE LVGG+AYD HGV ++D  M KA
Sbjct: 5   SILILPGDGIGPEVMTEVRKIIGWFGEKRDISFDVSEDLVGGAAYDKHGVPLADETMAKA 64

Query: 65  LAADAILFGAVGGPKWDGVPYEHRPEAGLLRLRKDLELFANLRPAICYPALAAASSLKPE 124
             ADA+L GAVGGPK+D + +  +PE GLLRLRK+++L++NLRPA C+ ALA  SSLK +
Sbjct: 65  QEADAVLLGAVGGPKYDDLDFSVKPERGLLRLRKEMDLYSNLRPAQCFDALADFSSLKKD 124

Query: 125 LVEGLDILIVRELTGGVYFGEPKQIIDLGNGQKRGIDTQIYDTFEIERIASVAFELARSR 184
           +V GLDI+IVRELT GVYFGEP+ I + GN ++ GI+TQ Y   EIER A  AFELA  R
Sbjct: 125 IVAGLDIMIVRELTSGVYFGEPRGIFEEGN-ERVGINTQRYTESEIERAARSAFELAMRR 183

Query: 185 DNRVCSMEKRNVMKSGVLWNQVVTETHAAKYKDVQLEHMLADAGGMQLVRKPKQFDVIVT 244
             +VCSMEK NVM+SG+LW +VVT   AA Y +V+L HM AD G MQLVR PKQFDVI+T
Sbjct: 184 GKKVCSMEKANVMESGILWREVVTRV-AADYPEVELSHMYADNGAMQLVRAPKQFDVILT 242

Query: 245 DNLFGDMLSDVAAMLTGSLGMLPSASLGAPDAKTGKRKAMYEPVHGSAPDIAGKSIANPI 304
           DNLFGD+LSD AAMLTGSLGMLPSASLGAP  + G+ KA+YEPVHGSAPDI G+  ANPI
Sbjct: 243 DNLFGDILSDCAAMLTGSLGMLPSASLGAP-MENGRPKALYEPVHGSAPDITGQGKANPI 301

Query: 305 AMIASFAMCLRYSFNMVDEATKLEAAIANVLDKGIRTADIMA-DGCRQVGTSDMGDAVLA 363
           A + SFAM LRYSF++  EA +LEAA+  VL  G+RTAD++A +G   V TS+MGDA++A
Sbjct: 302 ACVLSFAMALRYSFDLGAEADRLEAAVEKVLADGVRTADLLASEGVSPVSTSEMGDAIVA 361

Query: 364 EFKA 367
              A
Sbjct: 362 ALNA 365


Lambda     K      H
   0.319    0.135    0.387 

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: 449
Number of extensions: 19
Number of successful extensions: 5
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: 370
Length of database: 367
Length adjustment: 30
Effective length of query: 340
Effective length of database: 337
Effective search space:   114580
Effective search space used:   114580
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate WP_090219905.1 CV091_RS15535 (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.3074489.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.9e-148  480.1   0.0   2.2e-148  479.9   0.0    1.0  1  NCBI__GCF_002796795.1:WP_090219905.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002796795.1:WP_090219905.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  479.9   0.0  2.2e-148  2.2e-148       2     348 ..       6     358 ..       5     359 .. 0.98

  Alignments for each domain:
  == domain 1  score: 479.9 bits;  conditional E-value: 2.2e-148
                             TIGR00169   2 iavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGGp 74 
                                           i +LpGDgiGpev++e  k++    e+ +++++ +e l+GGaa d++g Pl++et+++++eadavLlgavGGp
  NCBI__GCF_002796795.1:WP_090219905.1   6 ILILPGDGIGPEVMTEVRKIIGWFGEKRDISFDVSEDLVGGAAYDKHGVPLADETMAKAQEADAVLLGAVGGP 78 
                                           889********************************************************************** PP

                             TIGR00169  75 kWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYfGepkeree 147
                                           k+d+l  +v+Pe+gLL+lrke+dl++nLrPa+ f++L ++s+lk++iv g+D+++vreLt+G+YfGep++++e
  NCBI__GCF_002796795.1:WP_090219905.1  79 KYDDLDFSVKPERGLLRLRKEMDLYSNLRPAQCFDALADFSSLKKDIVAGLDIMIVRELTSGVYFGEPRGIFE 151
                                           ************************************************************************* PP

                             TIGR00169 148 aeeekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPdvelehlyiD 220
                                           +++e+ +++t++Yt++eier ar afela++r kkv+s++kanv+es++lWr++v+ +a +yP+vel+h+y D
  NCBI__GCF_002796795.1:WP_090219905.1 152 EGNERVGINTQRYTESEIERAARSAFELAMRRGKKVCSMEKANVMESGILWREVVTRVAADYPEVELSHMYAD 224
                                           ************************************************************************* PP

                             TIGR00169 221 naamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslss.....kglalfepvhgsapdiagkgi 288
                                           n amqLv++P+q+dv++t+nlfGDilsD a+++tGslG+LPsasl+      + +al+epvhgsapdi+g+g 
  NCBI__GCF_002796795.1:WP_090219905.1 225 NGAMQLVRAPKQFDVILTDNLFGDILSDCAAMLTGSLGMLPSASLGApmengRPKALYEPVHGSAPDITGQGK 297
                                           **********************************************9898888899***************** PP

                             TIGR00169 289 anpiaailsaalllryslnleeaaeaieaavkkvleegkrtedl.aseattavstkeveee 348
                                           anpia +ls a+ lrys++l  +a+++eaav+kvl++g rt+dl ase+   vst+e+++ 
  NCBI__GCF_002796795.1:WP_090219905.1 298 ANPIACVLSFAMALRYSFDLGAEADRLEAAVEKVLADGVRTADLlASEGVSPVSTSEMGDA 358
                                           *****************************************99725677789999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (367 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 22.16
//
[ok]

This GapMind analysis is from Jul 26 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