GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Phaeobacter inhibens BS107

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate GFF2936 PGA1_c29830 3-isopropylmalate dehydrogenase LeuB

Query= BRENDA::P24404
         (370 letters)



>FitnessBrowser__Phaeo:GFF2936
          Length = 367

 Score =  423 bits (1088), Expect = e-123
 Identities = 222/364 (60%), Positives = 273/364 (75%), Gaps = 4/364 (1%)

Query: 1   MTVRSLFLLPGDGIGPEAMTEVRKLIEYMNSAHNAGFTVSEGLVGGSAYDAHGVAISDAD 60
           M+  S+ +LPGDGIGPE M EVRK+I +     +  F VSE LVGG+AYD HG  ++D  
Sbjct: 1   MSNPSILILPGDGIGPEVMAEVRKVISWYGEKRDLQFDVSEDLVGGAAYDVHGKPLADET 60

Query: 61  MEKALAADAILFGAVGGPKWDGVPYEHRPEAGLLRLRKDLELFANLRPAICYPALAAASS 120
           MEKA   DA+L GAVGGPK+D + +  +PE GLLRLRK+++L++NLRPA C+ ALA  SS
Sbjct: 61  MEKAQEVDAVLLGAVGGPKYDDLDFSVKPERGLLRLRKEMDLYSNLRPAQCFDALADFSS 120

Query: 121 LKPELVEGLDILIVRELTGGVYFGEPKQIIDLGNGQKRGIDTQIYDTFEIERIASVAFEL 180
           LK ++V GLDI+IVRELT GVYFGEP+ I + GN ++ GI+TQ Y   EIER A  AFEL
Sbjct: 121 LKKDIVAGLDIMIVRELTSGVYFGEPRGIFEEGN-ERVGINTQRYTESEIERAARSAFEL 179

Query: 181 ARSRDNRVCSMEKRNVMKSGVLWNQVVTETHAAKYKDVQLEHMLADAGGMQLVRKPKQFD 240
           A  R+ ++CSMEK NVM+SG+LW +VVT   AA Y +V+L HM AD G MQLVR PKQFD
Sbjct: 180 AMRRNKKLCSMEKANVMESGILWREVVTRV-AADYPEVELSHMYADNGAMQLVRAPKQFD 238

Query: 241 VIVTDNLFGDMLSDVAAMLTGSLGMLPSASLGAPDAKTGKRKAMYEPVHGSAPDIAGKSI 300
           VI+TDNLFGD+LSD AAMLTGSLGMLPSASLGAP A  G+ KA+YEPVHGSAPDIAG+  
Sbjct: 239 VILTDNLFGDILSDCAAMLTGSLGMLPSASLGAPMA-NGRPKALYEPVHGSAPDIAGQGK 297

Query: 301 ANPIAMIASFAMCLRYSFNMVDEATKLEAAIANVLDKGIRTADIMA-DGCRQVGTSDMGD 359
           ANPIA I SFAM LRYSF+   EA +LE A+  VL  G RT D++  +G   + TS+MGD
Sbjct: 298 ANPIACILSFAMALRYSFDQGSEADRLETAVEKVLADGHRTGDLLGEEGVSPISTSEMGD 357

Query: 360 AVLA 363
            ++A
Sbjct: 358 VIIA 361


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: 447
Number of extensions: 17
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 GFF2936 PGA1_c29830 (3-isopropylmalate dehydrogenase LeuB)
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.4682.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   3.6e-150  485.8   0.0   4.1e-150  485.6   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF2936  PGA1_c29830 3-isopropylmalate de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF2936  PGA1_c29830 3-isopropylmalate dehydrogenase LeuB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  485.6   0.0  4.1e-150  4.1e-150       2     348 ..       6     358 ..       5     359 .. 0.97

  Alignments for each domain:
  == domain 1  score: 485.6 bits;  conditional E-value: 4.1e-150
                          TIGR00169   2 iavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGGpkWd 77 
                                        i +LpGDgiGpev+ae  kv+    e+ +l+++ +e l+GGaa d +g+Pl++et+++++e+davLlgavGGpk+d
  lcl|FitnessBrowser__Phaeo:GFF2936   6 ILILPGDGIGPEVMAEVRKVISWYGEKRDLQFDVSEDLVGGAAYDVHGKPLADETMEKAQEVDAVLLGAVGGPKYD 81 
                                        889************************************************************************* PP

                          TIGR00169  78 nlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYfGepkereeaeeekk 153
                                        +l  +v+Pe+gLL+lrke+dl++nLrPa+ f++L ++s+lk++iv g+D+++vreLt+G+YfGep++++e+++e+ 
  lcl|FitnessBrowser__Phaeo:GFF2936  82 DLDFSVKPERGLLRLRKEMDLYSNLRPAQCFDALADFSSLKKDIVAGLDIMIVRELTSGVYFGEPRGIFEEGNERV 157
                                        **************************************************************************** PP

                          TIGR00169 154 aldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPdvelehlyiDnaamqLvks 229
                                        +++t++Yt++eier ar afela++r+kk++s++kanv+es++lWr++v+ +a +yP+vel+h+y Dn amqLv++
  lcl|FitnessBrowser__Phaeo:GFF2936 158 GINTQRYTESEIERAARSAFELAMRRNKKLCSMEKANVMESGILWREVVTRVAADYPEVELSHMYADNGAMQLVRA 233
                                        **************************************************************************** PP

                          TIGR00169 230 PeqldvvvtsnlfGDilsDeasvitGslGlLPsaslss.....kglalfepvhgsapdiagkgianpiaailsaal 300
                                        P+q+dv++t+nlfGDilsD a+++tGslG+LPsasl+      + +al+epvhgsapdiag+g anpia ils a+
  lcl|FitnessBrowser__Phaeo:GFF2936 234 PKQFDVILTDNLFGDILSDCAAMLTGSLGMLPSASLGApmangRPKALYEPVHGSAPDIAGQGKANPIACILSFAM 309
                                        *************************************9998888899***************************** PP

                          TIGR00169 301 llryslnleeaaeaieaavkkvleegkrtedlaseat.tavstkeveee 348
                                         lrys+++  +a+++e+av+kvl++g+rt dl +e++    st+e++++
  lcl|FitnessBrowser__Phaeo:GFF2936 310 ALRYSFDQGSEADRLETAVEKVLADGHRTGDLLGEEGvSPISTSEMGDV 358
                                        ******************************9877664166788888776 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.93
//
[ok]

This GapMind analysis is from Apr 09 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:

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:

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:

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:

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