Alignments for a candidate for leuB in Phaeobacter inhibens BS107

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.28453.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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.23
//
[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:

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