Alignments for a candidate for leuB in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuB in Dinoroseobacter shibae DFL-12

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate 3606650 Dshi_0081 3-isopropylmalate dehydrogenase (RefSeq)

Query= BRENDA::P24404
         (370 letters)



>FitnessBrowser__Dino:3606650
          Length = 368

 Score =  446 bits (1147), Expect = e-130
 Identities = 235/368 (63%), Positives = 279/368 (75%), Gaps = 3/368 (0%)

Query: 1   MTVRSLFLLPGDGIGPEAMTEVRKLIEYMNSAHNAGFTVSEGLVGGSAYDAHGVAISDAD 60
           M+  SL +L GDGIGPE M EVRK+I++  +  +  F VSE LVGG+AYD HGV ++D  
Sbjct: 1   MSTASLLILAGDGIGPEVMAEVRKIIDWYGAKRDLAFDVSEDLVGGAAYDVHGVPLADET 60

Query: 61  MEKALAADAILFGAVGGPKWDGVPYEHRPEAGLLRLRKDLELFANLRPAICYPALAAASS 120
           M KA A DA+L GAVGGPK+D + +  +PE GLLRLRK+++LFANLRPA C+ ALA  SS
Sbjct: 61  MAKAQAVDAVLLGAVGGPKYDTLDFSLKPERGLLRLRKEMDLFANLRPAQCFDALADFSS 120

Query: 121 LKPELVEGLDILIVRELTGGVYFGEPKQIIDLGNGQKRGIDTQIYDTFEIERIASVAFEL 180
           LK ++V GLDI+IVRELT GVYFGEP+ I   GN ++ GI+TQ Y   EI R+A  AFEL
Sbjct: 121 LKKDIVAGLDIMIVRELTSGVYFGEPRGIHKEGN-ERVGINTQRYTESEIARVARSAFEL 179

Query: 181 ARSRDNRVCSMEKRNVMKSGVLWNQVVTETHAAKYKDVQLEHMLADAGGMQLVRKPKQFD 240
           A+ R N+VCSMEK NVM+SG+LW  VVTE HAA+Y DV+L HM ADAG MQLVR PKQFD
Sbjct: 180 AKKRGNKVCSMEKANVMESGILWRDVVTEIHAAEYADVELSHMYADAGAMQLVRAPKQFD 239

Query: 241 VIVTDNLFGDMLSDVAAMLTGSLGMLPSASLGAPDAKTGKRKAMYEPVHGSAPDIAGKSI 300
           VIVTDNLFGD+LSD AAMLTGSLGMLPSASLG P  + G+ KA+YEPVHGSAPDIAG+  
Sbjct: 240 VIVTDNLFGDLLSDAAAMLTGSLGMLPSASLGLP-MENGRPKALYEPVHGSAPDIAGQGK 298

Query: 301 ANPIAMIASFAMCLRYSFNMVDEATKLEAAIANVLDKGIRTADIMADG-CRQVGTSDMGD 359
           ANP A I SFAM LRYSF+   EA +LEAA+  VL +GIRTAD+M  G      TS MGD
Sbjct: 299 ANPCACILSFAMALRYSFDQGAEADRLEAAVNQVLAQGIRTADLMQAGDTAPASTSQMGD 358

Query: 360 AVLAEFKA 367
           AV+A   A
Sbjct: 359 AVIAALDA 366


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: 448
Number of extensions: 14
Number of successful extensions: 4
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: 368
Length adjustment: 30
Effective length of query: 340
Effective length of database: 338
Effective search space:   114920
Effective search space used:   114920
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 3606650 Dshi_0081 (3-isopropylmalate dehydrogenase (RefSeq))
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.3280.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.4e-144  467.4   0.0   1.6e-144  467.2   0.0    1.0  1  lcl|FitnessBrowser__Dino:3606650  Dshi_0081 3-isopropylmalate dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3606650  Dshi_0081 3-isopropylmalate dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  467.2   0.0  1.6e-144  1.6e-144       3     348 ..       7     359 ..       5     360 .. 0.97

  Alignments for each domain:
  == domain 1  score: 467.2 bits;  conditional E-value: 1.6e-144
                         TIGR00169   3 avLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGGpkWdnl 79 
                                        +L+GDgiGpev+ae  k+++    + +l+++ +e l+GGaa d +g Pl++et+++++++davLlgavGGpk+d+l
  lcl|FitnessBrowser__Dino:3606650   7 LILAGDGIGPEVMAEVRKIIDWYGAKRDLAFDVSEDLVGGAAYDVHGVPLADETMAKAQAVDAVLLGAVGGPKYDTL 83 
                                       68*************************************************************************** PP

                         TIGR00169  80 prdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYfGepkereeaeeekkald 156
                                         + +Pe+gLL+lrke+dlfanLrPa+ f++L ++s+lk++iv g+D+++vreLt+G+YfGep++++++++e+ +++
  lcl|FitnessBrowser__Dino:3606650  84 DFSLKPERGLLRLRKEMDLFANLRPAQCFDALADFSSLKKDIVAGLDIMIVRELTSGVYFGEPRGIHKEGNERVGIN 160
                                       ***************************************************************************** PP

                         TIGR00169 157 tekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiak.eyPdvelehlyiDnaamqLvksPeq 232
                                       t++Yt++ei r+ar afela+kr +kv+s++kanv+es++lWr++v+ei+  ey dvel+h+y D+ amqLv++P+q
  lcl|FitnessBrowser__Dino:3606650 161 TQRYTESEIARVARSAFELAKKRGNKVCSMEKANVMESGILWRDVVTEIHAaEYADVELSHMYADAGAMQLVRAPKQ 237
                                       *************************************************999************************* PP

                         TIGR00169 233 ldvvvtsnlfGDilsDeasvitGslGlLPsaslss.....kglalfepvhgsapdiagkgianpiaailsaalllry 304
                                       +dv+vt+nlfGD+lsD a+++tGslG+LPsasl+      + +al+epvhgsapdiag+g anp+a ils a+ lry
  lcl|FitnessBrowser__Dino:3606650 238 FDVIVTDNLFGDLLSDAAAMLTGSLGMLPSASLGLpmengRPKALYEPVHGSAPDIAGQGKANPCACILSFAMALRY 314
                                       *********************************98777778899********************************* PP

                         TIGR00169 305 slnleeaaeaieaavkkvleegkrtedlasea.ttavstkeveee 348
                                       s+++  +a+++eaav++vl++g+rt+dl++ + t+ +st+++++ 
  lcl|FitnessBrowser__Dino:3606650 315 SFDQGAEADRLEAAVNQVLAQGIRTADLMQAGdTAPASTSQMGDA 359
                                       ***************************988652667888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (368 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: 00:00:00.01
# Mc/sec: 11.10
//
[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