GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Azospirillum brasilense Sp245

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate AZOBR_RS14130 AZOBR_RS14130 3-isopropylmalate dehydrogenase

Query= BRENDA::P24404
         (370 letters)



>FitnessBrowser__azobra:AZOBR_RS14130
          Length = 371

 Score =  472 bits (1214), Expect = e-138
 Identities = 235/368 (63%), Positives = 291/368 (79%), Gaps = 2/368 (0%)

Query: 4   RSLFLLPGDGIGPEAMTEVRKLIEYMNSAHNAGFTVSEGLVGGSAYDAHGVAISDADMEK 63
           + L  LPGDGIGPE M +VR++I++++   N  F V+EGLVGG+A DA+GV + D  +  
Sbjct: 5   KKLLFLPGDGIGPEVMRQVRRVIDWLDRKRNVTFDVTEGLVGGAAIDAYGVPLKDETLAD 64

Query: 64  ALAADAILFGAVGGPKWDG-VPYEHRPEAGLLRLRKDLELFANLRPAICYPALAAASSLK 122
           ALAADA++ GAVGGPKWD    Y  RPEAGLL LRK+L LFANLRPA+ + AL  AS+LK
Sbjct: 65  ALAADAVMLGAVGGPKWDNPTDYTKRPEAGLLSLRKELNLFANLRPAVVFDALVDASTLK 124

Query: 123 PELVEGLDILIVRELTGGVYFGEPKQIIDLGNGQKRGIDTQIYDTFEIERIASVAFELAR 182
            ++++GLDILIVRELTGGVYFGEP+ I D+GNG++RG++TQ+Y T EI R+A VAFELAR
Sbjct: 125 ADVIKGLDILIVRELTGGVYFGEPRGITDIGNGERRGVNTQVYTTSEIRRVARVAFELAR 184

Query: 183 SRDNRVCSMEKRNVMKSGVLWNQVVTETHAAKYKDVQLEHMLADAGGMQLVRKPKQFDVI 242
            R N++ SMEK NVM+SG+LW Q VT+ H  ++ DV LEHM AD G MQL++ PKQFDVI
Sbjct: 185 KRGNKLHSMEKANVMESGLLWRQEVTKLHQEEFSDVTLEHMYADNGAMQLLKNPKQFDVI 244

Query: 243 VTDNLFGDMLSDVAAMLTGSLGMLPSASLGAPDAKTGKRKAMYEPVHGSAPDIAGKSIAN 302
           VTDNLFGD+LSD AAM+TGSLGMLPSASLGAPDA  G+RKA+YEPVHGSAPDIAG+ +AN
Sbjct: 245 VTDNLFGDILSDEAAMMTGSLGMLPSASLGAPDA-NGQRKALYEPVHGSAPDIAGRDLAN 303

Query: 303 PIAMIASFAMCLRYSFNMVDEATKLEAAIANVLDKGIRTADIMADGCRQVGTSDMGDAVL 362
           P A + SFAMCLRYSFNM +EA  LE A+ NVL  G+RTADIMA G  +  T+ MGD++L
Sbjct: 304 PCATLLSFAMCLRYSFNMDEEAKMLEKAVQNVLSGGMRTADIMAPGMARCSTTVMGDSIL 363

Query: 363 AEFKALSA 370
            E   L++
Sbjct: 364 RELDKLAS 371


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: 450
Number of extensions: 11
Number of successful extensions: 3
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: 371
Length adjustment: 30
Effective length of query: 340
Effective length of database: 341
Effective search space:   115940
Effective search space used:   115940
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 AZOBR_RS14130 AZOBR_RS14130 (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.12927.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.1e-148  480.0   0.0   2.4e-148  479.8   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS14130  AZOBR_RS14130 3-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS14130  AZOBR_RS14130 3-isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  479.8   0.0  2.4e-148  2.4e-148       2     348 ..       7     361 ..       6     362 .. 0.98

  Alignments for each domain:
  == domain 1  score: 479.8 bits;  conditional E-value: 2.4e-148
                                 TIGR00169   2 iavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlga 70 
                                               +  LpGDgiGpev+ +  +v++ ++ + ++ ++  e l+GGaaida+g Pl +etl+ + +adav+lga
  lcl|FitnessBrowser__azobra:AZOBR_RS14130   7 LLFLPGDGIGPEVMRQVRRVIDWLDRKRNVTFDVTEGLVGGAAIDAYGVPLKDETLADALAADAVMLGA 75 
                                               5689***************************************************************** PP

                                 TIGR00169  71 vGGpkWdnlpr.dvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiY 138
                                               vGGpkWdn     +rPe gLL+lrkel+lfanLrPa +f++L+++s+lk++++kg+D+++vreLtgG+Y
  lcl|FitnessBrowser__azobra:AZOBR_RS14130  76 VGGPKWDNPTDyTKRPEAGLLSLRKELNLFANLRPAVVFDALVDASTLKADVIKGLDILIVRELTGGVY 144
                                               ********864368******************************************************* PP

                                 TIGR00169 139 fGepkereeaee.ekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeia 206
                                               fGep+++++ ++ e+++++t++Yt++ei+r+arvafelarkr +k+ s++kanv+es+ lWr+ v++++
  lcl|FitnessBrowser__azobra:AZOBR_RS14130 145 FGEPRGITDIGNgERRGVNTQVYTTSEIRRVARVAFELARKRGNKLHSMEKANVMESGLLWRQEVTKLH 213
                                               *********9999*******************************************************9 PP

                                 TIGR00169 207 k.eyPdvelehlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslss.....kg 269
                                               + e+ dv+leh+y Dn amqL+k+P+q+dv+vt+nlfGDilsDea+++tGslG+LPsasl+      ++
  lcl|FitnessBrowser__azobra:AZOBR_RS14130 214 QeEFSDVTLEHMYADNGAMQLLKNPKQFDVIVTDNLFGDILSDEAAMMTGSLGMLPSASLGApdangQR 282
                                               999**********************************************************99999999 PP

                                 TIGR00169 270 lalfepvhgsapdiagkgianpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseatt 338
                                               +al+epvhgsapdiag+++anp+a++ls a+ lrys+n++e+a+++e+av++vl+ g+rt+d++  + +
  lcl|FitnessBrowser__azobra:AZOBR_RS14130 283 KALYEPVHGSAPDIAGRDLANPCATLLSFAMCLRYSFNMDEEAKMLEKAVQNVLSGGMRTADIMAPGMA 351
                                               *******************************************************************99 PP

                                 TIGR00169 339 avstkeveee 348
                                               + st+ ++++
  lcl|FitnessBrowser__azobra:AZOBR_RS14130 352 RCSTTVMGDS 361
                                               9999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (371 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.15
//
[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