GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Acidovorax sp. GW101-3H11

Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 (characterized)
to candidate Ac3H11_1528 3-isopropylmalate dehydrogenase (EC 1.1.1.85)

Query= SwissProt::Q56268
         (358 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1528
          Length = 357

 Score =  403 bits (1036), Expect = e-117
 Identities = 219/358 (61%), Positives = 261/358 (72%), Gaps = 10/358 (2%)

Query: 3   KIAIFAGDGIGPEIVAAARQVLDAVDQAAHLGLRCTEGLVGGAALDASDDPLPAASLQLA 62
           KIA+  GDGIG EIVA A +VL A+D    L       LVGGAA +A   PLP ++L+LA
Sbjct: 2   KIAVLPGDGIGTEIVAEAVKVLKALD----LKFEMESALVGGAAYEAHGHPLPESTLKLA 57

Query: 63  MAADAVILGAVGGPRWDAYPPAKRPEQGLLRLRKGLDLYANLRPAQIFPQLLDASPLRPE 122
             ADA++ GAVG  ++D      RPEQ +L LRK L L+AN RPA  + QL+ AS L+PE
Sbjct: 58  KEADAILFGAVGDWKYDKLDRPLRPEQAILGLRKNLGLFANFRPAICYEQLVGASSLKPE 117

Query: 123 LVRDVDILVVRELTGDIYFGQPRGLEV-----IDGKRRGFNTMVYDEDEIRRIAHVAFRA 177
           L+  +DIL++RELTGDIYFGQPRG  V       G    F+TM Y   EI RIAHVAF+A
Sbjct: 118 LIAGLDILIIRELTGDIYFGQPRGRRVATDGHFPGAEEAFDTMRYSRPEIERIAHVAFQA 177

Query: 178 AQGRRKQLCSVDKANVLETTRLWREVVTEVARDYPDVRLSHMYVDNAAMQLIRAPAQFDV 237
           A+ R K++ SVDKANVLET + W++VVT+V ++YPDV L HMYVDNAAMQL++AP  FDV
Sbjct: 178 ARKRNKKVTSVDKANVLETFQFWKDVVTDVHKEYPDVELQHMYVDNAAMQLVKAPKAFDV 237

Query: 238 LLTGNMFGDILSDEASQLTGSIGMLPSASL-GEGRAMYEPIHGSAPDIAGQDKANPLATI 296
           ++TGNMFGDILSDEAS LTGSIGMLPSASL    + +YEP HGSAPDIAG+  ANPLATI
Sbjct: 238 VVTGNMFGDILSDEASMLTGSIGMLPSASLNSSNQGLYEPSHGSAPDIAGKGVANPLATI 297

Query: 297 LSVAMMLRHSLNAEPWAQRVEAAVQRVLDQGLRTADIAAPGTPVIGTKAMGAAVVNAL 354
           LS AMMLR SLN E  AQR+EAAVQ+VL QGLRT DI + GT  +GT  MG AVV AL
Sbjct: 298 LSAAMMLRFSLNQEAAAQRIEAAVQKVLAQGLRTPDIYSEGTTKVGTAQMGDAVVKAL 355


Lambda     K      H
   0.320    0.137    0.396 

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: 392
Number of extensions: 13
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: 358
Length of database: 357
Length adjustment: 29
Effective length of query: 329
Effective length of database: 328
Effective search space:   107912
Effective search space used:   107912
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 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate Ac3H11_1528 (3-isopropylmalate dehydrogenase (EC 1.1.1.85))
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.15855.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   7.9e-157  507.7   0.0   9.1e-157  507.5   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1528  3-isopropylmalate dehydrogenase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1528  3-isopropylmalate dehydrogenase (EC 1.1.1.85)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  507.5   0.0  9.1e-157  9.1e-157       1     348 [.       2     350 ..       2     351 .. 0.97

  Alignments for each domain:
  == domain 1  score: 507.5 bits;  conditional E-value: 9.1e-157
                                        TIGR00169   1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkacke 62 
                                                      kiavLpGDgiG e+vaea+kvLka+    +lk+e+e+al+GGaa +a+g+Plpe tlk +ke
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1528   2 KIAVLPGDGIGTEIVAEAVKVLKAL----DLKFEMESALVGGAAYEAHGHPLPESTLKLAKE 59 
                                                      79*********************98....589999*************************** PP

                                        TIGR00169  63 adavLlgavGGpkWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkg 124
                                                      ada+L+gavG  k+d+l r  rPe+++L lrk+l+lfan+rPa  +++L+ +s+lk+e++ g
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1528  60 ADAILFGAVGDWKYDKLDRPLRPEQAILGLRKNLGLFANFRPAICYEQLVGASSLKPELIAG 121
                                                      ************************************************************** PP

                                        TIGR00169 125 vDlvvvreLtgGiYfGepkereeaee.....ekkaldtekYtkeeieriarvafelarkrrk 181
                                                      +D++++reLtg iYfG+p++r+ a++      ++a+dt++Y+++eieria+vaf++arkr+k
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1528 122 LDILIIRELTGDIYFGQPRGRRVATDghfpgAEEAFDTMRYSRPEIERIAHVAFQAARKRNK 183
                                                      ********************99876433445689**************************** PP

                                        TIGR00169 182 kvtsvDkanvLessrlWrktveeiakeyPdvelehlyiDnaamqLvksPeqldvvvtsnlfG 243
                                                      kvtsvDkanvLe+ ++W+++v++++keyPdvel+h+y+DnaamqLvk+P+ +dvvvt+n+fG
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1528 184 KVTSVDKANVLETFQFWKDVVTDVHKEYPDVELQHMYVDNAAMQLVKAPKAFDVVVTGNMFG 245
                                                      ************************************************************** PP

                                        TIGR00169 244 DilsDeasvitGslGlLPsaslsskglalfepvhgsapdiagkgianpiaailsaalllrys 305
                                                      DilsDeas++tGs+G+LPsasl+s+ ++l+ep hgsapdiagkg+anp+a+ilsaa++lr s
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1528 246 DILSDEASMLTGSIGMLPSASLNSSNQGLYEPSHGSAPDIAGKGVANPLATILSAAMMLRFS 307
                                                      ************************************************************** PP

                                        TIGR00169 306 lnleeaaeaieaavkkvleegkrtedlaseattavstkeveee 348
                                                      ln+e aa++ieaav+kvl++g rt+d++se+tt+v+t+++++ 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1528 308 LNQEAAAQRIEAAVQKVLAQGLRTPDIYSEGTTKVGTAQMGDA 350
                                                      ****************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (357 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: 6.89
//
[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