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

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.7540.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: 8.97
//
[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