Alignments for a candidate for leuB in Alicycliphilus denitrificans K601

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuB in Alicycliphilus denitrificans K601

Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 (characterized)
to candidate WP_013519946.1 ALIDE2_RS06510 3-isopropylmalate dehydrogenase

Query= SwissProt::Q56268
         (358 letters)



>NCBI__GCF_000204645.1:WP_013519946.1
          Length = 356

 Score =  400 bits (1029), Expect = e-116
 Identities = 220/358 (61%), Positives = 261/358 (72%), Gaps = 10/358 (2%)

Query: 3   KIAIFAGDGIGPEIVAAARQVLDAVDQAAHLGLRCTEGLVGGAALDASDDPLPAASLQLA 62
           KIA+  GDGIGPEIVA A +VL+A+D    L L      VGGAA + +  PLP ++L LA
Sbjct: 2   KIAVLPGDGIGPEIVAEAVKVLEALD----LKLEMETAPVGGAAYEVAGHPLPESTLGLA 57

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

Query: 123 LVRDVDILVVRELTGDIYFGQPRGLEV-----IDGKRRGFNTMVYDEDEIRRIAHVAFRA 177
           LV  +DIL++RELTGDIYFGQPRG          G    F+TM Y   EI RIA VAF A
Sbjct: 118 LVAGLDILIIRELTGDIYFGQPRGRRTAPDGHFPGAEEAFDTMRYSRPEIERIARVAFEA 177

Query: 178 AQGRRKQLCSVDKANVLETTRLWREVVTEVARDYPDVRLSHMYVDNAAMQLIRAPAQFDV 237
           A+ R K++ SVDKANVLET +LW++VVTEV +DYPDV+L HMYVDNAAMQL++AP  FDV
Sbjct: 178 ARKRSKRVTSVDKANVLETFQLWKDVVTEVHKDYPDVQLDHMYVDNAAMQLVKAPKAFDV 237

Query: 238 LLTGNMFGDILSDEASQLTGSIGMLPSASLGEGR-AMYEPIHGSAPDIAGQDKANPLATI 296
           ++TGNMFGDILSDEAS LTGSIGMLPSASL + +  +YEP HGSAPDIAG+  ANPLATI
Sbjct: 238 IVTGNMFGDILSDEASMLTGSIGMLPSASLNDKKQGLYEPSHGSAPDIAGKGVANPLATI 297

Query: 297 LSVAMMLRHSLNAEPWAQRVEAAVQRVLDQGLRTADIAAPGTPVIGTKAMGAAVVNAL 354
           LS AMMLR SL  E  A+R+EAAVQ+VL QGLRT DI + GT  +GT  MG AVVNAL
Sbjct: 298 LSAAMMLRFSLGQEEAARRIEAAVQKVLAQGLRTPDIHSEGTTRVGTVQMGDAVVNAL 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: 406
Number of extensions: 16
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: 356
Length adjustment: 29
Effective length of query: 329
Effective length of database: 327
Effective search space:   107583
Effective search space used:   107583
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 WP_013519946.1 ALIDE2_RS06510 (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.2779.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.2e-155  501.2   0.0   8.2e-155  501.0   0.0    1.0  1  lcl|NCBI__GCF_000204645.1:WP_013519946.1  ALIDE2_RS06510 3-isopropylmalate


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000204645.1:WP_013519946.1  ALIDE2_RS06510 3-isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  501.0   0.0  8.2e-155  8.2e-155       1     348 [.       2     350 ..       2     351 .. 0.97

  Alignments for each domain:
  == domain 1  score: 501.0 bits;  conditional E-value: 8.2e-155
                                 TIGR00169   1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlg 69 
                                               kiavLpGDgiGpe+vaea+kvL+a+    +lkle+e+a +GGaa +  g+Plpe tl  ++eada+L+g
  lcl|NCBI__GCF_000204645.1:WP_013519946.1   2 KIAVLPGDGIGPEIVAEAVKVLEAL----DLKLEMETAPVGGAAYEVAGHPLPESTLGLAREADAILFG 66 
                                               79********************987....699************************************* PP

                                 TIGR00169  70 avGGpkWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiY 138
                                               avG  k+d+l r  rPe+++L lrk+l+lfan+rPa  +++L+++s+lk+e+v g+D++++reLtg iY
  lcl|NCBI__GCF_000204645.1:WP_013519946.1  67 AVGDWKYDKLDRPLRPEQAILGLRKHLGLFANFRPAICYEQLTHASSLKPELVAGLDILIIRELTGDIY 135
                                               ********************************************************************* PP

                                 TIGR00169 139 fGepkereeaee.....ekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktv 202
                                               fG+p++r+ a +      ++a+dt++Y+++eieriarvafe+arkr k+vtsvDkanvLe+ +lW+++v
  lcl|NCBI__GCF_000204645.1:WP_013519946.1 136 FGQPRGRRTAPDghfpgAEEAFDTMRYSRPEIERIARVAFEAARKRSKRVTSVDKANVLETFQLWKDVV 204
                                               ******98764322345799************************************************* PP

                                 TIGR00169 203 eeiakeyPdvelehlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskgla 271
                                               +e++k+yPdv+l+h+y+DnaamqLvk+P+ +dv+vt+n+fGDilsDeas++tGs+G+LPsasl++k+++
  lcl|NCBI__GCF_000204645.1:WP_013519946.1 205 TEVHKDYPDVQLDHMYVDNAAMQLVKAPKAFDVIVTGNMFGDILSDEASMLTGSIGMLPSASLNDKKQG 273
                                               ********************************************************************* PP

                                 TIGR00169 272 lfepvhgsapdiagkgianpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattav 340
                                               l+ep hgsapdiagkg+anp+a+ilsaa++lr sl++eeaa++ieaav+kvl++g rt+d+ se+tt+v
  lcl|NCBI__GCF_000204645.1:WP_013519946.1 274 LYEPSHGSAPDIAGKGVANPLATILSAAMMLRFSLGQEEAARRIEAAVQKVLAQGLRTPDIHSEGTTRV 342
                                               ********************************************************************* PP

                                 TIGR00169 341 stkeveee 348
                                               +t ++++ 
  lcl|NCBI__GCF_000204645.1:WP_013519946.1 343 GTVQMGDA 350
                                               ***99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (356 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: 11.99
//
[ok]

This GapMind analysis is from Apr 10 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