Alignments for a candidate for leuB in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuB in Dyella japonica UNC79MFTsu3.2

Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 (characterized)
to candidate N515DRAFT_0570 N515DRAFT_0570 3-isopropylmalate dehydrogenase

Query= SwissProt::P12010
         (366 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0570
          Length = 365

 Score =  362 bits (929), Expect = e-105
 Identities = 183/365 (50%), Positives = 247/365 (67%), Gaps = 8/365 (2%)

Query: 1   MKMKLAVLPGDGIGPEVMDAAIRVLKTVLDNDGHEAVFENALIGGAAIDEAGTPLPEETL 60
           MK ++  LPGDG+GPEV  AA+ VL  V  +  H   +E  LIGG AID  G PLP + L
Sbjct: 1   MKARIVTLPGDGVGPEVTAAAVAVLDAVAAHYDHTFDYEQHLIGGCAIDATGEPLPADAL 60

Query: 61  DICRRSDAILLGAVGGPKWDHNPASLRPEKGLLGLRKEMGLFANLRPVKAYATLLNASPL 120
             C+ +DA+LLGAVGGPKW    A +RPE+GLL LR  +G++ANLRP++ +  L   SPL
Sbjct: 61  AACKSADAVLLGAVGGPKWSDPSAPVRPEQGLLALRAALGVYANLRPLQVHPALTALSPL 120

Query: 121 KRERVENVDLVIVRELTGGLYFGRPSERRGPGENEVVDTLAYTREEIERIIEKAFQLAQI 180
           K +++ NVD++ VRELTGG YFG  +       +   D   YT  E+ER++ +AF+LA+ 
Sbjct: 121 KDDKLRNVDVLFVRELTGGAYFGAKTRT----VDTATDECKYTVVEVERVVRRAFELARG 176

Query: 181 RRKKLASVDKANVLESSRMWREIAEETAKKYPDVELSHMLVDSTSMQLIANPGQFDVIVT 240
           RR K+ SVDKANVLE+SR+WR   +  A  YPDV+L H LVDS +M L+  P  +DV+VT
Sbjct: 177 RRHKVTSVDKANVLETSRLWRSTVQRIAADYPDVKLEHQLVDSMAMLLLTQPASYDVVVT 236

Query: 241 ENMFGDILSDEASVITGSLGMLPSASLRSDRFGMYEPVHGSAPDIAGQGKANPLGTVLSA 300
           EN+FGDIL+DEA+ + GSLG+LPSASL     G+YEP+HGSAPDIAG+G ANP+G +LSA
Sbjct: 237 ENLFGDILTDEAAALAGSLGLLPSASLGEGARGLYEPIHGSAPDIAGKGVANPVGAILSA 296

Query: 301 ALMLRYSFGLEKEAAAIEKAVDDVLQDGYCTGDLQVANGKVVSTIELTDRLIEKLNNSAA 360
           A++LR+S GLE+EA A+E AV+ VL+ G  + D+    G    T  + + ++  L+   A
Sbjct: 297 AMLLRHSLGLEEEAGAVEAAVEHVLEHGPRSRDI----GGDAGTAAIREAVVAALDEHVA 352

Query: 361 RPRIF 365
               F
Sbjct: 353 NSEAF 357


Lambda     K      H
   0.316    0.135    0.379 

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: 402
Number of extensions: 10
Number of successful extensions: 2
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: 366
Length of database: 365
Length adjustment: 30
Effective length of query: 336
Effective length of database: 335
Effective search space:   112560
Effective search space used:   112560
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate N515DRAFT_0570 N515DRAFT_0570 (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.21560.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   4.4e-150  485.5   0.0     5e-150  485.3   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_0570  N515DRAFT_0570 3-isopropylmalate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_0570  N515DRAFT_0570 3-isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  485.3   0.0    5e-150    5e-150       1     346 [.       4     344 ..       4     347 .. 0.98

  Alignments for each domain:
  == domain 1  score: 485.3 bits;  conditional E-value: 5e-150
                                    TIGR00169   1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadav 66 
                                                  +i+ LpGDg+Gpev+a+a++vL+av+ ++++ +++e++liGG aidatgePlp+++l+ack+adav
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0570   4 RIVTLPGDGVGPEVTAAAVAVLDAVAAHYDHTFDYEQHLIGGCAIDATGEPLPADALAACKSADAV 69 
                                                  699*************************************************************** PP

                                    TIGR00169  67 LlgavGGpkWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvre 132
                                                  LlgavGGpkW +  + vrPe+gLL+lr  l+++anLrP +++++L++lsplk++  ++vD++ vre
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0570  70 LLGAVGGPKWSDPSAPVRPEQGLLALRAALGVYANLRPLQVHPALTALSPLKDDKLRNVDVLFVRE 135
                                                  ****************************************************************** PP

                                    TIGR00169 133 LtgGiYfGepkereeaeeekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlW 198
                                                  LtgG YfG ++ + +     +a d  kYt+ e+er++r afelar rr+kvtsvDkanvLe+srlW
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0570 136 LTGGAYFGAKTRTVD-----TATDECKYTVVEVERVVRRAFELARGRRHKVTSVDKANVLETSRLW 196
                                                  ********9988777.....7********************************************* PP

                                    TIGR00169 199 rktveeiakeyPdvelehlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsas 264
                                                  r tv+ ia +yPdv+leh+++D++am L+ +P+++dvvvt+nlfGDil Dea+ ++GslGlLPsas
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0570 197 RSTVQRIAADYPDVKLEHQLVDSMAMLLLTQPASYDVVVTENLFGDILTDEAAALAGSLGLLPSAS 262
                                                  ****************************************************************** PP

                                    TIGR00169 265 lsskglalfepvhgsapdiagkgianpiaailsaalllryslnleeaaeaieaavkkvleegkrte 330
                                                  l++   +l+ep+hgsapdiagkg+anp++ailsaa+llr+sl+lee+a a+eaav++vle+g r++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0570 263 LGEGARGLYEPIHGSAPDIAGKGVANPVGAILSAAMLLRHSLGLEEEAGAVEAAVEHVLEHGPRSR 328
                                                  ****************************************************************** PP

                                    TIGR00169 331 dlaseattavstkeve 346
                                                  d++++a+ta++ ++v+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0570 329 DIGGDAGTAAIREAVV 344
                                                  *******999998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (365 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.38
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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