Alignments for a candidate for leuB in Stenotrophomonas chelatiphaga DSM 21508

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuB in Stenotrophomonas chelatiphaga DSM 21508

Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 (characterized)
to candidate WP_057509305.1 ABB28_RS14510 3-isopropylmalate dehydrogenase

Query= SwissProt::P12010
         (366 letters)



>NCBI__GCF_001431535.1:WP_057509305.1
          Length = 354

 Score =  374 bits (961), Expect = e-108
 Identities = 198/357 (55%), Positives = 250/357 (70%), Gaps = 7/357 (1%)

Query: 1   MKMKLAVLPGDGIGPEVMDAAIRVLKTVLDNDGHEAVFENALIGGAAIDEAGTPLPEETL 60
           M  ++ VLPGDGIGPEV  AA+ VL+ V     H   F    IGG AID  G PLP  TL
Sbjct: 1   MHAEIVVLPGDGIGPEVAAAAVAVLEAVATRFNHTFNFNEHDIGGIAIDRHGEPLPASTL 60

Query: 61  DICRRSDAILLGAVGGPKWDHNPASLRPEKGLLGLRKEMGLFANLRPVKAYATLLNASPL 120
           D CR +DAILLGAVGGPKW    A +RPE+GLL +R+ +GL+ANLRPV+ +   L ASP+
Sbjct: 61  DACRAADAILLGAVGGPKWSDPNAKVRPEQGLLAIRRALGLYANLRPVRTHEAALGASPI 120

Query: 121 KRERVENVDLVIVRELTGGLYFGRPSERRGPGENEVVDTLAYTREEIERIIEKAFQLAQI 180
           K E +  VD V+VRELTGG+YFG  +       +   D  +Y+ EEIER++  AF+LA+ 
Sbjct: 121 KAELLRGVDFVVVRELTGGIYFGEKTRT----ADAASDLCSYSVEEIERVLRSAFELARQ 176

Query: 181 RRKKLASVDKANVLESSRMWREIAEETAKK-YPDVELSHMLVDSTSMQLIANPGQFDVIV 239
           RR K+ SVDKANVLE+SR+WR++A    +  +PDV L H LVDS +M L+A P ++DVIV
Sbjct: 177 RRGKVTSVDKANVLETSRLWRDVATRLGRDVFPDVALEHQLVDSMAMHLLAKPREYDVIV 236

Query: 240 TENMFGDILSDEASVITGSLGMLPSASL-RSDRFGMYEPVHGSAPDIAGQGKANPLGTVL 298
           TENMFGDIL+DEAS++ GSLG+LPSASL +    G+YEP+HGSAPDIAG+G ANP  T+ 
Sbjct: 237 TENMFGDILTDEASMLAGSLGLLPSASLGQPGAVGIYEPIHGSAPDIAGKGIANPYATIF 296

Query: 299 SAALMLRYSFGLEKEAAAIEKAVDDVLQDGYCTGDLQVANGKVVSTIELTDRLIEKL 355
           SAA++LR+S GLE EAAA+E AV   L  G  T DL  A G  VST E T  ++E+L
Sbjct: 297 SAAMLLRHSLGLEAEAAAVEAAVHAALDAGVFTADLAAA-GAAVSTAEATAAVLERL 352


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: 397
Number of extensions: 18
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: 366
Length of database: 354
Length adjustment: 29
Effective length of query: 337
Effective length of database: 325
Effective search space:   109525
Effective search space used:   109525
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 WP_057509305.1 ABB28_RS14510 (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.18758.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.8e-149  482.4   0.1   4.6e-149  482.1   0.1    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057509305.1  ABB28_RS14510 3-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057509305.1  ABB28_RS14510 3-isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  482.1   0.1  4.6e-149  4.6e-149       2     346 ..       5     345 ..       4     349 .. 0.97

  Alignments for each domain:
  == domain 1  score: 482.1 bits;  conditional E-value: 4.6e-149
                                 TIGR00169   2 iavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlga 70 
                                               i+vLpGDgiGpev a+a++vL+av+ rf++ ++f+e++iGG aid++gePlp+ tl+ac++ada+Llga
  lcl|NCBI__GCF_001431535.1:WP_057509305.1   5 IVVLPGDGIGPEVAAAAVAVLEAVATRFNHTFNFNEHDIGGIAIDRHGEPLPASTLDACRAADAILLGA 73 
                                               9******************************************************************** PP

                                 TIGR00169  71 vGGpkWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYf 139
                                               vGGpkW +  ++vrPe+gLL++r+ l+l+anLrP++ +++ + +sp+k+e+ +gvD+vvvreLtgGiYf
  lcl|NCBI__GCF_001431535.1:WP_057509305.1  74 VGGPKWSDPNAKVRPEQGLLAIRRALGLYANLRPVRTHEAALGASPIKAELLRGVDFVVVRELTGGIYF 142
                                               ********************************************************************* PP

                                 TIGR00169 140 GepkereeaeeekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiak. 207
                                               Ge++ + +      a d  +Y++eeier+ r afelar+rr kvtsvDkanvLe+srlWr++++ + + 
  lcl|NCBI__GCF_001431535.1:WP_057509305.1 143 GEKTRTAD-----AASDLCSYSVEEIERVLRSAFELARQRRGKVTSVDKANVLETSRLWRDVATRLGRd 206
                                               **998887.....79***************************************************996 PP

                                 TIGR00169 208 eyPdvelehlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslss.kglalfep 275
                                                +Pdv+leh+++D++am+L+ +P+++dv+vt+n+fGDil Deas+++GslGlLPsasl++   ++++ep
  lcl|NCBI__GCF_001431535.1:WP_057509305.1 207 VFPDVALEHQLVDSMAMHLLAKPREYDVIVTENMFGDILTDEASMLAGSLGLLPSASLGQpGAVGIYEP 275
                                               7**********************************************************955678**** PP

                                 TIGR00169 276 vhgsapdiagkgianpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstke 344
                                               +hgsapdiagkgianp a+i saa+llr+sl+le +a+a+eaav+ +l+ g  t+dla  + +avst+e
  lcl|NCBI__GCF_001431535.1:WP_057509305.1 276 IHGSAPDIAGKGIANPYATIFSAAMLLRHSLGLEAEAAAVEAAVHAALDAGVFTADLAAAG-AAVSTAE 343
                                               *********************************************************9988.7777777 PP

                                 TIGR00169 345 ve 346
                                               ++
  lcl|NCBI__GCF_001431535.1:WP_057509305.1 344 AT 345
                                               65 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (354 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: 10.15
//
[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