Alignments for a candidate for leuB in Methylocella silvestris BL2

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuB in Methylocella silvestris BL2

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate WP_012592468.1 MSIL_RS17820 3-isopropylmalate dehydrogenase

Query= BRENDA::P24404
         (370 letters)



>NCBI__GCF_000021745.1:WP_012592468.1
          Length = 370

 Score =  516 bits (1329), Expect = e-151
 Identities = 258/366 (70%), Positives = 298/366 (81%)

Query: 1   MTVRSLFLLPGDGIGPEAMTEVRKLIEYMNSAHNAGFTVSEGLVGGSAYDAHGVAISDAD 60
           MT   L +LPGDGIGPE M EV K+  ++       F + +GLVGGSAYD +G AIS+ D
Sbjct: 1   MTTYKLLVLPGDGIGPEVMAEVEKIAAFLTYEGLVKFEIEKGLVGGSAYDVYGAAISEDD 60

Query: 61  MEKALAADAILFGAVGGPKWDGVPYEHRPEAGLLRLRKDLELFANLRPAICYPALAAASS 120
           M +A  ADA+L  AVGGPKWD VPYE+RPEAGLLRLRKD++LFANLRPAICYPALA ASS
Sbjct: 61  MARAQEADAVLLAAVGGPKWDQVPYENRPEAGLLRLRKDMQLFANLRPAICYPALADASS 120

Query: 121 LKPELVEGLDILIVRELTGGVYFGEPKQIIDLGNGQKRGIDTQIYDTFEIERIASVAFEL 180
           LK E+V+GLDILIVRELTGGVYFGEPKQIIDLGNGQKR IDTQ+YDT+EIERI  +AFEL
Sbjct: 121 LKREVVDGLDILIVRELTGGVYFGEPKQIIDLGNGQKRAIDTQVYDTYEIERIGRIAFEL 180

Query: 181 ARSRDNRVCSMEKRNVMKSGVLWNQVVTETHAAKYKDVQLEHMLADAGGMQLVRKPKQFD 240
           AR R N+V S EKRNVMKSGVLW++V++  H  ++ DV+LEH LADA GMQLVR+PKQFD
Sbjct: 181 ARKRRNKVTSSEKRNVMKSGVLWHEVISALHTREFPDVELEHQLADALGMQLVRRPKQFD 240

Query: 241 VIVTDNLFGDMLSDVAAMLTGSLGMLPSASLGAPDAKTGKRKAMYEPVHGSAPDIAGKSI 300
           VIVTDNLFGDMLSDVAAMLTGSLGMLPSASLG  +A TG RKA+YEPVHGSAPDIAGK I
Sbjct: 241 VIVTDNLFGDMLSDVAAMLTGSLGMLPSASLGERNATTGARKALYEPVHGSAPDIAGKGI 300

Query: 301 ANPIAMIASFAMCLRYSFNMVDEATKLEAAIANVLDKGIRTADIMADGCRQVGTSDMGDA 360
           ANPIAMI+S  M LRYSFN+ D A +++ +IA VL+KG+RT DI       + T+ MGDA
Sbjct: 301 ANPIAMISSLVMALRYSFNLEDLADRIDRSIAAVLEKGLRTGDIAGGAQNTISTAQMGDA 360

Query: 361 VLAEFK 366
           +L E K
Sbjct: 361 ILEELK 366


Lambda     K      H
   0.319    0.135    0.387 

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: 508
Number of extensions: 15
Number of successful extensions: 1
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: 370
Length of database: 370
Length adjustment: 30
Effective length of query: 340
Effective length of database: 340
Effective search space:   115600
Effective search space used:   115600
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate WP_012592468.1 MSIL_RS17820 (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.30503.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     4e-140  452.7   0.1   4.6e-140  452.5   0.1    1.0  1  lcl|NCBI__GCF_000021745.1:WP_012592468.1  MSIL_RS17820 3-isopropylmalate d


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021745.1:WP_012592468.1  MSIL_RS17820 3-isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  452.5   0.1  4.6e-140  4.6e-140       2     348 ..       6     360 ..       5     361 .. 0.98

  Alignments for each domain:
  == domain 1  score: 452.5 bits;  conditional E-value: 4.6e-140
                                 TIGR00169   2 iavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlga 70 
                                               + vLpGDgiGpev+ae  k+   ++ +  +k+e e+ l+GG a d +g  ++e+ ++ ++eadavLl+a
  lcl|NCBI__GCF_000021745.1:WP_012592468.1   6 LLVLPGDGIGPEVMAEVEKIAAFLTYEGLVKFEIEKGLVGGSAYDVYGAAISEDDMARAQEADAVLLAA 74 
                                               689****************************************************************** PP

                                 TIGR00169  71 vGGpkWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYf 139
                                               vGGpkWd+ p + rPe gLL+lrk+++lfanLrPa  +++L ++s+lk+e+v+g+D+++vreLtgG+Yf
  lcl|NCBI__GCF_000021745.1:WP_012592468.1  75 VGGPKWDQVPYENRPEAGLLRLRKDMQLFANLRPAICYPALADASSLKREVVDGLDILIVRELTGGVYF 143
                                               ********************************************************************* PP

                                 TIGR00169 140 Gepkereeaee.ekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiak 207
                                               Gepk++ + ++ +k+a+dt++Y ++eieri r+afelarkrr+kvts +k nv++s+ lW ++++++++
  lcl|NCBI__GCF_000021745.1:WP_012592468.1 144 GEPKQIIDLGNgQKRAIDTQVYDTYEIERIGRIAFELARKRRNKVTSSEKRNVMKSGVLWHEVISALHT 212
                                               ******999999*******************************************************99 PP

                                 TIGR00169 208 .eyPdvelehlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslss......kg 269
                                                e+Pdveleh++ D+  mqLv++P+q+dv+vt+nlfGD+lsD a+++tGslG+LPsasl++      ++
  lcl|NCBI__GCF_000021745.1:WP_012592468.1 213 rEFPDVELEHQLADALGMQLVRRPKQFDVIVTDNLFGDMLSDVAAMLTGSLGMLPSASLGErnattgAR 281
                                               9************************************************************99999999 PP

                                 TIGR00169 270 lalfepvhgsapdiagkgianpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseatt 338
                                               +al+epvhgsapdiagkgianpia+i+s+ + lrys+nle+ a++i+++++ vle+g rt d+a+ a +
  lcl|NCBI__GCF_000021745.1:WP_012592468.1 282 KALYEPVHGSAPDIAGKGIANPIAMISSLVMALRYSFNLEDLADRIDRSIAAVLEKGLRTGDIAGGAQN 350
                                               9******************************************************************** PP

                                 TIGR00169 339 avstkeveee 348
                                               + st+++++ 
  lcl|NCBI__GCF_000021745.1:WP_012592468.1 351 TISTAQMGDA 360
                                               ******9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (370 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: 10.94
//
[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