Alignments for a candidate for leuB in Methylomonas methanica MC09

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuB in Methylomonas methanica MC09

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate WP_013817575.1 METME_RS04395 3-isopropylmalate dehydrogenase

Query= BRENDA::P31958
         (357 letters)



>NCBI__GCF_000214665.1:WP_013817575.1
          Length = 368

 Score =  288 bits (737), Expect = 2e-82
 Identities = 159/364 (43%), Positives = 234/364 (64%), Gaps = 9/364 (2%)

Query: 1   MKEFKIAVIPGDGIGPDIVREAVKIMTKVGEKYDTKFNFVEVKAGGDAIDAYGEPLPKET 60
           MK +KIAV+ GDGIGP+I +EA+K++  + E+ D  F  +    G  A    G+  P+ T
Sbjct: 1   MKHYKIAVLAGDGIGPEITQEALKVLKVIEERNDVTFELMPALFGACAYFETGDAFPQAT 60

Query: 61  IDVCKSSAAVLLGAVGGPKWDN--LEGSKRPER-ALLGLRGALGLYANLRPAKVYNVLKS 117
           ID+C  + A+L G +G    ++  +   K+PER ALL +R     YAN RP  +   L  
Sbjct: 61  IDICDQADAILKGPIGLSHEESKKIPVDKQPERGALLPMRRRYNTYANFRPVSLPKSLAH 120

Query: 118 ASPLKNEIIDEGVDLLVVRELIGGIYFG--DRGTKEVNGVETAFDTEKYNVDEVKRIAHS 175
            SPLK EII EG+DL++VREL+GG+YFG  +RG  +  G+    +T +Y+ ++++RI H 
Sbjct: 121 FSPLKPEIIGEGIDLIMVRELVGGLYFGNKERGVND-KGLRYVRETLEYDEEQIRRIMHE 179

Query: 176 AFKAAMKRRKKVTSVDKANVLDASRLWRKTVNEVSKEYPEVELSHLYVDNTAMQLVRKPS 235
           AFK A KRRK + ++ K+NVL +S LW + + EV+K+YP+VE+ +  VD  A  L  KP+
Sbjct: 180 AFKLASKRRKLLHNIHKSNVLMSSVLWNEVMEEVAKDYPDVEVVNYLVDAAATALCLKPT 239

Query: 236 QFDVILTNNIFGDILSDEASMITGSIGMLASSSIREDSFGMYEPIHGSAPDIAGLDIANP 295
           QFDV++  N+FGDILSD+   + GS+G++ S+ I  +    YEP HGSAPDIAG +IANP
Sbjct: 240 QFDVMVMENMFGDILSDQGGGVLGSLGLMPSACIGPEK-AYYEPSHGSAPDIAGKNIANP 298

Query: 296 LAQILSAAMLMEYSLDMSEAARDVEAAVEKVLNEGYRTADIYI--EGTKKVGTSEMGNLV 353
            + I S AM++E S DM+  A++V AA++ V  +GY TAD+     G   + T E G+ V
Sbjct: 299 YSMIGSVAMMLENSFDMAAEAKNVWAAMQGVFADGYSTADLSKPGSGVTMISTVEFGDKV 358

Query: 354 LERL 357
           +E+L
Sbjct: 359 VEKL 362


Lambda     K      H
   0.315    0.134    0.372 

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: 344
Number of extensions: 17
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: 357
Length of database: 368
Length adjustment: 29
Effective length of query: 328
Effective length of database: 339
Effective search space:   111192
Effective search space used:   111192
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: 42 (22.0 bits)
S2: 49 (23.5 bits)

Align candidate WP_013817575.1 METME_RS04395 (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.3558111.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     1e-113  365.8   0.0   1.2e-113  365.6   0.0    1.0  1  NCBI__GCF_000214665.1:WP_013817575.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000214665.1:WP_013817575.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  365.6   0.0  1.2e-113  1.2e-113       1     339 [.       5     346 ..       5     358 .. 0.95

  Alignments for each domain:
  == domain 1  score: 365.6 bits;  conditional E-value: 1.2e-113
                             TIGR00169   1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGG 73 
                                           kiavL+GDgiGpe+++ealkvLk++eer ++ +e   al+G  a  +tg+ +p++t++ c++ada+L g +G 
  NCBI__GCF_000214665.1:WP_013817575.1   5 KIAVLAGDGIGPEITQEALKVLKVIEERNDVTFELMPALFGACAYFETGDAFPQATIDICDQADAILKGPIGL 77 
                                           79**********************************************************************7 PP

                             TIGR00169  74 p..kWdnlprdvrPek.gLLklrkeldlfanLrPaklfksLeklsplkeeiv.kgvDlvvvreLtgGiYfGep 142
                                              + ++ p d++Pe+ +LL++r++ + +an+rP+ l ksL ++splk+ei+ +g+Dl++vreL+gG+YfG++
  NCBI__GCF_000214665.1:WP_013817575.1  78 SheESKKIPVDKQPERgALLPMRRRYNTYANFRPVSLPKSLAHFSPLKPEIIgEGIDLIMVRELVGGLYFGNK 150
                                           6115567899******88**********************************9******************99 PP

                             TIGR00169 143 kereeaeeekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPdvele 215
                                           +   +++  ++  +t +Y +e i+ri+++af+la krrk +  + k+nvL ss lW +++ee+ak+yPdve+ 
  NCBI__GCF_000214665.1:WP_013817575.1 151 ERGVNDKGLRYVRETLEYDEEQIRRIMHEAFKLASKRRKLLHNIHKSNVLMSSVLWNEVMEEVAKDYPDVEVV 223
                                           888877779**************************************************************** PP

                             TIGR00169 216 hlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvhgsapdiagkgi 288
                                           + ++D+aa  L  +P+q+dv+v +n+fGDilsD+ + + GslGl+Psa ++   +a++ep hgsapdiagk+i
  NCBI__GCF_000214665.1:WP_013817575.1 224 NYLVDAAATALCLKPTQFDVMVMENMFGDILSDQGGGVLGSLGLMPSACIG-PEKAYYEPSHGSAPDIAGKNI 295
                                           ***************************************************.7889***************** PP

                             TIGR00169 289 anpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseatta 339
                                           anp ++i s+a++l+ s+++  +a+ + aa++ v ++g+ t+dl + ++  
  NCBI__GCF_000214665.1:WP_013817575.1 296 ANPYSMIGSVAMMLENSFDMAAEAKNVWAAMQGVFADGYSTADLSKPGSGV 346
                                           ********************************************9877543 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (368 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: 00:00:00.00
# Mc/sec: 20.08
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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