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; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 (characterized)
to candidate WP_013820591.1 METME_RS20195 3-isopropylmalate dehydrogenase

Query= SwissProt::Q56268
         (358 letters)



>NCBI__GCF_000214665.1:WP_013820591.1
          Length = 359

 Score =  442 bits (1136), Expect = e-129
 Identities = 227/355 (63%), Positives = 278/355 (78%), Gaps = 2/355 (0%)

Query: 2   KKIAIFAGDGIGPEIVAAARQVLDAVDQAAHLGLRCTEGLVGGAALDASDDPLPAASLQL 61
           KKIA+ AGDGIGPEIVA A +VL  ++   +LGL     L+GGAA DA   PLP  +L L
Sbjct: 3   KKIAVLAGDGIGPEIVAEALKVLSYLNTDMNLGLVFENALIGGAAYDAFGTPLPQTTLNL 62

Query: 62  AMAADAVILGAVGGPRWDAYPPAKRPEQGLLRLRKGLDLYANLRPAQIFPQLLDASPLRP 121
              ADAV+LGAVGGP+W+  P A RPE+GLL +R  L+L++NLRPA ++PQL DAS L+P
Sbjct: 63  CKNADAVLLGAVGGPKWEPLPHAVRPERGLLGVRSELNLFSNLRPAILYPQLADASTLKP 122

Query: 122 ELVRDVDILVVRELTGDIYFGQPRGLEVID-GKRRGFNTMVYDEDEIRRIAHVAFRAAQG 180
           E+V  +DI++VRELTG IYFGQPRG+ +++ G+++GFNT+VY E EIRRIAH AF+ AQ 
Sbjct: 123 EVVAGLDIMIVRELTGGIYFGQPRGIRLLENGEQQGFNTLVYCESEIRRIAHSAFKTAQK 182

Query: 181 RRKQLCSVDKANVLETTRLWREVVTEVARDYPDVRLSHMYVDNAAMQLIRAPAQFDVLLT 240
           R  +LCSVDKANVLE T LWR+VV+EV R+YPDV+LSHMYVDNAAMQL+R P QFDV++T
Sbjct: 183 RHNKLCSVDKANVLEVTDLWRKVVSEVGREYPDVQLSHMYVDNAAMQLVRNPKQFDVIVT 242

Query: 241 GNMFGDILSDEASQLTGSIGMLPSASL-GEGRAMYEPIHGSAPDIAGQDKANPLATILSV 299
            NMFGDILSD A+ LTGSIGMLPSASL   G+ MYEPIHGSAPDIAGQ  ANPLAT+LSV
Sbjct: 243 TNMFGDILSDTAAMLTGSIGMLPSASLDANGKGMYEPIHGSAPDIAGQGIANPLATLLSV 302

Query: 300 AMMLRHSLNAEPWAQRVEAAVQRVLDQGLRTADIAAPGTPVIGTKAMGAAVVNAL 354
           AMMLR++ N    A+R+E AV + LD G+RTADI + G   + T  MG AV+NAL
Sbjct: 303 AMMLRYTFNETAAAERIEQAVNQALDSGVRTADIYSEGMTQVSTSGMGDAVLNAL 357


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: 401
Number of extensions: 15
Number of successful extensions: 3
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: 359
Length adjustment: 29
Effective length of query: 329
Effective length of database: 330
Effective search space:   108570
Effective search space used:   108570
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_013820591.1 METME_RS20195 (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.6199.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.2e-161  521.7   0.0   4.9e-161  521.5   0.0    1.0  1  lcl|NCBI__GCF_000214665.1:WP_013820591.1  METME_RS20195 3-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000214665.1:WP_013820591.1  METME_RS20195 3-isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  521.5   0.0  4.9e-161  4.9e-161       1     348 [.       4     352 ..       4     353 .. 0.99

  Alignments for each domain:
  == domain 1  score: 521.5 bits;  conditional E-value: 4.9e-161
                                 TIGR00169   1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlg 69 
                                               kiavL+GDgiGpe+vaealkvL  ++  ++l l fe+aliGGaa da g+Plp+ tl+ ck+adavLlg
  lcl|NCBI__GCF_000214665.1:WP_013820591.1   4 KIAVLAGDGIGPEIVAEALKVLSYLNTDMNLGLVFENALIGGAAYDAFGTPLPQTTLNLCKNADAVLLG 72 
                                               79******************************************************************* PP

                                 TIGR00169  70 avGGpkWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiY 138
                                               avGGpkW+ lp+ vrPe+gLL +r el+lf+nLrPa l+++L ++s+lk+e+v g+D+++vreLtgGiY
  lcl|NCBI__GCF_000214665.1:WP_013820591.1  73 AVGGPKWEPLPHAVRPERGLLGVRSELNLFSNLRPAILYPQLADASTLKPEVVAGLDIMIVRELTGGIY 141
                                               ********************************************************************* PP

                                 TIGR00169 139 fGepkereeaee.ekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeia 206
                                               fG+p++++  e+ e+++++t +Y ++ei+ria+ af++a+kr++k++svDkanvLe++ lWrk+v+e+ 
  lcl|NCBI__GCF_000214665.1:WP_013820591.1 142 FGQPRGIRLLENgEQQGFNTLVYCESEIRRIAHSAFKTAQKRHNKLCSVDKANVLEVTDLWRKVVSEVG 210
                                               *******999998******************************************************** PP

                                 TIGR00169 207 keyPdvelehlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfep 275
                                               +eyPdv+l+h+y+DnaamqLv++P+q+dv+vt n+fGDilsD a+++tGs+G+LPsasl  +g++++ep
  lcl|NCBI__GCF_000214665.1:WP_013820591.1 211 REYPDVQLSHMYVDNAAMQLVRNPKQFDVIVTTNMFGDILSDTAAMLTGSIGMLPSASLDANGKGMYEP 279
                                               ********************************************************************* PP

                                 TIGR00169 276 vhgsapdiagkgianpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstke 344
                                               +hgsapdiag+gianp+a++ls+a++lry++n   aae+ie+av+++l++g rt+d++se+ t+vst+ 
  lcl|NCBI__GCF_000214665.1:WP_013820591.1 280 IHGSAPDIAGQGIANPLATLLSVAMMLRYTFNETAAAERIEQAVNQALDSGVRTADIYSEGMTQVSTSG 348
                                               *******************************************************************99 PP

                                 TIGR00169 345 veee 348
                                               +++ 
  lcl|NCBI__GCF_000214665.1:WP_013820591.1 349 MGDA 352
                                               9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (359 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.29
//
[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