Alignments for a candidate for leuC in Methanobacterium lacus AL-21

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Methanobacterium lacus AL-21

Align Probable 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate WP_013645640.1 METBO_RS10230 3-isopropylmalate dehydratase large subunit

Query= curated2:O27439
         (419 letters)



>NCBI__GCF_000191585.1:WP_013645640.1
          Length = 414

 Score =  498 bits (1282), Expect = e-145
 Identities = 233/413 (56%), Positives = 311/413 (75%), Gaps = 1/413 (0%)

Query: 3   MTVSEKILARASGKDRVEAGEIVMADIDVAMTHDLTGPLSVESFRAIGEDRVWDPEKIVV 62
           M ++EKILARA+GK+ V  GEI+  D+D+AM HD T P ++ +F+ I +D+VWDPEKIV+
Sbjct: 1   MNITEKILARAAGKEEVHPGEIIEVDVDLAMAHDGTSPPTINNFKKI-QDKVWDPEKIVI 59

Query: 63  IFDHQVPADSIEAAQNHMIMRDFVEEQGIRNFYDVREGVCHQVLPEKGHVVPGEVVVGTD 122
           I DH VP ++I +A+ H + R+F  +QGI+N+ +  EG+CHQVLPE G V PGEVVVG D
Sbjct: 60  ICDHTVPPNTIGSAEFHKVSREFARDQGIKNYLNHGEGICHQVLPEYGFVKPGEVVVGAD 119

Query: 123 SHTCTHGALGAFATGIGSTDMAMVFATGKLWFRVPETLRFDVRGKLREHVYAKDVILNII 182
           SHTCTHGA GAFATG+G+TDMA +FATG+ WFRVPE  +  V GKL   V AKDVILN+I
Sbjct: 120 SHTCTHGAFGAFATGVGATDMAFIFATGQTWFRVPEAYKITVDGKLGNFVSAKDVILNVI 179

Query: 183 GRVGADGATYMACEFAGETVAEMSVSDRMVLSNMAIEMGGKTGIVEPDEKTLNYVRRRSG 242
           G +G  GATY + EF G T+  M V+ RM + NMAIE G K GI+EP++ TL Y++ R+ 
Sbjct: 180 GEIGTYGATYKSLEFCGNTIENMDVAGRMTICNMAIESGAKNGIMEPNKATLQYLKDRNV 239

Query: 243 KPWRVFKTDPDAPSLSVMEVDVSDLEPQVACPHNVDNVKPVTEVEGTEIDQVFLGSCTNG 302
           K + V  +DPD         DV D+EPQVACPHNVDNVKP+++V G  I+Q F+GSCTNG
Sbjct: 240 KGFDVVTSDPDYTYEKEYFFDVDDMEPQVACPHNVDNVKPLSKVTGKTINQAFIGSCTNG 299

Query: 303 RLSDLRDAAAILKNRKVSDSVRMLVIPASREVYRRALDEGLIEIFVDAGALVCNPCCGPC 362
           R+ DL  AA +L+ ++V   VR+L+IPAS E+YR+A++ GL++IF+D+GA++CNP CGPC
Sbjct: 300 RMEDLVAAAEVLEGKRVHPDVRLLIIPASAEIYRKAINSGLVDIFMDSGAIICNPGCGPC 359

Query: 363 LGGHVGLVGPGEVSLSTSNRNFRGRQGSPEAEVYLSSAAVAAASAVKGSITHP 415
           LGGH+G++  GEV ++T+NRNF GR G PE+EVYL++ AV A+SA+ G I  P
Sbjct: 360 LGGHMGVLAAGEVCVATTNRNFLGRMGDPESEVYLANPAVVASSALSGEINDP 412


Lambda     K      H
   0.318    0.135    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: 578
Number of extensions: 24
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: 419
Length of database: 414
Length adjustment: 31
Effective length of query: 388
Effective length of database: 383
Effective search space:   148604
Effective search space used:   148604
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: 50 (23.9 bits)

Align candidate WP_013645640.1 METBO_RS10230 (3-isopropylmalate dehydratase large subunit)
to HMM TIGR02086 (3-isopropylmalate dehydratase, large subunit)

# 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/TIGR02086.hmm
# target sequence database:        /tmp/gapView.25949.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02086  [M=411]
Accession:   TIGR02086
Description: IPMI_arch: 3-isopropylmalate dehydratase, large subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.9e-192  624.1   1.0   5.5e-192  623.9   1.0    1.0  1  lcl|NCBI__GCF_000191585.1:WP_013645640.1  METBO_RS10230 3-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000191585.1:WP_013645640.1  METBO_RS10230 3-isopropylmalate dehydratase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  623.9   1.0  5.5e-192  5.5e-192       1     411 []       1     414 []       1     414 [] 0.99

  Alignments for each domain:
  == domain 1  score: 623.9 bits;  conditional E-value: 5.5e-192
                                 TIGR02086   1 ktlaekilsekvGke.vkaGeivevkvDlvmvhDgtgplvikalrelgakvekkekivlvfDhvvPapt 68 
                                               ++++ekil++++Gke v++Gei+ev vDl+m+hDgt+p +i++++++++kv+++ekiv++ Dh+vP++t
  lcl|NCBI__GCF_000191585.1:WP_013645640.1   1 MNITEKILARAAGKEeVHPGEIIEVDVDLAMAHDGTSPPTINNFKKIQDKVWDPEKIVIICDHTVPPNT 69 
                                               689**********988***************************************************** PP

                                 TIGR02086  69 veaaelqkeirefakelgikv.fdvgeGichqvlvekgyakpgkvvvgaDshtttsGalgafatGlGat 136
                                               + +ae++k+ refa+ +gik+  + geGichqvl e g++kpg+vvvgaDsht+t+Ga+gafatG+Gat
  lcl|NCBI__GCF_000191585.1:WP_013645640.1  70 IGSAEFHKVSREFARDQGIKNyLNHGEGICHQVLPEYGFVKPGEVVVGADSHTCTHGAFGAFATGVGAT 138
                                               *********************9999******************************************** PP

                                 TIGR02086 137 DvalalatGktWlkvPesikveleGkleekvtakDvileivkelgadgatykaieftgeeiealsldeR 205
                                               D+a+++atG+tW++vPe+ k++++Gkl + v+akDvil++++e+g+ gatyk++ef g++ie++++ +R
  lcl|NCBI__GCF_000191585.1:WP_013645640.1 139 DMAFIFATGQTWFRVPEAYKITVDGKLGNFVSAKDVILNVIGEIGTYGATYKSLEFCGNTIENMDVAGR 207
                                               ********************************************************************* PP

                                 TIGR02086 206 ltlsnlaveagakaglvepdeetleylkkrrge.frilkadedakyeeeieidlseleplvavPhsvdn 273
                                               +t++n+a+e gak+g++ep++ tl+ylk r+ + f ++++d+d +ye+e+ +d++++ep+va+Ph+vdn
  lcl|NCBI__GCF_000191585.1:WP_013645640.1 208 MTICNMAIESGAKNGIMEPNKATLQYLKDRNVKgFDVVTSDPDYTYEKEYFFDVDDMEPQVACPHNVDN 276
                                               ****************************999888*********************************** PP

                                 TIGR02086 274 vkeveevegteidqvfiGsCtnGRledlkiaaeilegrevhkdvrlivvPasrkvyekaleeGlietlv 342
                                               vk++++v g++i+q+fiGsCtnGR+edl +aae+leg++vh+dvrl+++Pas ++y+ka+++Gl+++++
  lcl|NCBI__GCF_000191585.1:WP_013645640.1 277 VKPLSKVTGKTINQAFIGSCTNGRMEDLVAAAEVLEGKRVHPDVRLLIIPASAEIYRKAINSGLVDIFM 345
                                               ********************************************************************* PP

                                 TIGR02086 343 eaGaiiltpgCGPClGahlGvladgevivsttnRnfkGRmGspkaeiYLasPavaavsaveGeitdpee 411
                                               + Gaii++pgCGPClG h+Gvla gev+v+ttnRnf GRmG+p++e+YLa+Pav+a sa++Gei dp++
  lcl|NCBI__GCF_000191585.1:WP_013645640.1 346 DSGAIICNPGCGPCLGGHMGVLAAGEVCVATTNRNFLGRMGDPESEVYLANPAVVASSALSGEINDPRD 414
                                               *******************************************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (411 nodes)
Target sequences:                          1  (414 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: 12.20
//
[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