Alignments for a candidate for leuC in Methanosarcina acetivorans C2A

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Methanosarcina acetivorans C2A

Align 3-isopropylmalate dehydratase (EC 4.2.1.33); homoaconitate hydratase (EC 4.2.1.36) (characterized)
to candidate WP_011021410.1 MA_RS07220 3-isopropylmalate dehydratase large subunit

Query= BRENDA::P81291
         (424 letters)



>NCBI__GCF_000007345.1:WP_011021410.1
          Length = 420

 Score =  481 bits (1238), Expect = e-140
 Identities = 240/424 (56%), Positives = 311/424 (73%), Gaps = 10/424 (2%)

Query: 3   MTIVEKILAKASGKKEVSPGDIVMANIDVAMVHDITGPLTVN----TLKEYGIEKVWNPE 58
           MT+ EKI +KASG   V  GD V+ANID+AM HDITGPL V      +++   +KVW+P 
Sbjct: 1   MTVSEKIFSKASGTP-VKAGDFVLANIDLAMTHDITGPLAVQGFYEIMRDEEEKKVWDPS 59

Query: 59  KIVILFDHQVPADSIKAAENHILMRKFVKEQGIKYFYDIREGVCHQVLPEKGHVAPGEVV 118
           KIVI+FDHQVPADSI AAENHI++RKF KEQGI   YD+ EGVCHQVLPEKGHV PG+++
Sbjct: 60  KIVIIFDHQVPADSINAAENHIMLRKFAKEQGILN-YDVYEGVCHQVLPEKGHVLPGDLI 118

Query: 119 VGADSHTCTHGAFGAFATGIGSTDMAHVFATGKLWFKVPETIYFNITGDLQPYVTSKDVI 178
           VG+DSHTC +G+ GAF+TGIGSTDMA VFATGKLWF+VPET  F + G L   V SKD+I
Sbjct: 119 VGSDSHTCAYGSLGAFSTGIGSTDMAAVFATGKLWFRVPETFRFEVEGKLPERVYSKDLI 178

Query: 179 LSIIGEVGVDGATYKACQFGGETVKKMSIASRMTMTNMAIEMGGKTGIIEPDEKTIQYVK 238
           L +IG+VGV+GA Y A ++ G T++ +SI  RMT++NMAIEMGGK GIIE DE T  Y++
Sbjct: 179 LHLIGDVGVEGARYMAAEYAGSTIRSLSIPERMTISNMAIEMGGKAGIIEADEVTEAYLQ 238

Query: 239 EAMKKHGTERPFEVIKGDEDAEFAEVYEIEADKIEPVFACPHNVDNVKQAREVAGKPIDQ 298
           E +  +  + P+   K DE+A++ ++   +   +EP  ACPHNVDNVK   EV G  +DQ
Sbjct: 239 ERIPGYKLD-PY--WKSDEEAKYLDIRHYDVSDLEPQVACPHNVDNVKSVSEVEGTKLDQ 295

Query: 299 VFIGSCTNGRLEDLRMAIKIIEKHGGIADDVRVVVTPASREEYLKALKEGIIEKFLKYGC 358
           VF+GSCTNGR ED+++   I+     +A  VR++V PAS+ EY+K LK G +EK +  G 
Sbjct: 296 VFMGSCTNGRFEDIKIMADIMGDE-PVAKGVRLLVVPASKTEYMKLLKAGYVEKLMNAGA 354

Query: 359 VVTNPSCSACMGSLYGVLGPGEVCVSTSNRNFRGRQGSLEAEIYLASPITAAACAVKGEL 418
           +V  P C  CMG  +G+LGPGEV ++TSNRNF+GR+GS E+ +YL+SP TA A A+ GE+
Sbjct: 355 IVEAPCCGPCMGGSFGLLGPGEVGLATSNRNFKGREGSAESFVYLSSPATAGASALTGEI 414

Query: 419 VDPR 422
            DPR
Sbjct: 415 TDPR 418


Lambda     K      H
   0.318    0.136    0.400 

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: 587
Number of extensions: 34
Number of successful extensions: 6
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: 424
Length of database: 420
Length adjustment: 32
Effective length of query: 392
Effective length of database: 388
Effective search space:   152096
Effective search space used:   152096
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_011021410.1 MA_RS07220 (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.13374.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.5e-170  552.1   0.0     4e-170  551.9   0.0    1.0  1  lcl|NCBI__GCF_000007345.1:WP_011021410.1  MA_RS07220 3-isopropylmalate deh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000007345.1:WP_011021410.1  MA_RS07220 3-isopropylmalate dehydratase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  551.9   0.0    4e-170    4e-170       1     410 [.       1     418 [.       1     419 [. 0.98

  Alignments for each domain:
  == domain 1  score: 551.9 bits;  conditional E-value: 4e-170
                                 TIGR02086   1 ktlaekilsekvGkevkaGeivevkvDlvmvhDgtgplvikalrelg.....akvekkekivlvfDhvv 64 
                                               +t+ eki+s+++G++vkaG+ v++++Dl+m+hD tgpl+++ + e+      +kv++++kiv++fDh+v
  lcl|NCBI__GCF_000007345.1:WP_011021410.1   1 MTVSEKIFSKASGTPVKAGDFVLANIDLAMTHDITGPLAVQGFYEIMrdeeeKKVWDPSKIVIIFDHQV 69 
                                               799************************************9999998777778899************** PP

                                 TIGR02086  65 PaptveaaelqkeirefakelgikvfdvgeGichqvlvekgyakpgkvvvgaDshtttsGalgafatGl 133
                                               Pa +++aae + ++r+fake+gi ++dv eG+chqvl ekg++ pg+++vg+Dsht+ +G+lgaf+tG+
  lcl|NCBI__GCF_000007345.1:WP_011021410.1  70 PADSINAAENHIMLRKFAKEQGILNYDVYEGVCHQVLPEKGHVLPGDLIVGSDSHTCAYGSLGAFSTGI 138
                                               ********************************************************************* PP

                                 TIGR02086 134 GatDvalalatGktWlkvPesikveleGkleekvtakDvileivkelgadgatykaieftgeeiealsl 202
                                               G+tD+a+++atGk+W++vPe+++ e+eGkl e v++kD+il++++++g +ga y+a e+ g++i++ls+
  lcl|NCBI__GCF_000007345.1:WP_011021410.1 139 GSTDMAAVFATGKLWFRVPETFRFEVEGKLPERVYSKDLILHLIGDVGVEGARYMAAEYAGSTIRSLSI 207
                                               ********************************************************************* PP

                                 TIGR02086 203 deRltlsnlaveagakaglvepdeetleylkkrrge...frilkadedakyeeeieidlseleplvavP 268
                                                eR+t+sn+a+e+g+kag++e+de t+ yl++r +        k+de+aky +  + d+s+lep+va+P
  lcl|NCBI__GCF_000007345.1:WP_011021410.1 208 PERMTISNMAIEMGGKAGIIEADEVTEAYLQERIPGyklDPYWKSDEEAKYLDIRHYDVSDLEPQVACP 276
                                               *********************************98855544689************************* PP

                                 TIGR02086 269 hsvdnvkeveevegteidqvfiGsCtnGRledlkiaaeilegrevhkdvrlivvPasrkvyekaleeGl 337
                                               h+vdnvk+v+evegt++dqvf+GsCtnGR+ed+ki+a+i+ ++ v+k vrl+vvPas++ y+k l++G+
  lcl|NCBI__GCF_000007345.1:WP_011021410.1 277 HNVDNVKSVSEVEGTKLDQVFMGSCTNGRFEDIKIMADIMGDEPVAKGVRLLVVPASKTEYMKLLKAGY 345
                                               ********************************************************************* PP

                                 TIGR02086 338 ietlveaGaiiltpgCGPClGahlGvladgevivsttnRnfkGRmGspkaeiYLasPavaavsaveGei 406
                                               +e+l++aGai+  p CGPC+G  +G l++gev ++t+nRnfkGR Gs ++ +YL+sPa+a +sa++Gei
  lcl|NCBI__GCF_000007345.1:WP_011021410.1 346 VEKLMNAGAIVEAPCCGPCMGGSFGLLGPGEVGLATSNRNFKGREGSAESFVYLSSPATAGASALTGEI 414
                                               ********************************************************************* PP

                                 TIGR02086 407 tdpe 410
                                               tdp+
  lcl|NCBI__GCF_000007345.1:WP_011021410.1 415 TDPR 418
                                               ***8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (411 nodes)
Target sequences:                          1  (420 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: 9.44
//
[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