Alignments for a candidate for leuC in Malonomonas rubra DSM 5091

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Malonomonas rubra DSM 5091

Align isopropylmalate/citramalate isomerase large subunit LeuC (EC 4.2.1.33; EC 4.2.1.35) (characterized)
to candidate WP_072905201.1 BUB13_RS02530 3-isopropylmalate dehydratase large subunit

Query= reanno::DvH:208495
         (419 letters)



>NCBI__GCF_900142125.1:WP_072905201.1
          Length = 426

 Score =  352 bits (902), Expect = e-101
 Identities = 193/429 (44%), Positives = 265/429 (61%), Gaps = 13/429 (3%)

Query: 1   MAHTLAQKILQRHTDEAITDAGQIVRCRVSMVLANDITAPLAIKSFRAMGAKRVFDKDRV 60
           M  TLA+KI   H  +   +  +++   +  VL ++IT P+AI      G  RVFDKD++
Sbjct: 1   MGKTLAEKIFDAHLKDEPFEGTKVLS--LDRVLCHEITTPVAIADLEWRGKDRVFDKDKI 58

Query: 61  ALVMDHFTPQKDIEAAQQVKLTREFAREMGVTHYYEGGDCGVEHALLPELGLVGPGDVVV 120
            +V+DH TP KD + A Q  + RE+AR   +  +++ G  GV HA+ PE G + PG  V+
Sbjct: 59  KVVIDHVTPAKDSKTATQALILREWARRHDIPDFFDVGRNGVCHAIFPEKGYIRPGFTVI 118

Query: 121 GADSHTCTYGGLGAFATGLGSTDVAGAMALGETWFKVPPTIRATFTGTLPAYVGAKDLIL 180
             DSHTCT+G  GAFA G+G+TD+   +  G   F+ P ++R    G+LP  V AKD+IL
Sbjct: 119 MGDSHTCTHGAFGAFAAGVGTTDLEVGILKGVCSFREPKSLRVNLNGSLPQGVFAKDVIL 178

Query: 181 TLIGAIGVDGALYRALEFDGAAIEALDVEGRMTMANMAIEAGGKAGLFAADAKTLTY--- 237
            +IG +GV+GA  R +EF G  ++ + +E RMT+ NMAIEAGG +G+   D  T+ Y   
Sbjct: 179 YVIGQLGVNGATDRVIEFRGPIVDQMSMEARMTLCNMAIEAGGTSGVCMPDMTTVEYLWP 238

Query: 238 -------CTTAGRTGDTAFSADAGAVYERELSFDVTGMTPVVACPHLPDNVKPVSEVKDV 290
                     A     + + +D  A Y++ +  DV+ M P+V   + PD VK V E+   
Sbjct: 239 FIQDEFASKEAALEEYSKWISDDDASYDKVVDIDVSSMEPMVTFDYKPDCVKTVPEMAGT 298

Query: 291 TVQQVVIGSCTNGRIGDLREAAAVLRGRKVSRDVRCIVLPATPGIWRQALREGLIETFME 350
            V Q+ IGSCTNGRI DLREAAAVL+G+ V+  VR IV PATP I+++AL EG+I+ FM+
Sbjct: 299 KVDQIYIGSCTNGRIEDLREAAAVLKGKTVADSVRGIVSPATPKIFQEALAEGIIQVFMD 358

Query: 351 AGCIVGPATCGPCLGGHMGILADGERAIATTNRNFKGRMGSLESEVYLSGPATAAASAVT 410
           AG  V   TCG CLG   G+LA+GE   +TTNRNF GRMG     V+L  PATAAA+A+T
Sbjct: 359 AGFCVTNPTCGACLGMSNGVLAEGEVCASTTNRNFSGRMGK-GGMVHLMSPATAAATAIT 417

Query: 411 GVITDPSTL 419
           GVITD  TL
Sbjct: 418 GVITDARTL 426


Lambda     K      H
   0.320    0.136    0.401 

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: 501
Number of extensions: 17
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: 419
Length of database: 426
Length adjustment: 32
Effective length of query: 387
Effective length of database: 394
Effective search space:   152478
Effective search space used:   152478
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: 50 (23.9 bits)

Align candidate WP_072905201.1 BUB13_RS02530 (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.16437.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-134  434.8   0.8   1.7e-134  434.6   0.8    1.0  1  lcl|NCBI__GCF_900142125.1:WP_072905201.1  BUB13_RS02530 3-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900142125.1:WP_072905201.1  BUB13_RS02530 3-isopropylmalate dehydratase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  434.6   0.8  1.7e-134  1.7e-134       1     410 [.       3     424 ..       3     425 .. 0.96

  Alignments for each domain:
  == domain 1  score: 434.6 bits;  conditional E-value: 1.7e-134
                                 TIGR02086   1 ktlaekilsekvGkevkaGeivevkvDlvmvhDgtgplvikalrelg.akvekkekivlvfDhvvPapt 68 
                                               ktlaeki+ ++   e   G  v+   D v+ h+ t+p +i  l+  g ++v++k+ki +v+Dhv+Pa++
  lcl|NCBI__GCF_900142125.1:WP_072905201.1   3 KTLAEKIFDAHLKDEPFEGTKVL-SLDRVLCHEITTPVAIADLEWRGkDRVFDKDKIKVVIDHVTPAKD 70 
                                               69*********999999999886.69******************99999******************** PP

                                 TIGR02086  69 veaaelqkeirefakelgikv.fdvg.eGichqvlvekgyakpgkvvvgaDshtttsGalgafatGlGa 135
                                                ++a     +re+a+++ i+  fdvg +G+ch ++ ekgy++pg  v+ +Dsht+t+Ga+gafa G+G+
  lcl|NCBI__GCF_900142125.1:WP_072905201.1  71 SKTATQALILREWARRHDIPDfFDVGrNGVCHAIFPEKGYIRPGFTVIMGDSHTCTHGAFGAFAAGVGT 139
                                               *********************9999746***************************************** PP

                                 TIGR02086 136 tDvalalatGktWlkvPesikveleGkleekvtakDvileivkelgadgatykaieftgeeiealslde 204
                                               tD+ + ++ G   ++ P+s++v+l+G+l + v akDvil ++++lg +gat ++ief g  ++++s++ 
  lcl|NCBI__GCF_900142125.1:WP_072905201.1 140 TDLEVGILKGVCSFREPKSLRVNLNGSLPQGVFAKDVILYVIGQLGVNGATDRVIEFRGPIVDQMSMEA 208
                                               ********************************************************************* PP

                                 TIGR02086 205 Rltlsnlaveagakaglvepdeetleylkkrrge...........frilkadedakyeeeieidlsele 262
                                               R+tl+n+a+eag+ +g+  pd +t+eyl    ++           +    +d+da+y++ ++id+s++e
  lcl|NCBI__GCF_900142125.1:WP_072905201.1 209 RMTLCNMAIEAGGTSGVCMPDMTTVEYLWPFIQDefaskeaaleeYSKWISDDDASYDKVVDIDVSSME 277
                                               ***************************976555556667788777667789****************** PP

                                 TIGR02086 263 plvavPhsvdnvkeveevegteidqvfiGsCtnGRledlkiaaeilegrevhkdvrlivvPasrkvyek 331
                                               p+v+  +++d vk+v e+ gt++dq++iGsCtnGR+edl++aa +l+g++v+ +vr iv+Pa  k++++
  lcl|NCBI__GCF_900142125.1:WP_072905201.1 278 PMVTFDYKPDCVKTVPEMAGTKVDQIYIGSCTNGRIEDLREAAAVLKGKTVADSVRGIVSPATPKIFQE 346
                                               ********************************************************************* PP

                                 TIGR02086 332 aleeGlietlveaGaiiltpgCGPClGahlGvladgevivsttnRnfkGRmGspkaeiYLasPavaavs 400
                                               al eG+i+++++aG  +++p+CG ClG   Gvla+gev+ sttnRnf GRmG+    ++L sPa+aa++
  lcl|NCBI__GCF_900142125.1:WP_072905201.1 347 ALAEGIIQVFMDAGFCVTNPTCGACLGMSNGVLAEGEVCASTTNRNFSGRMGKG-GMVHLMSPATAAAT 414
                                               ****************************************************75.78************ PP

                                 TIGR02086 401 aveGeitdpe 410
                                               a++G+itd +
  lcl|NCBI__GCF_900142125.1:WP_072905201.1 415 AITGVITDAR 424
                                               *******976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (411 nodes)
Target sequences:                          1  (426 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: 00:00:00.02
# Mc/sec: 6.97
//
[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