Alignments for a candidate for leuC in Chlorobium limicola DSM 245

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Chlorobium limicola DSM 245

Align 2-(omega-methylthio)alkylmalate dehydratase (subunit 2/2) (EC 4.2.1.170); 3-isopropylmalate dehydratase (EC 4.2.1.33) (characterized)
to candidate WP_012465698.1 CLIM_RS03700 3-isopropylmalate dehydratase large subunit

Query= BRENDA::Q94AR8
         (509 letters)



>NCBI__GCF_000020465.1:WP_012465698.1
          Length = 431

 Score =  518 bits (1333), Expect = e-151
 Identities = 258/441 (58%), Positives = 322/441 (73%), Gaps = 13/441 (2%)

Query: 68  TMTEKILARASEKSLVVPGDNIWVNVDVLMTHDVCGPGAFGIFKREFGEKAKVWDPEKIV 127
           T+T+KIL+RA+ +  V  G+N+W+NVD+L+THDVCGP  F IFK+EFG  AKVWDPEK+V
Sbjct: 4   TITQKILSRAANRKFVDAGENVWLNVDILLTHDVCGPPTFDIFKQEFGPDAKVWDPEKVV 63

Query: 128 VIPDHYIFTADKRANRNVDIMREHCREQNIKYFYDITDLGNFKANPDYKGVCHVALAQEG 187
           V+PDHYIFTA++ A+RN+D++R+   EQ++  +YD+           YKGVCHVALA+EG
Sbjct: 64  VLPDHYIFTANEHAHRNIDLLRQFASEQSLPNYYDV-------GTDRYKGVCHVALAEEG 116

Query: 188 HCRPGEVLLGTDSHTCTAGAFGQFATGIGNTDAGFVLGTGKILLKVPPTMRFILDGEMPS 247
              PG VL GTDSHTCT+GAFG F +GIGNTDA F+LGTGK+  KVP +M+FI +G+MP 
Sbjct: 117 FNIPGTVLFGTDSHTCTSGAFGMFGSGIGNTDAAFILGTGKLWEKVPESMKFIFEGDMPE 176

Query: 248 YLQAKDLILQIIGEISVAGATYKTMEFSGTTIESLSMEERMTLCNMVVEAGGKNGVIPPD 307
           YL AKDLILQI+G+I   GATY+ MEF G  + SL ++ERMTLCNM +EAGG NG+I  D
Sbjct: 177 YLCAKDLILQILGDIGTDGATYRAMEFDGEAVYSLPVDERMTLCNMAIEAGGMNGIIAAD 236

Query: 308 ATTLNYVENRTSVPFEPVYSDGNASFVADYRFDVSKLEPVVAKPHSPDNRALARECKDVK 367
           A T  YV+  +S P+E   SD +A + + YR++  +LEPVVAKPHSPDNRA  R  +  K
Sbjct: 237 AVTEAYVKAHSSKPYEIFQSDPDADYHSVYRYNARELEPVVAKPHSPDNRATVRSMQGTK 296

Query: 368 IDRVYIGSCTGGKTEDFMAAAKLFHAAGRKVKVPTFLVPATQKVWMDVYALPVPGAGGKT 427
           I + YIGSCTGGK  DFM AAK+    G++V VPT +VPAT  V     AL      G T
Sbjct: 297 ITKSYIGSCTGGKLTDFMLAAKIL--KGKQVTVPTNIVPATVLV---ARALECETWEGVT 351

Query: 428 CAQIFEEAGCDTPASPSCGACLGGPADTYARLNEPQVCVSTTNRNFPGRMGHKEGQIYLA 487
             +IFE+AGC   A PSC ACLGGPADT  R  +  V VSTTNRNFPGRMG K+  +YLA
Sbjct: 352 LKKIFEDAGCSI-ALPSCAACLGGPADTVGRSADQDVVVSTTNRNFPGRMGSKKADVYLA 410

Query: 488 SPYTAAASALTGRVADPREFL 508
           SP TAAASA+TG++ DPREFL
Sbjct: 411 SPLTAAASAVTGKLTDPREFL 431


Lambda     K      H
   0.318    0.134    0.404 

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: 715
Number of extensions: 26
Number of successful extensions: 5
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: 509
Length of database: 431
Length adjustment: 33
Effective length of query: 476
Effective length of database: 398
Effective search space:   189448
Effective search space used:   189448
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: 51 (24.3 bits)

Align candidate WP_012465698.1 CLIM_RS03700 (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.26728.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.8e-128  414.1   0.0   3.1e-128  413.9   0.0    1.0  1  lcl|NCBI__GCF_000020465.1:WP_012465698.1  CLIM_RS03700 3-isopropylmalate d


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020465.1:WP_012465698.1  CLIM_RS03700 3-isopropylmalate dehydratase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  413.9   0.0  3.1e-128  3.1e-128       1     411 []       3     429 ..       3     429 .. 0.94

  Alignments for each domain:
  == domain 1  score: 413.9 bits;  conditional E-value: 3.1e-128
                                 TIGR02086   1 ktlaekilsekvGke.vkaGeivevkvDlvmvhDgtgplvikalrelg...akvekkekivlvfDhvvP 65 
                                               +t+++kils+++ ++ v aGe v  +vD+ ++hD  gp ++  +++     akv+++ek+v++ Dh + 
  lcl|NCBI__GCF_000020465.1:WP_012465698.1   3 QTITQKILSRAANRKfVDAGENVWLNVDILLTHDVCGPPTFDIFKQEFgpdAKVWDPEKVVVLPDHYIF 71 
                                               699*********9999****************************9754599****************** PP

                                 TIGR02086  66 aptveaaelqkeirefakelgikv.fdvg....eGichqvlvekgyakpgkvvvgaDshtttsGalgaf 129
                                               +++ +a      +r+fa e+ +++ +dvg    +G+ch  l+e+g+  pg+v++g+Dsht+tsGa+g f
  lcl|NCBI__GCF_000020465.1:WP_012465698.1  72 TANEHAHRNIDLLRQFASEQSLPNyYDVGtdryKGVCHVALAEEGFNIPGTVLFGTDSHTCTSGAFGMF 140
                                               ***9999999*************98887644447*********************************** PP

                                 TIGR02086 130 atGlGatDvalalatGktWlkvPesikveleGkleekvtakDvileivkelgadgatykaieftgeeie 198
                                               + G+G tD a++l+tGk+W kvPes+k  +eG++ e++ akD+il+i++++g+dgaty+a+ef ge + 
  lcl|NCBI__GCF_000020465.1:WP_012465698.1 141 GSGIGNTDAAFILGTGKLWEKVPESMKFIFEGDMPEYLCAKDLILQILGDIGTDGATYRAMEFDGEAVY 209
                                               ********************************************************************* PP

                                 TIGR02086 199 alsldeRltlsnlaveagakaglvepdeetleylkkrrge.frilkadedakyeeeieidlseleplva 266
                                               +l +deR+tl+n+a+eag+ +g++ +d  t+ y+k+++++ ++i+++d+da y+  ++ ++ elep+va
  lcl|NCBI__GCF_000020465.1:WP_012465698.1 210 SLPVDERMTLCNMAIEAGGMNGIIAADAVTEAYVKAHSSKpYEIFQSDPDADYHSVYRYNARELEPVVA 278
                                               *************************************999899************************** PP

                                 TIGR02086 267 vPhsvdnvkeveevegteidqvfiGsCtnGRledlkiaaeilegrevhkdvrlivvPasrkvyek...a 332
                                               +Phs+dn  +v+ ++gt+i++ +iGsCt G+l d+  aa+il+g++  ++v + +vPa   v +     
  lcl|NCBI__GCF_000020465.1:WP_012465698.1 279 KPHSPDNRATVRSMQGTKITKSYIGSCTGGKLTDFMLAAKILKGKQ--VTVPTNIVPATVLVARAlecE 345
                                               **********************************************..778888899987664431114 PP

                                 TIGR02086 333 leeGli..etlveaGaiiltpgCGPClGa...hlGvladgevivsttnRnfkGRmGspkaeiYLasPav 396
                                               + eG++  +++ +aG+ i+ p+C  ClG     +G  ad++v+vsttnRnf GRmGs+ka++YLasP +
  lcl|NCBI__GCF_000020465.1:WP_012465698.1 346 TWEGVTlkKIFEDAGCSIALPSCAACLGGpadTVGRSADQDVVVSTTNRNFPGRMGSKKADVYLASPLT 414
                                               5578762245779***************633368999******************************** PP

                                 TIGR02086 397 aavsaveGeitdpee 411
                                               aa+sav+G++tdp+e
  lcl|NCBI__GCF_000020465.1:WP_012465698.1 415 AAASAVTGKLTDPRE 429
                                               *************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (411 nodes)
Target sequences:                          1  (431 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: 10.33
//
[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