Alignments for a candidate for leuC in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Dyella japonica UNC79MFTsu3.2

Align 3-isopropylmalate dehydratase large subunit; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase; EC 4.2.1.33 (characterized)
to candidate N515DRAFT_0572 N515DRAFT_0572 3-isopropylmalate/(R)-2-methylmalate dehydratase large subunit

Query= SwissProt::Q7TXH6
         (473 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0572
          Length = 471

 Score =  544 bits (1401), Expect = e-159
 Identities = 270/468 (57%), Positives = 339/468 (72%), Gaps = 13/468 (2%)

Query: 9   RTLAEKIWDDHIVVSGGGCAPDLIYIDLHLVHEVTSPQAFDGLRLAGRRVRRPELTLATE 68
           RTL EK+WD H+V       P ++YIDLHLVHEVTSPQAF  LR  G ++RRP+  LAT 
Sbjct: 4   RTLFEKLWDAHVVAPETADTPAILYIDLHLVHEVTSPQAFSELRERGLKLRRPDRALATL 63

Query: 69  DHNVPTVDI----DQPIADPVSRTQVETLRRNCAEFGIRLHSMGDIEQGIVHVVGPQLGL 124
           DH+ PT+      ++P A+  ++ QV  L  NC EFG+ LH     E+GIVHV+GP+LG 
Sbjct: 64  DHSTPTLPANDKGERPYANEEAKAQVAQLEANCREFGVELHGWDSSERGIVHVIGPELGA 123

Query: 125 TQPGMTIVCGDSHTSTHGAFGALAMGIGTSEVEHVLATQTLPLRPFKTMAVNVDGRLPDG 184
           TQPGMTIVCGDSHTSTHGAFGALA GIGT+EV HV+ATQ L  R  KT+A++VDG+LP G
Sbjct: 124 TQPGMTIVCGDSHTSTHGAFGALAFGIGTTEVGHVMATQCLLQRKPKTLAIHVDGQLPKG 183

Query: 185 VSAKDIILALIAKIGTGGGQGHVIEYRGSAIESLSMEGRMTICNMSIEAGARAGMVAPDE 244
           + AKD+IL +I +IG  GG GHVIEYRG AIE+LSM+ RMT+CNMSIEAGARAG++APD+
Sbjct: 184 IGAKDLILHIIGEIGVDGGTGHVIEYRGEAIEALSMDERMTVCNMSIEAGARAGLIAPDD 243

Query: 245 TTYAFLRGRPHAPTGAQWDTALVYWQRLRTDVGAVFDTEVYLDAASLSPFVTWGTNPGQG 304
           TT+A+L+GRP  P GA WD A+  W+ LRTD GA +D EV +DA+ + P VT+GT+PG  
Sbjct: 244 TTFAWLKGRPRVPQGAAWDAAVAKWRALRTDAGASYDREVRIDASKVKPTVTYGTHPGMA 303

Query: 305 VPLAAAVPDPQLMTDDAERQAAE-KALAYMDLRPGTAMREIAVDAVFVGSCTNGRIEDLR 363
           + + A VP        A R A E +AL YM  +PG  M+   VD VF+GSCTN R+ DLR
Sbjct: 304 IAMDAPVP--------AARSAQETRALDYMRAQPGKPMQGTPVDVVFIGSCTNSRLSDLR 355

Query: 364 VVAEVLRGRKVADGVRMLIVPGSMRVRAQAEAEGLGEIFTDAGAQWRQAGCSMCLGMNPD 423
             A +LRGR++A+GVRML+VPGS  VR  AE EGL ++FT AGA+WR  GCSMC+ MN D
Sbjct: 356 EAAAILRGRRIAEGVRMLVVPGSEAVRRDAEREGLHQVFTAAGAEWRVPGCSMCIAMNGD 415

Query: 424 QLASGERCAATSNRNFEGRQGAGGRTHLVSPAVAAATAVRGTLSSPAD 471
               G+   +TSNRNFEGRQG G RT L SPA AAA+A+ G+++ P +
Sbjct: 416 LAQPGQLVVSTSNRNFEGRQGKGARTVLASPATAAASALAGSIADPRE 463


Lambda     K      H
   0.319    0.135    0.402 

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: 699
Number of extensions: 26
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: 473
Length of database: 471
Length adjustment: 33
Effective length of query: 440
Effective length of database: 438
Effective search space:   192720
Effective search space used:   192720
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: 51 (24.3 bits)

Align candidate N515DRAFT_0572 N515DRAFT_0572 (3-isopropylmalate/(R)-2-methylmalate dehydratase large subunit)
to HMM TIGR00170 (leuC: 3-isopropylmalate dehydratase, large subunit (EC 4.2.1.33))

# 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/TIGR00170.hmm
# target sequence database:        /tmp/gapView.15910.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00170  [M=466]
Accession:   TIGR00170
Description: leuC: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   2.4e-202  658.6   0.0   2.8e-202  658.3   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_0572  N515DRAFT_0572 3-isopropylmalate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_0572  N515DRAFT_0572 3-isopropylmalate/(R)-2-methylmalate dehydratase large su
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  658.3   0.0  2.8e-202  2.8e-202       2     465 ..       3     463 ..       2     464 .. 0.97

  Alignments for each domain:
  == domain 1  score: 658.3 bits;  conditional E-value: 2.8e-202
                                    TIGR00170   2 aktlyeklfdahvvkeaen.etdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnis 66 
                                                  a+tl+ekl+dahvv  + +  + +lyid+hlvhevtspqaf  lr++g k+rr+d++latldh+ +
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0572   3 ARTLFEKLWDAHVVAPETAdTPAILYIDLHLVHEVTSPQAFSELRERGLKLRRPDRALATLDHSTP 68 
                                                  89************9666505679*****************************************9 PP

                                    TIGR00170  67 tesr....dveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgd 128
                                                  t       +    +e+ak qv +le n++efgv+l++ +s+e+givhv+gpe g t pg+tivcgd
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0572  69 TLPAndkgERPYANEEAKAQVAQLEANCREFGVELHGWDSSERGIVHVIGPELGATQPGMTIVCGD 134
                                                  97553334566789**************************************************** PP

                                    TIGR00170 129 shtathgafgalafgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigva 194
                                                  sht+thgafgalafgigt+ev hv+atq l q ++ktl i+v+g+l kgi akd+il iig igv 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0572 135 SHTSTHGAFGALAFGIGTTEVGHVMATQCLLQRKPKTLAIHVDGQLPKGIGAKDLILHIIGEIGVD 200
                                                  ****************************************************************** PP

                                    TIGR00170 195 ggtgyvvefageairdlsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekava 260
                                                  ggtg+v+e+ geai++lsm+ermtvcnm+ieaga+agliapd+ttf+++k+r+  p+g+ ++ ava
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0572 201 GGTGHVIEYRGEAIEALSMDERMTVCNMSIEAGARAGLIAPDDTTFAWLKGRPRVPQGAAWDAAVA 266
                                                  ****************************************************************** PP

                                    TIGR00170 261 ywktlktdegakfdkvvtleakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalayl 326
                                                  +w++l+td ga +d++v ++a+++ p+vt+gt pg++++++  vp+ +s       a+  +al+y+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0572 267 KWRALRTDAGASYDREVRIDASKVKPTVTYGTHPGMAIAMDAPVPAARS-------AQETRALDYM 325
                                                  ******************************************9998776.......45679***** PP

                                    TIGR00170 327 glepgtklkdikvdkvfigsctnsriedlraaaevvkgkkvadnvklalvvpgsglvkkqaekegl 392
                                                    +pg++++   vd vfigsctnsr+ dlr+aa++++g+++a++v+ +lvvpgs++v+++ae+egl
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0572 326 RAQPGKPMQGTPVDVVFIGSCTNSRLSDLREAAAILRGRRIAEGVR-MLVVPGSEAVRRDAEREGL 390
                                                  **********************************************.9****************** PP

                                    TIGR00170 393 dkifleagfewreagcslclgmnndvldeyercastsnrnfegrqgkgarthlvspamaaaaavag 458
                                                   ++f +ag+ewr +gcs+c++mn d  ++++   stsnrnfegrqgkgart l spa aaa+a+ag
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0572 391 HQVFTAAGAEWRVPGCSMCIAMNGDLAQPGQLVVSTSNRNFEGRQGKGARTVLASPATAAASALAG 456
                                                  ****************************************************************** PP

                                    TIGR00170 459 kfvdire 465
                                                   ++d re
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0572 457 SIADPRE 463
                                                  ***9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (471 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: 11.59
//
[ok]

This GapMind analysis is from Apr 09 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