Alignments for a candidate for leuC in Cupriavidus basilensis 4G11

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Cupriavidus basilensis 4G11

Align 3-isopropylmalate dehydratase large subunit 1; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1; EC 4.2.1.33 (characterized)
to candidate RR42_RS22770 RR42_RS22770 3-isopropylmalate dehydratase

Query= SwissProt::P15717
         (466 letters)



>FitnessBrowser__Cup4G11:RR42_RS22770
          Length = 466

 Score =  499 bits (1285), Expect = e-146
 Identities = 251/466 (53%), Positives = 321/466 (68%), Gaps = 2/466 (0%)

Query: 1   MAKTLYEKLFDAHVVFEAPNETPLLYIDRHLVHEVTSPQAFDGLRAHHRPVRQPGKTFAT 60
           MA+TL++KL+DAHVV E  +   LL+IDRHL+H+++ P A   + A   P+  P   F+T
Sbjct: 1   MARTLFDKLWDAHVVRELGDGWALLHIDRHLLHDLSGPPALAEVAARGLPLHDPALVFST 60

Query: 61  MDHNVSTQT-KDINASGEMARIQMQELIKNCNEFGVELYDLNHPYQGIVHVMGPEQGVTL 119
            DH VS+Q  +D N      R+    L       GV ++DL  P QGIVHVMGPE G+ L
Sbjct: 61  PDHAVSSQPGRDGNTHVPGGRL-WSALRDRSAAAGVTMFDLGQPGQGIVHVMGPELGIVL 119

Query: 120 PGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVTGNAAPGIT 179
           PG+T++CGDSHT T+G  GA+AFG+G+SE  H LATQTL+Q + + M+I   G  A GIT
Sbjct: 120 PGLTVICGDSHTCTNGGLGAMAFGVGSSESTHALATQTLRQQKPRRMRIRCDGVLAEGIT 179

Query: 180 AKDIVLAIIGKTGSAGGTGHVVEFCGDAIRALSMEGRMTLCNMAIEMGAKAGLVAPDETT 239
           AKD+ L IIG+ G+A G G+ +EF G AI AL +EGR+TLCN+++E+GA+ G+VAPD  T
Sbjct: 180 AKDLALHIIGRLGAAAGGGYAIEFAGTAIEALEVEGRLTLCNLSVELGARFGMVAPDART 239

Query: 240 FNYVKGRLHAPKGRDFDEAVEYWKTLKTDDGATFDTVVALRAEEIAPQVTWGTNPGQVIS 299
             +++GR +AP G  FD A EYW+TL TD GA FD    + A  +AP +TWGT+P   I+
Sbjct: 240 IEWLRGRPYAPSGAQFDGAAEYWRTLATDAGAVFDREEVIDATAVAPTITWGTSPEHAIA 299

Query: 300 VTDIIPDPASFSDPVERASAEKALAYMGLQPGVPLTDVAIDKVFIGSCTNSRIEDLRAAA 359
           +   IPDPA+ SD    A+   AL YMGL P  P+    +D VFIGSC NSR+ DLRAAA
Sbjct: 300 IDGHIPDPAAASDQAASAAIGAALDYMGLAPNAPIAGTPVDWVFIGSCANSRLSDLRAAA 359

Query: 360 EVAKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLN 419
            VA+GR+VAPGV A VVPGS  VK  AEAEGL  +F +AGF WR PGCSMC+A N +++ 
Sbjct: 360 AVARGRRVAPGVTAWVVPGSENVKRAAEAEGLRTVFEDAGFGWREPGCSMCVAANGEQVP 419

Query: 420 PGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRSI 465
           PG+R  STSNRNF GRQG G RTHL SPAMAAAAAVTG   D+R +
Sbjct: 420 PGQRSVSTSNRNFVGRQGPGARTHLASPAMAAAAAVTGCMTDVRKL 465


Lambda     K      H
   0.318    0.134    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: 781
Number of extensions: 41
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: 466
Length of database: 466
Length adjustment: 33
Effective length of query: 433
Effective length of database: 433
Effective search space:   187489
Effective search space used:   187489
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 RR42_RS22770 RR42_RS22770 (3-isopropylmalate dehydratase)
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.26390.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     2e-179  583.0   0.0   2.3e-179  582.8   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS22770  RR42_RS22770 3-isopropylmalate d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS22770  RR42_RS22770 3-isopropylmalate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  582.8   0.0  2.3e-179  2.3e-179       1     466 []       1     465 [.       1     465 [. 0.98

  Alignments for each domain:
  == domain 1  score: 582.8 bits;  conditional E-value: 2.3e-179
                                 TIGR00170   1 maktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistes 69 
                                               ma+tl++kl+dahvv+e  ++  ll+idrhl+h+++ p a+  + a+g ++  +   ++t dh++s++ 
  lcl|FitnessBrowser__Cup4G11:RR42_RS22770   1 MARTLFDKLWDAHVVRELGDGWALLHIDRHLLHDLSGPPALAEVAARGLPLHDPALVFSTPDHAVSSQP 69 
                                               89****************************************************************995 PP

                                 TIGR00170  70 .rdveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgaf 137
                                                rd +++    +l   +l     + gv +fdl +  qgivhv+gpe g+ lpg t++cgdsht+t g +
  lcl|FitnessBrowser__Cup4G11:RR42_RS22770  70 gRDGNTHVPGGRL-WSALRDRSAAAGVTMFDLGQPGQGIVHVMGPELGIVLPGLTVICGDSHTCTNGGL 137
                                               3788877776666.678999999********************************************** PP

                                 TIGR00170 138 galafgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefage 206
                                               ga+afg+g+se  h latqtl+q++++ ++i+ +g la+gitakd+ l iig++g+a g gy +efag 
  lcl|FitnessBrowser__Cup4G11:RR42_RS22770 138 GAMAFGVGSSESTHALATQTLRQQKPRRMRIRCDGVLAEGITAKDLALHIIGRLGAAAGGGYAIEFAGT 206
                                               ********************************************************************* PP

                                 TIGR00170 207 airdlsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdk 275
                                               ai++l +e+r+t+cn+++e+ga+ g++apd  t+e++++r+yap g++f+ a +yw+tl td ga+fd+
  lcl|FitnessBrowser__Cup4G11:RR42_RS22770 207 AIEALEVEGRLTLCNLSVELGARFGMVAPDARTIEWLRGRPYAPSGAQFDGAAEYWRTLATDAGAVFDR 275
                                               ********************************************************************* PP

                                 TIGR00170 276 vvtleakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfi 344
                                               + +++a+ ++p++twgt+p++++++++++pdp+  +d+   a +  al+y+gl p+ ++    vd vfi
  lcl|FitnessBrowser__Cup4G11:RR42_RS22770 276 EEVIDATAVAPTITWGTSPEHAIAIDGHIPDPAAASDQAASAAIGAALDYMGLAPNAPIAGTPVDWVFI 344
                                               ********************************************************************* PP

                                 TIGR00170 345 gsctnsriedlraaaevvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclg 413
                                               gsc+nsr+ dlraaa+v++g++va++v  a vvpgs+ vk+ ae+egl  +f +agf wre+gcs+c++
  lcl|FitnessBrowser__Cup4G11:RR42_RS22770 345 GSCANSRLSDLRAAAAVARGRRVAPGVT-AWVVPGSENVKRAAEAEGLRTVFEDAGFGWREPGCSMCVA 412
                                               ***************************9.**************************************** PP

                                 TIGR00170 414 mnndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdirel 466
                                                n +++++++r  stsnrnf grqg garthl spamaaaaav+g + d+r+l
  lcl|FitnessBrowser__Cup4G11:RR42_RS22770 413 ANGEQVPPGQRSVSTSNRNFVGRQGPGARTHLASPAMAAAAAVTGCMTDVRKL 465
                                               ***************************************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (466 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: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.63
//
[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