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; EC 4.2.1.33 (characterized)
to candidate RR42_RS01530 RR42_RS01530 isopropylmalate isomerase

Query= CharProtDB::CH_024771
         (466 letters)



>FitnessBrowser__Cup4G11:RR42_RS01530
          Length = 472

 Score =  476 bits (1226), Expect = e-139
 Identities = 242/464 (52%), Positives = 310/464 (66%), Gaps = 1/464 (0%)

Query: 4   TLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMDH 63
           T Y KL D+H V   + +  LLY D HL++E TSPQAF GL A GR V  PG+  A +DH
Sbjct: 5   TYYRKLVDSHTVAALDADHVLLYADLHLMNEYTSPQAFAGLAAQGRGVPSPGQQVAVVDH 64

Query: 64  NVSTQTKDINACGEMAR-IQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLPGM 122
            + T  +      + A  +Q + L +NC + G+ L+D +   QGI HV+ PE G+  PGM
Sbjct: 65  IIPTHAESPRRIQDPASALQARNLKRNCDQHGIPLFDTDDALQGIEHVIAPEHGMIRPGM 124

Query: 123 TIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITAKD 182
            ++CGDSHT T+GA GAL FGIGTSEVEHVLATQTL    A  M+I V G    G TAKD
Sbjct: 125 VVLCGDSHTTTYGALGALGFGIGTSEVEHVLATQTLVYRVAMDMRIRVDGVLPCGATAKD 184

Query: 183 IVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTFNY 242
           ++L II +  + G  G+VVEF G AI  LS+E RMTLCNM +E GA+  L+APD     Y
Sbjct: 185 MILHIISRISAQGARGYVVEFTGSAIAALSIEARMTLCNMTVEAGARGALIAPDAAAIEY 244

Query: 243 VKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISVND 302
           V  R         + A+A W+ L +D  A FD+ +   A  ++P V+WGT+P Q I ++ 
Sbjct: 245 VLARAADIDATLRERALACWRALHSDADARFDSELVFDASNVAPYVSWGTSPDQAIPIDA 304

Query: 303 NIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAEIA 362
            +P      D   R++A KAL Y+GL+ G  L  + + +VFIGSCTN RIEDLRA A I 
Sbjct: 305 CVPPVEDAIDDTARSAAAKALDYIGLQAGATLEGLPVQRVFIGSCTNGRIEDLRAVAAIV 364

Query: 363 KGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNPGE 422
           +GRKVA GV+A+VVPGSG V+ QAE EG+ ++ ++AGFEWR PGCSMCLAMN+D L PGE
Sbjct: 365 RGRKVAAGVRAMVVPGSGAVRQQAEDEGIAQVLLDAGFEWRKPGCSMCLAMNDDVLAPGE 424

Query: 423 RCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNIK 466
           RCAST+NRNFEGRQGR GRTHL+SPAMAAAAA+TG   D+R ++
Sbjct: 425 RCASTTNRNFEGRQGRAGRTHLMSPAMAAAAALTGCITDVRRLE 468


Lambda     K      H
   0.317    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: 710
Number of extensions: 22
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: 466
Length of database: 472
Length adjustment: 33
Effective length of query: 433
Effective length of database: 439
Effective search space:   190087
Effective search space used:   190087
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_RS01530 RR42_RS01530 (isopropylmalate isomerase)
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.27646.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.3e-188  613.2   0.1   1.6e-188  613.0   0.1    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS01530  RR42_RS01530 isopropylmalate iso


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS01530  RR42_RS01530 isopropylmalate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  613.0   0.1  1.6e-188  1.6e-188       4     465 ..       5     466 ..       2     467 .. 0.99

  Alignments for each domain:
  == domain 1  score: 613.0 bits;  conditional E-value: 1.6e-188
                                 TIGR00170   4 tlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrd. 71 
                                               t y kl d+h v   +++  lly d+hl+ e tspqaf gl a+gr v  +++ +a +dh i+t++   
  lcl|FitnessBrowser__Cup4G11:RR42_RS01530   5 TYYRKLVDSHTVAALDADHVLLYADLHLMNEYTSPQAFAGLAAQGRGVPSPGQQVAVVDHIIPTHAESp 73 
                                               789*************************************************************99851 PP

                                 TIGR00170  72 veikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgal 140
                                                 i++  + lq ++l++n+++ g++lfd ++a qgi hv+ pe+g+  pg+ ++cgdsht+t+ga+gal
  lcl|FitnessBrowser__Cup4G11:RR42_RS01530  74 RRIQDPASALQARNLKRNCDQHGIPLFDTDDALQGIEHVIAPEHGMIRPGMVVLCGDSHTTTYGALGAL 142
                                               567788899************************************************************ PP

                                 TIGR00170 141 afgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageair 209
                                                fgigtsevehvlatqtl+   a  ++i+v+g l  g takd+il ii +i+++g  gyvvef+g ai 
  lcl|FitnessBrowser__Cup4G11:RR42_RS01530 143 GFGIGTSEVEHVLATQTLVYRVAMDMRIRVDGVLPCGATAKDMILHIISRISAQGARGYVVEFTGSAIA 211
                                               ********************************************************************* PP

                                 TIGR00170 210 dlsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvt 278
                                               +ls+e+rmt+cnm++eaga+  liapd +++eyv  r         e a+a w++l++d +a+fd +++
  lcl|FitnessBrowser__Cup4G11:RR42_RS01530 212 ALSIEARMTLCNMTVEAGARGALIAPDAAAIEYVLARAADIDATLRERALACWRALHSDADARFDSELV 280
                                               ********************************************************************* PP

                                 TIGR00170 279 leakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsc 347
                                               ++a++++p v+wgt+p+q+++++  vp  ++  d+  ++ a kal+y+gl++g  l+ + v++vfigsc
  lcl|FitnessBrowser__Cup4G11:RR42_RS01530 281 FDASNVAPYVSWGTSPDQAIPIDACVPPVEDAIDDTARSAAAKALDYIGLQAGATLEGLPVQRVFIGSC 349
                                               ********************************************************************* PP

                                 TIGR00170 348 tnsriedlraaaevvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnn 416
                                               tn+riedlra a++v+g+kva +v+ a+vvpgsg+v++qae eg+ +++l+agfewr++gcs+cl+mn+
  lcl|FitnessBrowser__Cup4G11:RR42_RS01530 350 TNGRIEDLRAVAAIVRGRKVAAGVR-AMVVPGSGAVRQQAEDEGIAQVLLDAGFEWRKPGCSMCLAMND 417
                                               *************************.******************************************* PP

                                 TIGR00170 417 dvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdire 465
                                               dvl ++ercast+nrnfegrqg+++rthl+spamaaaaa++g + d+r 
  lcl|FitnessBrowser__Cup4G11:RR42_RS01530 418 DVLAPGERCASTTNRNFEGRQGRAGRTHLMSPAMAAAAALTGCITDVRR 466
                                               ***********************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (472 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: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 6.95
//
[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