Alignments for a candidate for leuC in Pseudomonas simiae WCS417

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Pseudomonas simiae WCS417

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate GFF1850 PS417_09410 isopropylmalate isomerase

Query= CharProtDB::CH_024771
         (466 letters)



>FitnessBrowser__WCS417:GFF1850
          Length = 472

 Score =  505 bits (1301), Expect = e-147
 Identities = 250/466 (53%), Positives = 327/466 (70%), Gaps = 2/466 (0%)

Query: 2   AKTLYEKLFDAHVVYEAENETP-LLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFAT 60
           A+TLY+K  D+H V   +++   LLYIDR +++E TSPQAF GLR  GR V +PG   A 
Sbjct: 3   ARTLYDKHIDSHTVCPLDDQGHVLLYIDRQVINEYTSPQAFSGLREAGRNVWRPGTALAV 62

Query: 61  MDHNVSTQTKDINACGEMARI-QMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTL 119
           +DH   T  K I A  +     Q+  L +NC++FG+EL D+    QGI HV+ PEQG  L
Sbjct: 63  VDHVNPTTPKRIAAMPDAGGARQVSYLAENCRDFGIELLDILDKRQGIEHVIAPEQGFIL 122

Query: 120 PGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGIT 179
           PGM I  GDSHT T+GA GA  FGIGTSE+EH+LA+QTL   R KTM + V G  APG+T
Sbjct: 123 PGMVIAAGDSHTTTYGALGAFGFGIGTSEIEHLLASQTLVYKRLKTMCVSVDGDLAPGLT 182

Query: 180 AKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETT 239
           +KD+++A+IGK G++G TG+ +EF G  +  LS+E RMT+CNMA+E GA+   +APDE  
Sbjct: 183 SKDVIMALIGKIGASGATGYAIEFRGSTLDALSVEARMTICNMAVEAGARGAFMAPDEKV 242

Query: 240 FNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVIS 299
           F Y+KG+  AP+G+ +D A+A W+ L +D GA FD  V L A  + P VTWGT+P Q   
Sbjct: 243 FAYLKGKPRAPQGELWDQALAGWRLLHSDVGAVFDQEVQLDATTLEPMVTWGTSPDQAAP 302

Query: 300 VNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAA 359
           +   +PDP   +D + R    +AL YMGL+ G+ L+++ I   FIGSCTN+RIEDLR AA
Sbjct: 303 IGARVPDPQDVSDLILRQDMRRALNYMGLEAGMRLSDIVISHAFIGSCTNARIEDLRDAA 362

Query: 360 EIAKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLN 419
            + +G+ VA  V+A++VPGS  V+ QAEAEGL  IFI+AGFEWR  GCSMCLAMN+D L 
Sbjct: 363 SVVRGKHVAEHVRAMIVPGSTEVRDQAEAEGLAAIFIDAGFEWRQSGCSMCLAMNDDVLA 422

Query: 420 PGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465
           PG+RCAS++NRNFEGRQG G RTHL+SPAM AAAA+TG   DIR++
Sbjct: 423 PGDRCASSTNRNFEGRQGAGARTHLMSPAMVAAAAITGRLTDIRHV 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: 692
Number of extensions: 24
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 GFF1850 PS417_09410 (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.819.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.5e-200  652.6   0.0   1.7e-200  652.4   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF1850  PS417_09410 isopropylmalate isom


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF1850  PS417_09410 isopropylmalate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  652.4   0.0  1.7e-200  1.7e-200       2     466 .]       3     468 ..       2     468 .. 0.98

  Alignments for each domain:
  == domain 1  score: 652.4 bits;  conditional E-value: 1.7e-200
                           TIGR00170   2 aktlyeklfdahvvke.aenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdveik 75 
                                         a+tly+k  d+h v   ++++  llyidr ++ e tspqaf glr+agr+v r++++la +dh  +t+ + + ++
  lcl|FitnessBrowser__WCS417:GFF1850   3 ARTLYDKHIDSHTVCPlDDQGHVLLYIDRQVINEYTSPQAFSGLREAGRNVWRPGTALAVVDHVNPTTPKRIAAM 77 
                                         89**********997626677889***************************************999999888776 PP

                           TIGR00170  76 .eekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigtsev 149
                                          +    +qv  l +n+++fg++l+d+ +++qgi hv+ pe+g+ lpg+ i  gdsht+t+ga+ga+ fgigtse+
  lcl|FitnessBrowser__WCS417:GFF1850  78 pDAGGARQVSYLAENCRDFGIELLDILDKRQGIEHVIAPEQGFILPGMVIAAGDSHTTTYGALGAFGFGIGTSEI 152
                                         2666799******************************************************************** PP

                           TIGR00170 150 ehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtvcnmai 224
                                         eh+la+qtl+ +r kt+ + v+g la+g+t+kd+i+a+igkig++g tgy +ef g ++++ls+e+rmt+cnma+
  lcl|FitnessBrowser__WCS417:GFF1850 153 EHLLASQTLVYKRLKTMCVSVDGDLAPGLTSKDVIMALIGKIGASGATGYAIEFRGSTLDALSVEARMTICNMAV 227
                                         *************************************************************************** PP

                           TIGR00170 225 eagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgtnpgqvls 299
                                         eaga+  ++apde  f+y+k+++ ap+g+ +++a+a w+ l++d ga+fd++v+l+a+ + p+vtwgt+p+q+ +
  lcl|FitnessBrowser__WCS417:GFF1850 228 EAGARGAFMAPDEKVFAYLKGKPRAPQGELWDQALAGWRLLHSDVGAVFDQEVQLDATTLEPMVTWGTSPDQAAP 302
                                         *************************************************************************** PP

                           TIGR00170 300 vneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgkkvadnvkla 374
                                         +   vpdp++++d + ++++ +al+y+gle+g++l di + + figsctn+riedlr aa+vv+gk+va+ v+ a
  lcl|FitnessBrowser__WCS417:GFF1850 303 IGARVPDPQDVSDLILRQDMRRALNYMGLEAGMRLSDIVISHAFIGSCTNARIEDLRDAASVVRGKHVAEHVR-A 376
                                         *************************************************************************.* PP

                           TIGR00170 375 lvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqgkgarthlvspa 449
                                         ++vpgs  v+ qae+egl  if++agfewr++gcs+cl+mn+dvl +++rcas++nrnfegrqg+garthl+spa
  lcl|FitnessBrowser__WCS417:GFF1850 377 MIVPGSTEVRDQAEAEGLAAIFIDAGFEWRQSGCSMCLAMNDDVLAPGDRCASSTNRNFEGRQGAGARTHLMSPA 451
                                         *************************************************************************** PP

                           TIGR00170 450 maaaaavagkfvdirel 466
                                         m aaaa++g++ dir++
  lcl|FitnessBrowser__WCS417:GFF1850 452 MVAAAAITGRLTDIRHV 468
                                         ***************85 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 10.99
//
[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