GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Phaeobacter inhibens BS107

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate GFF2931 PGA1_c29780 3-isopropylmalate dehydratase large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>FitnessBrowser__Phaeo:GFF2931
          Length = 467

 Score =  619 bits (1597), Expect = 0.0
 Identities = 309/466 (66%), Positives = 370/466 (79%), Gaps = 6/466 (1%)

Query: 3   KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62
           KTLY+K++DAHV +EAE+ T LLYIDRHLVHEVTSPQAF+GLR  GR V  P KT A  D
Sbjct: 4   KTLYDKIWDAHVAHEAEDGTCLLYIDRHLVHEVTSPQAFEGLRMAGRKVHAPDKTIAVPD 63

Query: 63  HNVST---QTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTL 119
           HNV T   + K I    E +RIQ++ L KN +EFGV  Y ++   QGIVH++GPEQG TL
Sbjct: 64  HNVPTTLDRAKGIE--NEESRIQVEALDKNAREFGVHYYPVDDVRQGIVHIVGPEQGWTL 121

Query: 120 PGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGIT 179
           PGMT+VCGDSHTATHGAFGALA GIGTSEVEHVLATQTL Q ++K MK+E+ GK  PG+T
Sbjct: 122 PGMTVVCGDSHTATHGAFGALAHGIGTSEVEHVLATQTLIQKKSKNMKVEITGKLKPGVT 181

Query: 180 AKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETT 239
           AKDI LA+IG+TG+AGGTG+V+E+CGEAIRDL+MEGRMT+CNMAIE GA+AGL+APDETT
Sbjct: 182 AKDITLAVIGETGTAGGTGYVIEYCGEAIRDLTMEGRMTVCNMAIEGGARAGLIAPDETT 241

Query: 240 FNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVIS 299
           F YVKGR HAPKG  ++ A+ +WKTL TDEGA FD VVTL+ E+I P VTWGT+P  V+ 
Sbjct: 242 FEYVKGRPHAPKGAQWEAALNWWKTLFTDEGAHFDKVVTLKGEDIQPVVTWGTSPEDVLP 301

Query: 300 VNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAA 359
           +   +P P  F      A A ++L YMGL PG  LT++ ID VFIGSCTN RIEDLRA A
Sbjct: 302 ITGVVPAPEDFTGGKVEA-ARRSLEYMGLTPGQKLTDIEIDTVFIGSCTNGRIEDLRAVA 360

Query: 360 EIAKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLN 419
           E+ KG+K+  G++A+VVPGSG V+AQAE EG+ +I  +AGFEWRL GCSMCLAMN D+L+
Sbjct: 361 EVVKGKKIKDGMRAMVVPGSGLVRAQAEEEGIAEILQDAGFEWRLAGCSMCLAMNPDQLS 420

Query: 420 PGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465
            GERCA+TSNRNFEGRQG  GRTHLVSPAMAAAAA+TG   D+R +
Sbjct: 421 EGERCAATSNRNFEGRQGYKGRTHLVSPAMAAAAALTGKLTDVREL 466


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: 801
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: 466
Length of database: 467
Length adjustment: 33
Effective length of query: 433
Effective length of database: 434
Effective search space:   187922
Effective search space used:   187922
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 GFF2931 PGA1_c29780 (3-isopropylmalate 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.19993.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
     1e-243  794.9   0.7   1.2e-243  794.7   0.7    1.0  1  lcl|FitnessBrowser__Phaeo:GFF2931  PGA1_c29780 3-isopropylmalate de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF2931  PGA1_c29780 3-isopropylmalate dehydratase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  794.7   0.7  1.2e-243  1.2e-243       2     466 .]       3     466 ..       2     466 .. 0.98

  Alignments for each domain:
  == domain 1  score: 794.7 bits;  conditional E-value: 1.2e-243
                          TIGR00170   2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhniste.srdveike 76 
                                        +ktly+k++dahv +eae++t llyidrhlvhevtspqafeglr agrkv  +dkt+a  dhn++t+  r   i +
  lcl|FitnessBrowser__Phaeo:GFF2931   3 PKTLYDKIWDAHVAHEAEDGTCLLYIDRHLVHEVTSPQAFEGLRMAGRKVHAPDKTIAVPDHNVPTTlDRAKGIEN 78 
                                        89**************************************************************987257788999 PP

                          TIGR00170  77 ekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigtsevehv 152
                                        e++++qv++l+kn++efgv+++ +++++qgivh+vgpe+g tlpg+t+vcgdshtathgafgala gigtsevehv
  lcl|FitnessBrowser__Phaeo:GFF2931  79 EESRIQVEALDKNAREFGVHYYPVDDVRQGIVHIVGPEQGWTLPGMTVVCGDSHTATHGAFGALAHGIGTSEVEHV 154
                                        **************************************************************************** PP

                          TIGR00170 153 latqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtvcnmaieaga 228
                                        latqtl+q+++k++k+e+ gkl++g+takdi la+ig +g+aggtgyv+e++geairdl+me+rmtvcnmaie ga
  lcl|FitnessBrowser__Phaeo:GFF2931 155 LATQTLIQKKSKNMKVEITGKLKPGVTAKDITLAVIGETGTAGGTGYVIEYCGEAIRDLTMEGRMTVCNMAIEGGA 230
                                        **************************************************************************** PP

                          TIGR00170 229 kagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgtnpgqvlsvneev 304
                                        +agliapdettfeyvk+r++apkg+++e a++ wktl tdega+fdkvvtl+++di p vtwgt+p++vl++++ v
  lcl|FitnessBrowser__Phaeo:GFF2931 231 RAGLIAPDETTFEYVKGRPHAPKGAQWEAALNWWKTLFTDEGAHFDKVVTLKGEDIQPVVTWGTSPEDVLPITGVV 306
                                        **************************************************************************** PP

                          TIGR00170 305 pdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgkkvadnvklalvvpgs 380
                                        p+p++++   + + a ++l+y+gl+pg+kl+di++d vfigsctn+riedlra aevvkgkk+ d+++ a+vvpgs
  lcl|FitnessBrowser__Phaeo:GFF2931 307 PAPEDFTGG-KVEAARRSLEYMGLTPGQKLTDIEIDTVFIGSCTNGRIEDLRAVAEVVKGKKIKDGMR-AMVVPGS 380
                                        ******986.456789****************************************************.******* PP

                          TIGR00170 381 glvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqgkgarthlvspamaaaaav 456
                                        glv++qae+eg+ +i+++agfewr agcs+cl+mn+d+l+e+erca+tsnrnfegrqg ++rthlvspamaaaaa+
  lcl|FitnessBrowser__Phaeo:GFF2931 381 GLVRAQAEEEGIAEILQDAGFEWRLAGCSMCLAMNPDQLSEGERCAATSNRNFEGRQGYKGRTHLVSPAMAAAAAL 456
                                        **************************************************************************** PP

                          TIGR00170 457 agkfvdirel 466
                                        +gk+ d+rel
  lcl|FitnessBrowser__Phaeo:GFF2931 457 TGKLTDVREL 466
                                        ********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (467 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: 9.13
//
[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:

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:

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:

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:

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