Alignments for a candidate for leuC in Phaeobacter inhibens BS107

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.8793.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: 10.31
//
[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