Alignments for a candidate for ilvC in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvC in Herbaspirillum seropedicae SmR1

Align acetohydroxyacid isomeroreductase (EC 1.1.1.86) (characterized)
to candidate HSERO_RS08660 HSERO_RS08660 ketol-acid reductoisomerase

Query= metacyc::MONOMER-18814
         (338 letters)



>FitnessBrowser__HerbieS:HSERO_RS08660
          Length = 338

 Score =  583 bits (1503), Expect = e-171
 Identities = 289/338 (85%), Positives = 308/338 (91%)

Query: 1   MKVFYDKDADLSLIKGKNVTIIGYGSQGHAHALNLKDSGVNVTVGLRKSGASWNKAANAG 60
           MKVFYDKDADLSLIK KNVTIIGYGSQGHAHALNLKDSGV VTVGLRK GASWNKA  AG
Sbjct: 1   MKVFYDKDADLSLIKNKNVTIIGYGSQGHAHALNLKDSGVKVTVGLRKGGASWNKAEQAG 60

Query: 61  LQVKEVAEAVKGADVVMILLPDEQIADVYKNEVHDNIKEGAALAFAHGFNVHYGAVIPRA 120
           L+V EV EAVK ADV+MILLPDE I  VY   V    K+GA +AFAHGFN+HYG V+PRA
Sbjct: 61  LKVAEVNEAVKDADVIMILLPDENIGQVYAENVAPFAKQGATVAFAHGFNIHYGQVVPRA 120

Query: 121 DLDVIMIAPKAPGHTVRATYTQGGGVPHLIAVHQNKSGAARDIALSYATANGGGRAGIIE 180
           DLD+IMIAPKAPGHTVR+TY+QGGGVPHLIAVHQ+KSG+ARD+ALSYATANGGGRAGIIE
Sbjct: 121 DLDIIMIAPKAPGHTVRSTYSQGGGVPHLIAVHQDKSGSARDLALSYATANGGGRAGIIE 180

Query: 181 TNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIYE 240
           TNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIYE
Sbjct: 181 TNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIYE 240

Query: 241 GGIANMNYSISNNAEYGEYVTGPRVVTEETKKAMKQCLTDIQTGEYAKSFLLENKAGAPT 300
           GGIANMNYSISNNAEYGEYVTGPRV+  E+K AMK+ L DIQTGEYAKSF+LENKAGAPT
Sbjct: 241 GGIANMNYSISNNAEYGEYVTGPRVINAESKAAMKKVLEDIQTGEYAKSFILENKAGAPT 300

Query: 301 LISRRRLTAEHQIEEVGAKLRAMMPWIAKNKMVDQSKN 338
           L+SRRR+ AEHQIE VG KLRAMMPWI  NK+VDQSKN
Sbjct: 301 LMSRRRINAEHQIEIVGEKLRAMMPWIKANKLVDQSKN 338


Lambda     K      H
   0.316    0.133    0.379 

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: 534
Number of extensions: 15
Number of successful extensions: 1
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: 338
Length of database: 338
Length adjustment: 28
Effective length of query: 310
Effective length of database: 310
Effective search space:    96100
Effective search space used:    96100
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 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate HSERO_RS08660 HSERO_RS08660 (ketol-acid reductoisomerase)
to HMM TIGR00465 (ilvC: ketol-acid reductoisomerase (EC 1.1.1.86))

# 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/TIGR00465.hmm
# target sequence database:        /tmp/gapView.520942.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00465  [M=314]
Accession:   TIGR00465
Description: ilvC: ketol-acid reductoisomerase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
   1.6e-138  446.9   2.1   1.8e-138  446.7   2.1    1.0  1  FitnessBrowser__HerbieS:HSERO_RS08660  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__HerbieS:HSERO_RS08660  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  446.7   2.1  1.8e-138  1.8e-138       1     313 [.      14     327 ..      14     328 .. 0.99

  Alignments for each domain:
  == domain 1  score: 446.7 bits;  conditional E-value: 1.8e-138
                              TIGR00465   1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDevq 72 
                                            +k+k+v+iiGyGsqG+a+alnl+dsg++v+vglrk++asw+kAe+ G+kv +v+ea+k+ad+imiLlpDe  
  FitnessBrowser__HerbieS:HSERO_RS08660  14 IKNKNVTIIGYGSQGHAHALNLKDSGVKVTVGLRKGGASWNKAEQAGLKVAEVNEAVKDADVIMILLPDENI 85 
                                            689********************************************************************* PP

                              TIGR00465  73 kevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqdvt 144
                                             +vy ++++p+ k+g+++ f+HGfni++ q+v+++d+d++++APK+pG++vR++y +g Gvp+liAv+qd +
  FitnessBrowser__HerbieS:HSERO_RS08660  86 GQVYAENVAPFAKQGATVAFAHGFNIHYGQVVPRADLDIIMIAPKAPGHTVRSTYSQGGGVPHLIAVHQDKS 157
                                            ************************************************************************ PP

                              TIGR00465 145 geakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivh 216
                                            g a++ Al+yA a Gg+rag++et F+eE+e+DLfGEqavLcGg  +lika+f+tLveaGy+pe+Ayfe++h
  FitnessBrowser__HerbieS:HSERO_RS08660 158 GSARDLALSYATANGGGRAGIIETNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLH 229
                                            ************************************************************************ PP

                              TIGR00465 217 elklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefakewalekeagkpaf 287
                                            elklivdl++e+G+++m  ++sn A++g++ ++ +++++e k++m+k+l++iq+Ge+ak ++le++ag+p++
  FitnessBrowser__HerbieS:HSERO_RS08660 230 ELKLIVDLIYEGGIANMNYSISNNAEYGEYVTGpRVINAESKAAMKKVLEDIQTGEYAKSFILENKAGAPTL 301
                                            *********************************9************************************** PP

                              TIGR00465 288 eearkkekeqeiekvGkelralvkae 313
                                             + r+ + e++ie vG++lra++++ 
  FitnessBrowser__HerbieS:HSERO_RS08660 302 MSRRRINAEHQIEIVGEKLRAMMPWI 327
                                            ***********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (314 nodes)
Target sequences:                          1  (338 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 19.85
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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