Aligments for a candidate for ilvC in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Aligments for a candidate for ilvC in Dyella japonica UNC79MFTsu3.2

Align ketol-acid reductoisomerase (NAD+) (EC 1.1.1.382); ketol-acid reductoisomerase (NADP+) (EC 1.1.1.86) (characterized)
to candidate N515DRAFT_0568 N515DRAFT_0568 ketol-acid reductoisomerase

Query= BRENDA::C8WR67
         (344 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0568
          Length = 339

 Score =  395 bits (1015), Expect = e-115
 Identities = 194/316 (61%), Positives = 241/316 (76%), Gaps = 1/316 (0%)

Query: 15  LADKRIAVIGYGSQGHAHAQNLRDSGFDVVIGLRPGS-SWAKAEADGFRVMAVGEAVEES 73
           LA+ RIAV+GYGSQG AHA NLRDSG DVV+GLR G  SW +A A+GF V   GEAV  +
Sbjct: 10  LANARIAVLGYGSQGRAHALNLRDSGLDVVVGLRKGGPSWERASAEGFTVAEPGEAVRGA 69

Query: 74  DVIMILLPDERQPAVYEREIRPYLTAGKALAFAHGFNIHFSQIQPPKDVDVFMVAPKGPG 133
           D++ +L PD  QPA+Y+  I P + AG AL FAHGFN+HF QI P +D+DV +VAPKGPG
Sbjct: 70  DLVAVLTPDMVQPALYKESIEPNIKAGAALLFAHGFNVHFKQIAPREDIDVILVAPKGPG 129

Query: 134 HLVRRVYEAGGGVPALIAVHQDASGQAKDLALAYARGIGAGRAGILTTTFREETETDLFG 193
            LVRR YE G GVP++ A+HQD +GQA+  A AYA GIG GRA ++ T F+EETETDLFG
Sbjct: 130 ALVRREYEIGRGVPSIWAIHQDVTGQAEAKAKAYADGIGGGRALLIKTDFKEETETDLFG 189

Query: 194 EQAVLCGGLSALIKAGFETLVEAGYQPEIAYFECLHEMKLIVDLIYEGGLEYMRYSISDT 253
           EQAVLCGG S+L++AGFETLVEAGYQPEIAY+E LHE+KLIVDL YEGG+  M   +S+T
Sbjct: 190 EQAVLCGGASSLVQAGFETLVEAGYQPEIAYYEVLHELKLIVDLFYEGGIARMLEFVSET 249

Query: 254 AQWGDFTSGPRIINEETKKEMRRILADIQSGAFAKSWILENQANRPMFNAINRRELEHPI 313
           AQ+GD+ SGPR+I+  TK  M+ +L DIQ G FA++WI E QA  P +    + +LEHPI
Sbjct: 250 AQYGDYVSGPRVIDAGTKARMKDVLTDIQDGTFARNWIAEYQAGLPNYKRFKQADLEHPI 309

Query: 314 EVVGRKLRSMMPFIKA 329
           E VG KLR+ M +++A
Sbjct: 310 EQVGAKLRARMSWLQA 325


Lambda     K      H
   0.320    0.138    0.404 

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: 395
Number of extensions: 12
Number of successful extensions: 2
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: 344
Length of database: 339
Length adjustment: 29
Effective length of query: 315
Effective length of database: 310
Effective search space:    97650
Effective search space used:    97650
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate N515DRAFT_0568 N515DRAFT_0568 (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.31020.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   7.2e-134  431.6   0.0   8.3e-134  431.4   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_0568  N515DRAFT_0568 ketol-acid reduct


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_0568  N515DRAFT_0568 ketol-acid reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  431.4   0.0  8.3e-134  8.3e-134       1     313 [.      10     323 ..      10     324 .. 0.99

  Alignments for each domain:
  == domain 1  score: 431.4 bits;  conditional E-value: 8.3e-134
                                    TIGR00465   1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiL 66 
                                                  l++ ++a++GyGsqG+a+alnlrdsgl+v+vglrk++ sw++A+ +Gf v +  ea++ adl+++L
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0568  10 LANARIAVLGYGSQGRAHALNLRDSGLDVVVGLRKGGPSWERASAEGFTVAEPGEAVRGADLVAVL 75 
                                                  67899************************************************************* PP

                                    TIGR00465  67 lpDevqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrG 132
                                                  +pD+vq++ y+++i+p++k+g+allf+HGfn++fkqi +++d+dv+lvAPKgpGalvR+ey+ grG
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0568  76 TPDMVQPALYKESIEPNIKAGAALLFAHGFNVHFKQIAPREDIDVILVAPKGPGALVRREYEIGRG 141
                                                  ****************************************************************** PP

                                    TIGR00465 133 vpsliAveqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafd 198
                                                  vps+ A++qdvtg+a ++A+ayA +iGg+ra +++t FkeE+e+DLfGEqavLcGg + l++a+f+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0568 142 VPSIWAIHQDVTGQAEAKAKAYADGIGGGRALLIKTDFKEETETDLFGEQAVLCGGASSLVQAGFE 207
                                                  ****************************************************************** PP

                                    TIGR00465 199 tLveaGyqpelAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqki 263
                                                  tLveaGyqpe+Ay e++helklivdl +e+G++ m + vs+tA++g++ ++ +++++ +k++m+++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0568 208 TLVEAGYQPEIAYYEVLHELKLIVDLFYEGGIARMLEFVSETAQYGDYVSGpRVIDAGTKARMKDV 273
                                                  ***************************************************9************** PP

                                    TIGR00465 264 lkeiqnGefakewalekeagkpafeearkkekeqeiekvGkelralvkae 313
                                                  l +iq+G+fa++w+ e +ag p++++ ++++ e+ ie+vG +lra +++ 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0568 274 LTDIQDGTFARNWIAEYQAGLPNYKRFKQADLEHPIEQVGAKLRARMSWL 323
                                                  *********************************************99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (314 nodes)
Target sequences:                          1  (339 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: 00:00:00.01
# Mc/sec: 7.62
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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