Alignments for a candidate for ilvC in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvC in Echinicola vietnamensis KMM 6221, DSM 17526

Align Ketol-acid reductoisomerase (NAD(+)); KARI; Acetohydroxy-acid isomeroreductase; AHIR; Alpha-keto-beta-hydroxylacyl reductoisomerase; EC 1.1.1.382 (characterized)
to candidate Echvi_2058 Echvi_2058 ketol-acid reductoisomerase

Query= SwissProt::A8ZTR0
         (352 letters)



>FitnessBrowser__Cola:Echvi_2058
          Length = 347

 Score =  490 bits (1261), Expect = e-143
 Identities = 239/344 (69%), Positives = 283/344 (82%)

Query: 4   INFGGVEENVVTSEEFTLKKAREVLKNEVITVLGYGVQGPAQALNLKDNGFEVIIGQLEG 63
           + FG VEE+VVT EEF L+KAREVLK+EVI VLGYGVQGP QALNLKDNGF VI+GQ + 
Sbjct: 3   LKFGTVEEDVVTREEFPLEKAREVLKDEVIAVLGYGVQGPGQALNLKDNGFNVIVGQRKN 62

Query: 64  DAYWEKAIADGFVPGKTLFPIEEAAKKGTIIKMLLSDAGQVAVWPKVKKCLKKGDALYFS 123
              W+KA+ADG+VPG+TLF +EEA +KGTI++ LLSDAGQ+A+WP VKK L  G ALYFS
Sbjct: 63  SKTWDKAVADGWVPGETLFELEEACEKGTILQFLLSDAGQIALWPTVKKHLTPGKALYFS 122

Query: 124 HGFGIVYKDQTGIVPPKNVDVILVAPKGSGTNVRRNFKDGSGINSSYAVFQDATGRAEER 183
           HGFG+ YKDQTGIVPP++VDVILVAPKGSGT++RR F +G G+NSS+A++QDATG+A ER
Sbjct: 123 HGFGVTYKDQTGIVPPEDVDVILVAPKGSGTSLRRMFVEGRGLNSSFAIYQDATGKARER 182

Query: 184 TIALGIAIGSGYLFPTTFEKEVFSDLTGERGVLMGCLAGTMEAQYNVLRKHGHSPSEAFN 243
            IALGI +GSGYLF T F +EV SDLTGERG LMG + G   AQY VLR++GHSPSEAFN
Sbjct: 183 VIALGIGVGSGYLFETDFYREVTSDLTGERGTLMGAIQGIFAAQYEVLRENGHSPSEAFN 242

Query: 244 ETVEELTQSLIRLVAENGMDWMFANCSTTAQRGALDWAPKFRDAVAPVFDSLYRRVKNGA 303
           ETVEELTQSL+ LVAENGMDWM+ANCSTTAQRGALDW   FRDA  PVF+ LY+ VK+G 
Sbjct: 243 ETVEELTQSLMPLVAENGMDWMYANCSTTAQRGALDWWKPFRDASKPVFEQLYKSVKDGK 302

Query: 304 ETRRVLKVNSAPNYLEKLRKELDTIKNSEMWQAGAAVRALRPEN 347
           E  + ++ NS  +Y EKL  EL  ++ SEMW+AGA VR LRPEN
Sbjct: 303 EAAKSIESNSKADYREKLEVELKELRESEMWKAGATVRKLRPEN 346


Lambda     K      H
   0.316    0.134    0.391 

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: 464
Number of extensions: 9
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: 352
Length of database: 347
Length adjustment: 29
Effective length of query: 323
Effective length of database: 318
Effective search space:   102714
Effective search space used:   102714
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 Echvi_2058 Echvi_2058 (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.18363.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
    2.7e-98  314.8   0.0      3e-98  314.6   0.0    1.0  1  lcl|FitnessBrowser__Cola:Echvi_2058  Echvi_2058 ketol-acid reductoiso


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_2058  Echvi_2058 ketol-acid reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  314.6   0.0     3e-98     3e-98       1     313 [.      27     346 ..      27     347 .] 0.96

  Alignments for each domain:
  == domain 1  score: 314.6 bits;  conditional E-value: 3e-98
                            TIGR00465   1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeed....GfkvltveeaikkadlimiLlpDe 70 
                                          lk++ +a++GyG qG +qalnl+d+g nvivg rk++++w+kA  d    G  ++++eea +k+ ++  Ll+D+
  lcl|FitnessBrowser__Cola:Echvi_2058  27 LKDEVIAVLGYGVQGPGQALNLKDNGFNVIVGQRKNSKTWDKAVADgwvpGETLFELEEACEKGTILQFLLSDA 100
                                          68999*****************************************8888899********************* PP

                            TIGR00465  71 vqkevyeaeikpllkegkallfsHGfnivfkqiv...ipkdvdvvlvAPKgpGalvReeykegrGvpsliAveq 141
                                           q + +   +k  l+ gkal+fsHGf + +k+ +   +p+dvdv+lvAPKg+G+ +R+++ egrG++s++A++q
  lcl|FitnessBrowser__Cola:Echvi_2058 101 GQIALWPT-VKKHLTPGKALYFSHGFGVTYKDQTgivPPEDVDVILVAPKGSGTSLRRMFVEGRGLNSSFAIYQ 173
                                          **999998.*********************9755555************************************* PP

                            TIGR00465 142 dvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeiv 215
                                          d+tg+a+e   a+  ++G++  +++et F +Ev sDL GE++ L+G +++++ a++++L+e+G++p++A++e+v
  lcl|FitnessBrowser__Cola:Echvi_2058 174 DATGKARERVIALGIGVGSG--YLFETDFYREVTSDLTGERGTLMGAIQGIFAAQYEVLRENGHSPSEAFNETV 245
                                          **********9999999999..**************************************************** PP

                            TIGR00465 216 hel.klivdllkekGlelmrdavsntAklgalelreilkeelkkemqkilkeiqnGefakewalekeagkpafe 288
                                          +el +++++l+ e+G++ m+ ++s+tA++gal++ + ++++ k+++++++k++++G++a+  ++e+ ++k++++
  lcl|FitnessBrowser__Cola:Echvi_2058 246 EELtQSLMPLVAENGMDWMYANCSTTAQRGALDWWKPFRDASKPVFEQLYKSVKDGKEAA-KSIES-NSKADYR 317
                                          ***9*******************************************************9.55565.7999999 PP

                            TIGR00465 289 earkke....keqeiekvGkelralvkae 313
                                          e+ + e    +e e++k G ++r+l++++
  lcl|FitnessBrowser__Cola:Echvi_2058 318 EKLEVElkelRESEMWKAGATVRKLRPEN 346
                                          9999999899**************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (314 nodes)
Target sequences:                          1  (347 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: 11.82
//
[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