GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvC in Pontibacter ramchanderi LP43

Align Ketol-acid reductoisomerase (NAD(+)); KARI; Acetohydroxy-acid isomeroreductase; AHIR; Alpha-keto-beta-hydroxylacyl reductoisomerase; EC 1.1.1.382 (characterized)
to candidate WP_101445085.1 BD749_RS13340 ketol-acid reductoisomerase

Query= SwissProt::A8ZTR0
         (352 letters)



>NCBI__GCF_002846395.1:WP_101445085.1
          Length = 348

 Score =  466 bits (1199), Expect = e-136
 Identities = 226/348 (64%), Positives = 276/348 (79%)

Query: 1   MPTINFGGVEENVVTSEEFTLKKAREVLKNEVITVLGYGVQGPAQALNLKDNGFEVIIGQ 60
           M TINFGGV+E VVT EEF L KAREVL++E+I V+GYGVQGP QALNL+DNGF VI+GQ
Sbjct: 1   MATINFGGVDETVVTREEFPLAKAREVLQHELIAVIGYGVQGPGQALNLRDNGFNVIVGQ 60

Query: 61  LEGDAYWEKAIADGFVPGKTLFPIEEAAKKGTIIKMLLSDAGQVAVWPKVKKCLKKGDAL 120
            +  A W+KA+ADG+V G+TLF IEEAA++GTII  LLSDAGQ+AVWP +++ L  G  L
Sbjct: 61  RKDSASWQKALADGWVEGETLFSIEEAAERGTIIANLLSDAGQIAVWPTLRERLTAGKTL 120

Query: 121 YFSHGFGIVYKDQTGIVPPKNVDVILVAPKGSGTNVRRNFKDGSGINSSYAVFQDATGRA 180
           YFSHGFGI + + T IVPP +VDVIL APKGSGT++RR +  G G+NSS+AV+QDATG+A
Sbjct: 121 YFSHGFGITFHEHTNIVPPADVDVILAAPKGSGTSLRRLYLQGGGLNSSFAVYQDATGKA 180

Query: 181 EERTIALGIAIGSGYLFPTTFEKEVFSDLTGERGVLMGCLAGTMEAQYNVLRKHGHSPSE 240
            E+ +A+GI IGSGYLF T F KEV+SDLTGERGVLMG LAG +EAQY VLR+ GHSPSE
Sbjct: 181 YEKAVAMGIGIGSGYLFETDFRKEVYSDLTGERGVLMGALAGIIEAQYQVLRQRGHSPSE 240

Query: 241 AFNETVEELTQSLIRLVAENGMDWMFANCSTTAQRGALDWAPKFRDAVAPVFDSLYRRVK 300
           AFNETVEELTQSL+ LV ENGMDWMF+NCS TAQRGALDW  +F++A  PV   LY  V 
Sbjct: 241 AFNETVEELTQSLVPLVGENGMDWMFSNCSVTAQRGALDWKGRFKEATLPVLHELYDSVA 300

Query: 301 NGAETRRVLKVNSAPNYLEKLRKELDTIKNSEMWQAGAAVRALRPENR 348
           +G E +R ++  SAP Y  +L  EL  ++ SE+WQ GA VR LR +++
Sbjct: 301 SGTEAQRTIQRGSAPGYRTELEAELQELRESELWQTGARVRELRSQSK 348


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: 422
Number of extensions: 10
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: 348
Length adjustment: 29
Effective length of query: 323
Effective length of database: 319
Effective search space:   103037
Effective search space used:   103037
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 WP_101445085.1 BD749_RS13340 (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.239335.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.4e-99  319.0   0.0    1.6e-99  318.8   0.0    1.0  1  NCBI__GCF_002846395.1:WP_101445085.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002846395.1:WP_101445085.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  318.8   0.0   1.6e-99   1.6e-99       1     313 [.      28     347 ..      28     348 .] 0.95

  Alignments for each domain:
  == domain 1  score: 318.8 bits;  conditional E-value: 1.6e-99
                             TIGR00465   1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeed....GfkvltveeaikkadlimiLlpD 69 
                                           l+ + +a+iGyG qG +qalnlrd+g nvivg rk++asw+kA  d    G  ++++eea++++ +i++Ll+D
  NCBI__GCF_002846395.1:WP_101445085.1  28 LQHELIAVIGYGVQGPGQALNLRDNGFNVIVGQRKDSASWQKALADgwveGETLFSIEEAAERGTIIANLLSD 100
                                           57788****************************************98888899******************** PP

                             TIGR00465  70 evqkevyeaeikpllkegkallfsHGfnivfkqiv...ipkdvdvvlvAPKgpGalvReeykegrGvpsliAv 139
                                           + q +v+   +++ l++gk+l+fsHGf i f++ +   +p+dvdv+l+APKg+G+ +R+ y +g G++s++Av
  NCBI__GCF_002846395.1:WP_101445085.1 101 AGQIAVWPT-LRERLTAGKTLYFSHGFGITFHEHTnivPPADVDVILAAPKGSGTSLRRLYLQGGGLNSSFAV 172
                                           *******99.*******************998644444*********************************** PP

                             TIGR00465 140 eqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyf 212
                                           +qd+tg+a e+A a+  +iG++  +++et F++Ev sDL GE++vL+G l+++i+a++++L++ G++p++A++
  NCBI__GCF_002846395.1:WP_101445085.1 173 YQDATGKAYEKAVAMGIGIGSG--YLFETDFRKEVYSDLTGERGVLMGALAGIIEAQYQVLRQRGHSPSEAFN 243
                                           *********************9..************************************************* PP

                             TIGR00465 213 eivhel.klivdllkekGlelmrdavsntAklgalelreilkeelkkemqkilkeiqnGefakewalekeagk 284
                                           e+v+el +++v+l+ e+G++ m++++s tA++gal+++  +ke++ ++++++++++ +G++a+ +++++  ++
  NCBI__GCF_002846395.1:WP_101445085.1 244 ETVEELtQSLVPLVGENGMDWMFSNCSVTAQRGALDWKGRFKEATLPVLHELYDSVASGTEAQ-RTIQR-GSA 314
                                           ******9********************************************************.44444.577 PP

                             TIGR00465 285 pafeearkke....keqeiekvGkelralvkae 313
                                           p ++++ ++e    +e e++++G ++r+l++++
  NCBI__GCF_002846395.1:WP_101445085.1 315 PGYRTELEAElqelRESELWQTGARVRELRSQS 347
                                           88888877777777**************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (314 nodes)
Target sequences:                          1  (348 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: 27.07
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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