GapMind for Amino acid biosynthesis

 

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

Align Branched-chain-amino-acid transaminase 1; BCAT 1; EC 2.6.1.42 (characterized)
to candidate Echvi_1626 Echvi_1626 branched-chain amino acid aminotransferase, group II

Query= SwissProt::O31461
         (356 letters)



>FitnessBrowser__Cola:Echvi_1626
          Length = 355

 Score =  276 bits (705), Expect = 8e-79
 Identities = 147/332 (44%), Positives = 203/332 (61%), Gaps = 12/332 (3%)

Query: 24  FGQYFTDYMFVMDYEEGIGWHHPRIAPYAPLTLDPSSSVFHYGQAVFEGLKAYRTDDGRV 83
           FG   TD+M V  Y +G  WH   I PY  L L P +   HYGQ VFEGLKAYR +D  +
Sbjct: 23  FGVEATDHMLVARYSDG-HWHSATIQPYEQLVLSPLAMCLHYGQTVFEGLKAYRQEDDTI 81

Query: 84  LLFRPDQNIKRLNRSCERMSMPPLDEELVLEALTQLVELEKDWVPKEKGTSLYIRPFVIA 143
            +FR  ++ +R+N+S  RM+MP + EEL    + +LV+LE++W+   +G SLYIRPFVIA
Sbjct: 82  SIFRLARHHERINQSLRRMAMPEIPEELFETGIRELVDLEQEWIRGGEGNSLYIRPFVIA 141

Query: 144 TEPSLGVKASRSYTFMIVLSPVGSYYGDDQLKPVRIYVEDEYVRAVNGGVGFAKTAGNYA 203
           TE  LGV  S  Y FM+V +P+ +YY     KP+++ VE  Y RAV GGVG AK  GNY 
Sbjct: 142 TEARLGVSISTDYLFMVVCTPMAAYYA----KPLKVKVERHYTRAVPGGVGAAKNGGNYG 197

Query: 204 ASLQAQRKANELGYDQVLWLDAIEKKYVEEVGSMNIFFVINGEAVTPALSGSILSGVTRA 263
           A+      A + G+DQV+W DA + ++VEE G+MN+ F+I+G  +TP    ++L+GVTR 
Sbjct: 198 AAYYPAHLAQQAGFDQVIWTDARDHQFVEESGTMNLMFIIDGVLLTPPAGETVLAGVTRD 257

Query: 264 SAIELIRSWGIPVREERISIDEVYAASARGELTEVFGTGTAAVVTPVGELNIHG---KTV 320
           S + + R  G PV E  IS+ E+  A + G+  E FG GTAAVV P+  + I G   +  
Sbjct: 258 SLLSIARDMGWPVEERPISLKELEEAFSTGKKVEAFGAGTAAVVAPLELIQIDGQDFRPY 317

Query: 321 IVGDGQIGDLSKKLYETITDIQLGKVKGPFNW 352
           I  D Q+  L  +L    + I+ GK K P+ W
Sbjct: 318 IAEDAQMYQLKARL----SAIRAGKEKDPYAW 345


Lambda     K      H
   0.317    0.137    0.400 

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: 334
Number of extensions: 10
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: 356
Length of database: 355
Length adjustment: 29
Effective length of query: 327
Effective length of database: 326
Effective search space:   106602
Effective search space used:   106602
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_1626 Echvi_1626 (branched-chain amino acid aminotransferase, group II)
to HMM TIGR01123 (ilvE: branched-chain amino acid aminotransferase (EC 2.6.1.42))

# 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/TIGR01123.hmm
# target sequence database:        /tmp/gapView.97161.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01123  [M=313]
Accession:   TIGR01123
Description: ilvE_II: branched-chain amino acid aminotransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
    6.9e-97  310.2   0.0      8e-97  309.9   0.0    1.0  1  FitnessBrowser__Cola:Echvi_1626  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Cola:Echvi_1626  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  309.9   0.0     8e-97     8e-97       1     310 [.      41     346 ..      41     349 .. 0.97

  Alignments for each domain:
  == domain 1  score: 309.9 bits;  conditional E-value: 8e-97
                        TIGR01123   1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflealkqlv 78 
                                      W++a+++++++l l++ ++ lhYgq vfeGlkayR++d  i +fR  +  +R+++s +r+++Pe++eelf   +++lv
  FitnessBrowser__Cola:Echvi_1626  41 WHSATIQPYEQLVLSPLAMCLHYGQTVFEGLKAYRQEDDTISIFRLARHHERINQSLRRMAMPEIPEELFETGIRELV 118
                                      ****************************************************************************** PP

                        TIGR01123  79 kadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsifveteyvRaapkGtGavkv 156
                                       ++++w+   + ++sLY+RPf+iate+ lGv  +++ylf+v+++P+ aY+++ l++    ve +y+Ra+p+G+Ga+k 
  FitnessBrowser__Cola:Echvi_1626 119 DLEQEWIRGGE-GNSLYIRPFVIATEARLGVSISTDYLFMVVCTPMAAYYAKPLKV---KVERHYTRAVPGGVGAAKN 192
                                      *******9776.9*************************************998877...89***************** PP

                        TIGR01123 157 gGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttplsesiLegvtresllelakdlgle 234
                                      gGnY a+  + + a++ g+d+v++ d+ +++ +ee G++n+++i++ g l+t+p  e +L gvtr+sll++a+d+g  
  FitnessBrowser__Cola:Echvi_1626 193 GGNYGAAYYPAHLAQQAGFDQVIWTDARDHQFVEESGTMNLMFIID-GVLLTPPAGETVLAGVTRDSLLSIARDMGWP 269
                                      ********************************************97.8****************************** PP

                        TIGR01123 235 veereiaidelkaaveaGei..vfacGtaavitPvgelkiegkevevkseevGevtkklrdeltdiqyGkledkegWi 310
                                      veer i++ el++a  +G+   +f++Gtaav++P++ ++i+g+ ++ + +e     ++l+  l  i  Gk +d++ W 
  FitnessBrowser__Cola:Echvi_1626 270 VEERPISLKELEEAFSTGKKveAFGAGTAAVVAPLELIQIDGQDFRPYIAE-DAQMYQLKARLSAIRAGKEKDPYAWN 346
                                      ******************98789********************99988774.456799*******************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (313 nodes)
Target sequences:                          1  (355 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: 24.08
//
[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:

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