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

GapMind for catabolism of small carbon sources

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.carbon/TIGR01123.hmm
# target sequence database:        /tmp/gapView.16746.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  lcl|FitnessBrowser__Cola:Echvi_1626  Echvi_1626 branched-chain amino 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_1626  Echvi_1626 branched-chain amino acid aminotransferase, group II
   #    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 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelfleal 74 
                                          W++a+++++++l l++ ++ lhYgq vfeGlkayR++d  i +fR  +  +R+++s +r+++Pe++eelf   +
  lcl|FitnessBrowser__Cola:Echvi_1626  41 WHSATIQPYEQLVLSPLAMCLHYGQTVFEGLKAYRQEDDTISIFRLARHHERINQSLRRMAMPEIPEELFETGI 114
                                          ************************************************************************** PP

                            TIGR01123  75 kqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsifveteyvRaap 148
                                          ++lv ++++w+   + ++sLY+RPf+iate+ lGv  +++ylf+v+++P+ aY+++ l++    ve +y+Ra+p
  lcl|FitnessBrowser__Cola:Echvi_1626 115 RELVDLEQEWIRGGE-GNSLYIRPFVIATEARLGVSISTDYLFMVVCTPMAAYYAKPLKV---KVERHYTRAVP 184
                                          ***********9776.9*************************************998877...89********* PP

                            TIGR01123 149 kGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttplsesiLegvtre 222
                                          +G+Ga+k gGnY a+  + + a++ g+d+v++ d+ +++ +ee G++n+++i++ g l+t+p  e +L gvtr+
  lcl|FitnessBrowser__Cola:Echvi_1626 185 GGVGAAKNGGNYGAAYYPAHLAQQAGFDQVIWTDARDHQFVEESGTMNLMFIID-GVLLTPPAGETVLAGVTRD 257
                                          ****************************************************97.8****************** PP

                            TIGR01123 223 sllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkiegkevevkseevGevtkklrde 294
                                          sll++a+d+g  veer i++ el++a  +G+   +f++Gtaav++P++ ++i+g+ ++ + +e     ++l+  
  lcl|FitnessBrowser__Cola:Echvi_1626 258 SLLSIARDMGWPVEERPISLKELEEAFSTGKKveAFGAGTAAVVAPLELIQIDGQDFRPYIAE-DAQMYQLKAR 330
                                          ******************************98789********************99988774.456799**** PP

                            TIGR01123 295 ltdiqyGkledkegWi 310
                                          l  i  Gk +d++ W 
  lcl|FitnessBrowser__Cola:Echvi_1626 331 LSAIRAGKEKDPYAWN 346
                                          ***************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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.28
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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
the source code
instructions for running GapMind on your computer

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 catabolism of small carbon sources