Alignments for a candidate for ilvE in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvE in Shewanella oneidensis MR-1

Align Branched-chain-amino-acid aminotransferase 2; BCAT 2; Vegetative protein 85; VEG85; EC 2.6.1.42 (characterized)
to candidate 199535 SO0340 branched-chain amino acid aminotransferase (NCBI ptt file)

Query= SwissProt::P39576
         (363 letters)



>FitnessBrowser__MR1:199535
          Length = 363

 Score =  288 bits (737), Expect = 2e-82
 Identities = 153/347 (44%), Positives = 218/347 (62%), Gaps = 6/347 (1%)

Query: 13  TKKPKPDPNQLSFGRVFTDHMFVMDYAADKGWYDPRIIPYQPLSMDPAAMVYHYGQTVFE 72
           T++ KP+ N + FG + TDHMF+MDY  D  W DPRI+PY P  M P AM  HYGQ++FE
Sbjct: 15  TEQFKPEGN-VGFGSLRTDHMFLMDYH-DGEWRDPRIVPYGPFEMAPGAMALHYGQSIFE 72

Query: 73  GLKAYVSEDDHVLLFRPEKNMERLNQSNDRLCIPQIDEEQVLEGLKQLVAIDKDWIPNAE 132
           G KA++ ED  +  FR  KN ER+N+S D +CIP IDE+  ++ +  L+ +D+ W P  E
Sbjct: 73  GAKAFMHEDGEIYTFRINKNAERMNRSADIVCIPNIDEQMQIDAINALIDVDRLWFPMQE 132

Query: 133 GTSLYIRPFIIATEPFLGVAASHTYKLLIILSPVGSYYKEGI-KPVKIAVESEFVRAVKG 191
           G  LYIRPFI ATE  L V+ S  Y   ++LSP G+YY  G+ K +++ +   + RAV G
Sbjct: 133 GACLYIRPFIFATEDRLSVSPSSRYTFCVVLSPSGAYYAAGVNKGIRLLISKTYHRAVSG 192

Query: 192 GTGNAKTAGNYASSLKAQQVAEEKGFSQVLWLDGIEKKYIEEVGSMNIFFKI-NGEIVTP 250
           GTG +K AGNYA+SL+A + A + G SQVL+LD    + IEE G+MN F  + +G ++ P
Sbjct: 193 GTGASKAAGNYAASLRAGKAAAQFGASQVLYLDA-NNQQIEEAGAMNHFHILKDGTVIIP 251

Query: 251 MLNGSILEGITRNSVIALLKHWGLQVSERKIAIDEVIQAHKDGILEEAFGTGTAAVISPV 310
               +IL+ IT  S++ L +  G +V +  + +D+ I   + G + EA G GTAAV+S V
Sbjct: 252 TFTDTILKSITSQSIMELSELLGCEVRQETVMLDKFIADIESGEIIEAGGFGTAAVVSAV 311

Query: 311 GELIWQD-ETLSINNGETGEIAKKLYDTITGIQKGAVADEFGWTTEV 356
           G  I++D   +++ NGE GE  +++Y   T IQKG V    GW   V
Sbjct: 312 GSYIFEDGRVVTVGNGEVGEHIQRIYKLYTDIQKGHVQGPEGWVKRV 358


Lambda     K      H
   0.316    0.135    0.390 

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: 359
Number of extensions: 14
Number of successful extensions: 4
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: 363
Length of database: 363
Length adjustment: 29
Effective length of query: 334
Effective length of database: 334
Effective search space:   111556
Effective search space used:   111556
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 199535 SO0340 (branched-chain amino acid aminotransferase (NCBI ptt file))
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.17393.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   6.1e-102  326.7   0.1   7.1e-102  326.5   0.1    1.0  1  lcl|FitnessBrowser__MR1:199535  SO0340 branched-chain amino acid


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:199535  SO0340 branched-chain amino acid aminotransferase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  326.5   0.1  7.1e-102  7.1e-102       1     313 []      44     358 ..      44     358 .. 0.96

  Alignments for each domain:
  == domain 1  score: 326.5 bits;  conditional E-value: 7.1e-102
                       TIGR01123   1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflealkqlvk 79 
                                     W ++++++++++e+++g+++lhYgq +feG ka+ ++dG+i++fR ++na+R++rsa+++ +P+++e++ ++a++ l+ 
  lcl|FitnessBrowser__MR1:199535  44 WRDPRIVPYGPFEMAPGAMALHYGQSIFEGAKAFMHEDGEIYTFRINKNAERMNRSADIVCIPNIDEQMQIDAINALID 122
                                     99***************************************************************************** PP

                       TIGR01123  80 adkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglap.vsifveteyvRaapkGtGavkvg 157
                                     +d+ w p ++ +a LY+RPf++ated l v ++++y+f+v++sP GaY++ g+++ ++ ++++ y Ra+ +GtGa k +
  lcl|FitnessBrowser__MR1:199535 123 VDRLWFPMQE-GACLYIRPFIFATEDRLSVSPSSRYTFCVVLSPSGAYYAAGVNKgIRLLISKTYHRAVSGGTGASKAA 200
                                     *******777.*****************************************99978999******************* PP

                       TIGR01123 158 GnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttplsesiLegvtresllelakdlgleve 236
                                     GnYaasl+a k aa+ g ++v+yld++++ +iee+Ga+n f i+kdg+++++  ++ iL+++t +s++el + lg ev+
  lcl|FitnessBrowser__MR1:199535 201 GNYAASLRAGKAAAQFGASQVLYLDANNQ-QIEEAGAMNHFHILKDGTVIIPTFTDTILKSITSQSIMELSELLGCEVR 278
                                     **************************998.9************************************************ PP

                       TIGR01123 237 ereiaidelkaaveaGei..vfacGtaavitPvge.lkiegkevevkseevGevtkklrdeltdiqyGkledkegWive 312
                                      + + +d++ a  e+Gei  + + Gtaav++ vg+ +  +g+ v+v ++evGe  +++++  tdiq G+++++egW+ +
  lcl|FitnessBrowser__MR1:199535 279 QETVMLDKFIADIESGEIieAGGFGTAAVVSAVGSyIFEDGRVVTVGNGEVGEHIQRIYKLYTDIQKGHVQGPEGWVKR 357
                                     *****************96566679********9835566788899999***************************987 PP

                       TIGR01123 313 v 313
                                     v
  lcl|FitnessBrowser__MR1:199535 358 V 358
                                     6 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (313 nodes)
Target sequences:                          1  (363 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 8.56
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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