Alignments for a candidate for ilvE in Pelobacter propionicus DSM 2379

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvE in Pelobacter propionicus DSM 2379

Align Branched-chain-amino-acid aminotransferase 2; BCAT 2; Vegetative protein 85; VEG85; EC 2.6.1.42 (characterized)
to candidate WP_011735248.1 PPRO_RS06625 branched-chain amino acid aminotransferase

Query= SwissProt::P39576
         (363 letters)



>NCBI__GCF_000015045.1:WP_011735248.1
          Length = 357

 Score =  389 bits (998), Expect = e-113
 Identities = 190/357 (53%), Positives = 246/357 (68%)

Query: 1   MTKQTIRVELTSTKKPKPDPNQLSFGRVFTDHMFVMDYAADKGWYDPRIIPYQPLSMDPA 60
           M  Q + +     K+   D  +LSFGR FTD M ++++ AD+GW D RI PY P  +DP+
Sbjct: 1   MDIQVLPLPAEKMKQKAQDETKLSFGRQFTDRMLLVEWKADQGWCDARIQPYAPFVLDPS 60

Query: 61  AMVYHYGQTVFEGLKAYVSEDDHVLLFRPEKNMERLNQSNDRLCIPQIDEEQVLEGLKQL 120
            +V+HY Q +FEGLKAY   D  + LFRPE N  R NQS DRLC+P + EE  L G+++L
Sbjct: 61  CLVFHYAQEIFEGLKAYKWADGRIALFRPEMNARRFNQSADRLCMPDVPEELFLGGIEKL 120

Query: 121 VAIDKDWIPNAEGTSLYIRPFIIATEPFLGVAASHTYKLLIILSPVGSYYKEGIKPVKIA 180
           ++++K+WIP A GTSLYIRP +IA EP LGV  S  Y   +ILSPVG+YY  G  PV I 
Sbjct: 121 LSLEKEWIPGAPGTSLYIRPAMIAVEPVLGVKPSSHYYFFVILSPVGAYYSAGFNPVSIM 180

Query: 181 VESEFVRAVKGGTGNAKTAGNYASSLKAQQVAEEKGFSQVLWLDGIEKKYIEEVGSMNIF 240
           VE  +VRAV GGTG AKT GNYASSLK    A+ KG+ QVLWLDG E++Y+EEVGSMN+F
Sbjct: 181 VEDHYVRAVPGGTGEAKTGGNYASSLKGALEAKNKGYDQVLWLDGREQRYVEEVGSMNMF 240

Query: 241 FKINGEIVTPMLNGSILEGITRNSVIALLKHWGLQVSERKIAIDEVIQAHKDGILEEAFG 300
           F     IVT  +NGSIL GITR+S++ L    G +  ER I I+E++   + G + EAFG
Sbjct: 241 FVYGDTIVTAAMNGSILSGITRDSILKLAVSLGYRAEERSIEINELMDDIRGGKVTEAFG 300

Query: 301 TGTAAVISPVGELIWQDETLSINNGETGEIAKKLYDTITGIQKGAVADEFGWTTEVA 357
           +GTAAV+SPVG+L ++DE + ++ G  G I +KLYDT+TGIQ G + DEFGW   VA
Sbjct: 301 SGTAAVVSPVGKLCFKDEVVHLSGGTVGAITQKLYDTLTGIQTGKIKDEFGWVRFVA 357


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: 438
Number of extensions: 15
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: 363
Length of database: 357
Length adjustment: 29
Effective length of query: 334
Effective length of database: 328
Effective search space:   109552
Effective search space used:   109552
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_011735248.1 PPRO_RS06625 (branched-chain amino acid aminotransferase)
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.3947291.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.9e-124  399.3   0.0   5.6e-124  399.1   0.0    1.0  1  NCBI__GCF_000015045.1:WP_011735248.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000015045.1:WP_011735248.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  399.1   0.0  5.6e-124  5.6e-124       1     310 [.      44     353 ..      44     356 .. 0.99

  Alignments for each domain:
  == domain 1  score: 399.1 bits;  conditional E-value: 5.6e-124
                             TIGR01123   1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflea 73 
                                           W +a+++++a++ ld++  v+hY+qe+feGlkay++adG+i lfRp+ na+R+++sa+rl +P+++eelfl  
  NCBI__GCF_000015045.1:WP_011735248.1  44 WCDARIQPYAPFVLDPSCLVFHYAQEIFEGLKAYKWADGRIALFRPEMNARRFNQSADRLCMPDVPEELFLGG 116
                                           999********************************************************************** PP

                             TIGR01123  74 lkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsifveteyvRa 146
                                           +++l+ ++k+w+p a  ++sLY+RP +ia+e++lGvk++++y f+v++sPvGaY+  g +pvsi+ve++yvRa
  NCBI__GCF_000015045.1:WP_011735248.1 117 IEKLLSLEKEWIPGAP-GTSLYIRPAMIAVEPVLGVKPSSHYYFFVILSPVGAYYSAGFNPVSIMVEDHYVRA 188
                                           *************999.******************************************************** PP

                             TIGR01123 147 apkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttplsesiLegv 219
                                           +p+GtG +k+gGnYa+sl+   +a+++g+d+v++ld  e++++eevG++n+f++++d ++vt +  +siL+g+
  NCBI__GCF_000015045.1:WP_011735248.1 189 VPGGTGEAKTGGNYASSLKGALEAKNKGYDQVLWLDGREQRYVEEVGSMNMFFVYGD-TIVTAAMNGSILSGI 260
                                           *********************************************************.*************** PP

                             TIGR01123 220 tresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkiegkevevkseevGevtkk 290
                                           tr+s+l+la +lg+++eer+i+i+el +    G++  +f++Gtaav++Pvg+l  +++ v+++ + vG +t+k
  NCBI__GCF_000015045.1:WP_011735248.1 261 TRDSILKLAVSLGYRAEERSIEINELMDDIRGGKVteAFGSGTAAVVSPVGKLCFKDEVVHLSGGTVGAITQK 333
                                           *********************************9999************************************ PP

                             TIGR01123 291 lrdeltdiqyGkledkegWi 310
                                           l+d+lt+iq+Gk++d++gW+
  NCBI__GCF_000015045.1:WP_011735248.1 334 LYDTLTGIQTGKIKDEFGWV 353
                                           *******************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (313 nodes)
Target sequences:                          1  (357 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: 17.79
//
[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:

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