Alignments for a candidate for ilvE in Marinobacter adhaerens HP15

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvE in Marinobacter adhaerens HP15

Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate GFF448 HP15_436 branched-chain-amino-acid aminotransferase

Query= reanno::psRCH2:GFF445
         (307 letters)



>FitnessBrowser__Marino:GFF448
          Length = 308

 Score =  474 bits (1219), Expect = e-138
 Identities = 230/307 (74%), Positives = 261/307 (85%)

Query: 1   MSMADRDGVIWYDGELVQWRDATTHVLTHTLHYGMGVFEGVRAYNTPDGTAIFRLQAHTD 60
           MSMADRDGVIW DGE+V WRDA THVLTHTLHYG+G FEGVRAYNT +G AIFRL+ HTD
Sbjct: 1   MSMADRDGVIWMDGEMVPWRDAKTHVLTHTLHYGLGCFEGVRAYNTANGPAIFRLKEHTD 60

Query: 61  RLFDSAHIMNMPMPYSKEEINEATRAAVRENNLESAYIRPMVFYGSEGMGLRASGLKVHV 120
           RLF SAHI+NM MP+SK+EINEA RAAVRENNL+ AY+RPM F GSEGMGLRA  LKVHV
Sbjct: 61  RLFRSAHILNMKMPFSKDEINEAQRAAVRENNLDEAYLRPMAFLGSEGMGLRADNLKVHV 120

Query: 121 IVAAWHWGAYMGDEALELGIKVRTSSFTRHHVNITMTRAKSNGAYINSMLALQEAISGGA 180
           +VAAW W +YM  EA E+GIKVRTSS+TRHHVNITM +AK+NG YINSMLAL EAISGGA
Sbjct: 121 MVAAWSWPSYMSPEAKEMGIKVRTSSYTRHHVNITMCKAKANGNYINSMLALNEAISGGA 180

Query: 181 DEALMLDPEGYVAEGSGENIFIIKDGVIYTPEVTACLNGITRGTVLTLAAEHGLKIVEKR 240
           +EAL+LD EGYVAEGSGENIFI++DGV++TPE+T+CL GITR T++  A E  + I E+R
Sbjct: 181 EEALLLDNEGYVAEGSGENIFIMRDGVLHTPELTSCLEGITRATIMDFARELNIPIKERR 240

Query: 241 ITRDEVYIADEAFFTGTAAEVTPIREVDGRAIGIGRRGPITEKLQKAYFDLVTGKTDAHA 300
           ITRDEVYIADEAFFTGTAAEV PIRE+DGR IG G+RGP+TEKLQ  YFD V GK   H+
Sbjct: 241 ITRDEVYIADEAFFTGTAAEVLPIRELDGRVIGAGKRGPVTEKLQAMYFDAVKGKLAEHS 300

Query: 301 EWRTLVK 307
            W T VK
Sbjct: 301 GWLTHVK 307


Lambda     K      H
   0.319    0.135    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: 419
Number of extensions: 12
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: 307
Length of database: 308
Length adjustment: 27
Effective length of query: 280
Effective length of database: 281
Effective search space:    78680
Effective search space used:    78680
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate GFF448 HP15_436 (branched-chain-amino-acid aminotransferase)
to HMM TIGR01122 (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/TIGR01122.hmm
# target sequence database:        /tmp/gapView.32235.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01122  [M=298]
Accession:   TIGR01122
Description: ilvE_I: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
     1e-135  437.7   0.0   1.1e-135  437.5   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF448  HP15_436 branched-chain-amino-ac


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF448  HP15_436 branched-chain-amino-acid aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  437.5   0.0  1.1e-135  1.1e-135       1     298 []      11     306 ..      11     306 .. 0.99

  Alignments for each domain:
  == domain 1  score: 437.5 bits;  conditional E-value: 1.1e-135
                          TIGR01122   1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskeelvevtke 76 
                                        w+dGe+v+++dak+hvlth+lhYG g feG+RaY+t +g+aifrlkeh++Rl+ sa+il++++p+sk+e++e+++ 
  lcl|FitnessBrowser__Marino:GFF448  11 WMDGEMVPWRDAKTHVLTHTLHYGLGCFEGVRAYNTANGPAIFRLKEHTDRLFRSAHILNMKMPFSKDEINEAQRA 86 
                                        9*************************************************************************** PP

                          TIGR01122  77 vlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavnsiptkaka 152
                                        ++r+nnl++aY+Rp++++G+e++gl++  +lkv+v++aaw+w+ y+  ea e Gikv++ss++r++vn+ + kaka
  lcl|FitnessBrowser__Marino:GFF448  87 AVRENNLDEAYLRPMAFLGSEGMGLRA-DNLKVHVMVAAWSWPSYMSPEAKEMGIKVRTSSYTRHHVNITMCKAKA 161
                                        ***************************.899********************************************* PP

                          TIGR01122 153 agnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdaviklakelgiev 228
                                        +gnY+ns+la  ea++ G++ea+lLd+eGyvaeGsGenifi++dgvl tP++ +s+L+gitr +++++a+el i +
  lcl|FitnessBrowser__Marino:GFF448 162 NGNYINSMLALNEAISGGAEEALLLDNEGYVAEGSGENIFIMRDGVLHTPEL-TSCLEGITRATIMDFARELNIPI 236
                                        ****************************************************.78********************* PP

                          TIGR01122 229 keerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlvegktekkeewltyv 298
                                        ke+ri+r+e+y+aDe+f+tGtaaev Pire+Dgr ig+gkrGpvt+klq  +fd v+gk  ++++wlt+v
  lcl|FitnessBrowser__Marino:GFF448 237 KERRITRDEVYIADEAFFTGTAAEVLPIRELDGRVIGAGKRGPVTEKLQAMYFDAVKGKLAEHSGWLTHV 306
                                        *******************************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (308 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: 00:00:00.01
# Mc/sec: 7.81
//
[ok]

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