GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Lentibacillus jeotgali Grbi

Align Branched-chain-amino-acid aminotransferase 2; BCAT 2; Vegetative protein 85; VEG85; EC 2.6.1.42 (characterized)
to candidate WP_010532003.1 ON01_RS15935 branched-chain amino acid aminotransferase

Query= SwissProt::P39576
         (363 letters)



>NCBI__GCF_000224785.1:WP_010532003.1
          Length = 369

 Score =  505 bits (1300), Expect = e-148
 Identities = 240/360 (66%), Positives = 296/360 (82%), Gaps = 1/360 (0%)

Query: 3   KQTIRVELTSTKKPKPDPNQLSFGRVFTDHMFVMDYAADKGWYDPRIIPYQPLSMDPAAM 62
           +Q IR E+ S+ K KP  +QL FG +FTDHMF+MDY ADKGW+DPRI+PY+PL+++P+AM
Sbjct: 5   QQGIRTEICSSGKEKPKSDQLEFGTIFTDHMFMMDYTADKGWHDPRIVPYEPLNIEPSAM 64

Query: 63  VYHYGQTVFEGLKAYVSEDDHVLLFRPEKNMERLNQSNDRLCIPQIDEEQVLEGLKQLVA 122
           V+HYGQ+VFEG+KAY++ D    LFRP++N  R+N SN RLCIP IDE   L+ LKQLV 
Sbjct: 65  VFHYGQSVFEGMKAYLTSDGDAQLFRPQRNFSRMNHSNSRLCIPPIDEAFALKALKQLVG 124

Query: 123 IDKDWIPNAEGTSLYIRPFIIATEPFLGVAASHTYKLLIILSPVGSYYKEGIKPVKIAVE 182
           ++KDWIP AEGTSLYIRPFII+TE FLGVA S  YK +IILSPVG+YYKEGI PVKIAVE
Sbjct: 125 LEKDWIPEAEGTSLYIRPFIISTEAFLGVAPSSHYKFIIILSPVGAYYKEGINPVKIAVE 184

Query: 183 SEFVRAVKGGTGNAKTAGNYASSLKAQQVAEEKGFSQVLWLDGIEKKYIEEVGSMNIFFK 242
            ++VR VKGGTG AKT GNYA+SLKAQ++A E G +QVLWLDG+E+KYIEEVGSMN+FFK
Sbjct: 185 HDYVRTVKGGTGEAKTGGNYAASLKAQEMAAE-GIAQVLWLDGVERKYIEEVGSMNVFFK 243

Query: 243 INGEIVTPMLNGSILEGITRNSVIALLKHWGLQVSERKIAIDEVIQAHKDGILEEAFGTG 302
           I+G +VTP LNGSILEG+TRNSVI LLK+W + V ERK++++EVIQAHKDG LEEAFG G
Sbjct: 244 IDGTVVTPALNGSILEGVTRNSVIQLLKYWNVPVEERKLSMEEVIQAHKDGKLEEAFGAG 303

Query: 303 TAAVISPVGELIWQDETLSINNGETGEIAKKLYDTITGIQKGAVADEFGWTTEVAALTES 362
           TAAVISP+GEL+  ++ + IN G TG IAK+LYDT+TGIQ G + D F W  +V  L ++
Sbjct: 304 TAAVISPIGELVRGEKHIEINEGNTGAIAKRLYDTLTGIQYGKIEDPFDWVEKVKDLKQT 363


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: 510
Number of extensions: 16
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: 363
Length of database: 369
Length adjustment: 30
Effective length of query: 333
Effective length of database: 339
Effective search space:   112887
Effective search space used:   112887
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_010532003.1 ON01_RS15935 (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.1898044.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.7e-123  396.9   0.0   3.1e-123  396.7   0.0    1.0  1  NCBI__GCF_000224785.1:WP_010532003.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000224785.1:WP_010532003.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  396.7   0.0  3.1e-123  3.1e-123       1     313 []      46     357 ..      46     357 .. 0.98

  Alignments for each domain:
  == domain 1  score: 396.7 bits;  conditional E-value: 3.1e-123
                             TIGR01123   1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflea 73 
                                           W++++++++++l+++++++v+hYgq vfeG+kay t+dG + lfRp++n  R+++s +rl +P ++e+  l+a
  NCBI__GCF_000224785.1:WP_010532003.1  46 WHDPRIVPYEPLNIEPSAMVFHYGQSVFEGMKAYLTSDGDAQLFRPQRNFSRMNHSNSRLCIPPIDEAFALKA 118
                                           ************************************************************************* PP

                             TIGR01123  74 lkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsifveteyvRa 146
                                           lkqlv ++kdw+p+a+ ++sLY+RPf+i+te+ lGv+++++y f++++sPvGaY+k+g++pv+i ve +yvR+
  NCBI__GCF_000224785.1:WP_010532003.1 119 LKQLVGLEKDWIPEAE-GTSLYIRPFIISTEAFLGVAPSSHYKFIIILSPVGAYYKEGINPVKIAVEHDYVRT 190
                                           *************988.******************************************************** PP

                             TIGR01123 147 apkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttplsesiLegv 219
                                           +++GtG +k+gGnYaasl+aq++aa +g+++v++ld ve+k+ieevG++n+f+ ++ g++vt++l +siLegv
  NCBI__GCF_000224785.1:WP_010532003.1 191 VKGGTGEAKTGGNYAASLKAQEMAA-EGIAQVLWLDGVERKYIEEVGSMNVFFKID-GTVVTPALNGSILEGV 261
                                           ********************88775.69************************9775.9*************** PP

                             TIGR01123 220 tresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkiegkevevkseevGevtkk 290
                                           tr+s+++l k +++ veer+++++e+ +a + G++  +f++Gtaavi+P+gel  ++k++e++++++G ++k+
  NCBI__GCF_000224785.1:WP_010532003.1 262 TRNSVIQLLKYWNVPVEERKLSMEEVIQAHKDGKLeeAFGAGTAAVISPIGELVRGEKHIEINEGNTGAIAKR 334
                                           *********************************9889************************************ PP

                             TIGR01123 291 lrdeltdiqyGkledkegWivev 313
                                           l+d+lt+iqyGk+ed+++W+ +v
  NCBI__GCF_000224785.1:WP_010532003.1 335 LYDTLTGIQYGKIEDPFDWVEKV 357
                                           *******************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (313 nodes)
Target sequences:                          1  (369 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: 17.75
//
[ok]

This GapMind analysis is from Jul 26 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