GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ilvE in Lactobacillus shenzhenensis LY-73

Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_022529386.1 L248_RS06710 branched-chain amino acid aminotransferase

Query= BRENDA::Q8DTW7
         (341 letters)



>NCBI__GCF_000469325.1:WP_022529386.1
          Length = 345

 Score =  466 bits (1200), Expect = e-136
 Identities = 223/336 (66%), Positives = 269/336 (80%), Gaps = 2/336 (0%)

Query: 5   LDWKNLGFEYHKLPFRYISYYKDGKWDDGKLTEDATLHISESSPALHYGQEAFEGLKAYR 64
           +DW++LGFEY + P+R+ ++++DG W+ G+LT+D  + ++ESSP LHYGQ AFEG+KAYR
Sbjct: 8   IDWQHLGFEYMQTPYRFEAHWRDGAWEPGQLTKDPNMTMNESSPILHYGQGAFEGMKAYR 67

Query: 65  TKDGSVQLFRPNMNAERLQRTADRLLMPQVPTDKFIDAAKQVVRANEEYVPPYGTGATLY 124
            KDG + LFRP+ NA+RLQ +ADRLLMP+ PTD F++A K VV AN +YVPPYGTGATLY
Sbjct: 68  AKDGRILLFRPDQNAQRLQHSADRLLMPEYPTDDFLNAVKLVVAANADYVPPYGTGATLY 127

Query: 125 LRPLLIGVGDVIGVHPADEYIFTIFAMPVGNYFKGGLAPTNFLIQDDYDRAAPHGTGAAK 184
           +RPLLIGVG+ IGVHPA EY+  IFAMPVG YFKGGL PT+FL+  DYDRAA +GTG +K
Sbjct: 128 IRPLLIGVGENIGVHPAPEYVLRIFAMPVGPYFKGGLTPTSFLVV-DYDRAAHNGTGQSK 186

Query: 185 VGGNYAASLLPGKVAHERQFSDVIYLDPATHTKIEEVGSANFFGITKDNEFI-TPLSPSI 243
           VGGNYAASLL G+ AH   FSD IYLDP  H  IEEVGSANF   TKD + + TP SPSI
Sbjct: 187 VGGNYAASLLAGQEAHTHHFSDAIYLDPVHHRYIEEVGSANFLAFTKDGKTLKTPKSPSI 246

Query: 244 LPSVTKYSLLYLAEHRFGMKAIEGDVCVDELDKFVEAGACGTAAVISPIGGVQHGDDFHV 303
           LPS+TKYS LYLAEH  GMK  E  + +DELD+F EA ACGTAAVISPI G+Q+GD +HV
Sbjct: 247 LPSITKYSSLYLAEHVLGMKTEETRISIDELDEFGEAAACGTAAVISPIAGIQYGDHYHV 306

Query: 304 FYSETEVGPVTHKLYDELTGIQFGDVKAPEGWIYKV 339
           FY E +VGP+THKLYD LTGIQFGDV  P GW+ +V
Sbjct: 307 FYDEKKVGPITHKLYDLLTGIQFGDVDGPAGWVQEV 342


Lambda     K      H
   0.319    0.139    0.423 

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: 501
Number of extensions: 23
Number of successful extensions: 3
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: 341
Length of database: 345
Length adjustment: 29
Effective length of query: 312
Effective length of database: 316
Effective search space:    98592
Effective search space used:    98592
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate WP_022529386.1 L248_RS06710 (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.carbon/TIGR01123.hmm
# target sequence database:        /tmp/gapView.1265673.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.8e-127  409.2   0.0   5.5e-127  409.0   0.0    1.0  1  NCBI__GCF_000469325.1:WP_022529386.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000469325.1:WP_022529386.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  409.0   0.0  5.5e-127  5.5e-127       1     313 []      33     342 ..      33     342 .. 0.99

  Alignments for each domain:
  == domain 1  score: 409.0 bits;  conditional E-value: 5.5e-127
                             TIGR01123   1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflea 73 
                                           W+ ++l+++ +++++e+s +lhYgq  feG+kayR +dG+illfRpd+na+Rl++sa+rll+Pe +++ fl+a
  NCBI__GCF_000469325.1:WP_022529386.1  33 WEPGQLTKDPNMTMNESSPILHYGQGAFEGMKAYRAKDGRILLFRPDQNAQRLQHSADRLLMPEYPTDDFLNA 105
                                           9************************************************************************ PP

                             TIGR01123  74 lkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsifveteyvRa 146
                                           +k +v+a++d+vp+++++a+LY+RP+li++++n+Gv++a+ey++ ++a PvG+Yfkggl+p + f+  +y+Ra
  NCBI__GCF_000469325.1:WP_022529386.1 106 VKLVVAANADYVPPYGTGATLYIRPLLIGVGENIGVHPAPEYVLRIFAMPVGPYFKGGLTP-TSFLVVDYDRA 177
                                           *************************************************************.99999****** PP

                             TIGR01123 147 apkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttplsesiLegv 219
                                           a +GtG+ kvgGnYaaslla ++a+ ++++d++yldpv++++ieevG+an+++ tkdg+++ tp+s+siL+++
  NCBI__GCF_000469325.1:WP_022529386.1 178 AHNGTGQSKVGGNYAASLLAGQEAHTHHFSDAIYLDPVHHRYIEEVGSANFLAFTKDGKTLKTPKSPSILPSI 250
                                           ************************************************************************* PP

                             TIGR01123 220 tresllelakd.lgleveereiaidelkaaveaGeivfacGtaavitPvgelkiegkevevkse.evGevtkk 290
                                           t++s l la++ lg++ ee +i+idel+++ ea     acGtaavi+P+++++ +++ +++++e +vG++t+k
  NCBI__GCF_000469325.1:WP_022529386.1 251 TKYSSLYLAEHvLGMKTEETRISIDELDEFGEAA----ACGTAAVISPIAGIQYGDHYHVFYDEkKVGPITHK 319
                                           *******************************999....***********************99989******* PP

                             TIGR01123 291 lrdeltdiqyGkledkegWivev 313
                                           l+d lt+iq+G+++++ gW+ ev
  NCBI__GCF_000469325.1:WP_022529386.1 320 LYDLLTGIQFGDVDGPAGWVQEV 342
                                           *******************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (313 nodes)
Target sequences:                          1  (345 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 23.15
//
[ok]

This GapMind analysis is from Sep 24 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:

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