Alignments for a candidate for ilvE in Lactobacillus silagei IWT126

GapMind for catabolism of small carbon sources

Alignments for a candidate for ilvE in Lactobacillus silagei IWT126

Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_089136520.1 CES79_RS05205 branched-chain amino acid aminotransferase

Query= BRENDA::Q8DTW7
         (341 letters)



>NCBI__GCF_002217945.1:WP_089136520.1
          Length = 345

 Score =  530 bits (1365), Expect = e-155
 Identities = 249/337 (73%), Positives = 289/337 (85%), Gaps = 1/337 (0%)

Query: 4   DLDWKNLGFEYHKLPFRYISYYKDGKWDDGKLTEDATLHISESSPALHYGQEAFEGLKAY 63
           ++DW+NLGF Y  LP+R++++YKDG+WDDGKLTEDATLHISE S ALHYGQ  FEGLKAY
Sbjct: 9   EIDWQNLGFNYMDLPYRFLAHYKDGQWDDGKLTEDATLHISEGSTALHYGQADFEGLKAY 68

Query: 64  RTKDGSVQLFRPNMNAERLQRTADRLLMPQVPTDKFIDAAKQVVRANEEYVPPYGTGATL 123
           RTK+G +QLFRP+ NA R+Q++ +RLLMP  PTDKF+ A K VV+AN +YVPPYGTG TL
Sbjct: 69  RTKNGDIQLFRPDRNAARMQKSCERLLMPPFPTDKFVAAVKSVVKANADYVPPYGTGGTL 128

Query: 124 YLRPLLIGVGDVIGVHPADEYIFTIFAMPVGNYFKGGLAPTNFLIQDDYDRAAPHGTGAA 183
           YLRPL+IGVG+ IGVHPA EY+FT+FAMPVG Y+KGG+ PTNF     YDRAAPHGTG +
Sbjct: 129 YLRPLMIGVGENIGVHPAPEYLFTVFAMPVGAYYKGGVKPTNFTTSY-YDRAAPHGTGQS 187

Query: 184 KVGGNYAASLLPGKVAHERQFSDVIYLDPATHTKIEEVGSANFFGITKDNEFITPLSPSI 243
           KVGGNY  SLLPG  AH+  +SDVIYLDPATHTKIEE GSANFFGITK+NEF+TP S SI
Sbjct: 188 KVGGNYGGSLLPGSEAHKAGYSDVIYLDPATHTKIEEAGSANFFGITKNNEFVTPKSNSI 247

Query: 244 LPSVTKYSLLYLAEHRFGMKAIEGDVCVDELDKFVEAGACGTAAVISPIGGVQHGDDFHV 303
           LPS+TKYSLLYLAEH  GMKAIEGDV +++LD+F EAGA GTAAVI+PIGG+++ D  HV
Sbjct: 248 LPSITKYSLLYLAEHNLGMKAIEGDVFINDLDRFTEAGAMGTAAVIAPIGGIEYQDQLHV 307

Query: 304 FYSETEVGPVTHKLYDELTGIQFGDVKAPEGWIYKVD 340
           FYSETEVGPVT KLYD LTGIQFGDVKAPEGWI KV+
Sbjct: 308 FYSETEVGPVTQKLYDTLTGIQFGDVKAPEGWIQKVE 344


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: 521
Number of extensions: 20
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: 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_089136520.1 CES79_RS05205 (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.1274681.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     2e-130  420.3   0.0   2.4e-130  420.1   0.0    1.0  1  NCBI__GCF_002217945.1:WP_089136520.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002217945.1:WP_089136520.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  420.1   0.0  2.4e-130  2.4e-130       1     313 []      35     343 ..      35     343 .. 0.99

  Alignments for each domain:
  == domain 1  score: 420.1 bits;  conditional E-value: 2.4e-130
                             TIGR01123   1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflea 73 
                                           Wd+++l+++a+l+++egs++lhYgq+ feGlkayRt++G i lfRpd+na+R+++s+erll+P  +++ f+ a
  NCBI__GCF_002217945.1:WP_089136520.1  35 WDDGKLTEDATLHISEGSTALHYGQADFEGLKAYRTKNGDIQLFRPDRNAARMQKSCERLLMPPFPTDKFVAA 107
                                           ************************************************************************* PP

                             TIGR01123  74 lkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsifveteyvRa 146
                                           +k +vka++d+vp+++++ +LYlRP++i++++n+Gv++a+eylf+v+a PvGaY+kgg++p ++f ++ y+Ra
  NCBI__GCF_002217945.1:WP_089136520.1 108 VKSVVKANADYVPPYGTGGTLYLRPLMIGVGENIGVHPAPEYLFTVFAMPVGAYYKGGVKP-TNFTTSYYDRA 179
                                           *************************************************************.*********** PP

                             TIGR01123 147 apkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttplsesiLegv 219
                                           ap+GtG+ kvgGnY  sll+ ++a++ g++dv+yldp++++kiee+G+an+f+itk+ + ++tp+s+siL+++
  NCBI__GCF_002217945.1:WP_089136520.1 180 APHGTGQSKVGGNYGGSLLPGSEAHKAGYSDVIYLDPATHTKIEEAGSANFFGITKN-NEFVTPKSNSILPSI 251
                                           ********************************************************9.99************* PP

                             TIGR01123 220 tresllelakd.lgleveereiaidelkaaveaGeivfacGtaavitPvgelkiegkevevkse.evGevtkk 290
                                           t++sll la++ lg+++ e+++ i++l++++eaG    a Gtaavi+P+g+++ +++ ++++se evG+vt+k
  NCBI__GCF_002217945.1:WP_089136520.1 252 TKYSLLYLAEHnLGMKAIEGDVFINDLDRFTEAG----AMGTAAVIAPIGGIEYQDQLHVFYSEtEVGPVTQK 320
                                           **********99**********************....9***********************999******** PP

                             TIGR01123 291 lrdeltdiqyGkledkegWivev 313
                                           l+d+lt+iq+G+++++egWi +v
  NCBI__GCF_002217945.1:WP_089136520.1 321 LYDTLTGIQFGDVKAPEGWIQKV 343
                                           ********************987 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 24.62
//
[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:

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 2024 update 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

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 catabolism of small carbon sources