Alignments for a candidate for ilvE in Nocardiopsis lucentensis DSM 44048

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvE in Nocardiopsis lucentensis DSM 44048

Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_017598163.1 D471_RS0108160 branched-chain amino acid aminotransferase

Query= BRENDA::A0R066
         (368 letters)



>NCBI__GCF_000341125.1:WP_017598163.1
          Length = 371

 Score =  463 bits (1192), Expect = e-135
 Identities = 225/362 (62%), Positives = 278/362 (76%), Gaps = 2/362 (0%)

Query: 6   LEFTVSANTNPATDAVRESILANPGFGKYYTDHMVSIDYTVDEGWHNAQVIPYGPIQLDP 65
           L F +  +    T   RE +L NPGFG+ +TDHMV+I YT  +GWH+A++ PYGP+ LDP
Sbjct: 10  LTFDIQLSDQRKTPQEREELLENPGFGQVFTDHMVTIRYTEGKGWHDAKLEPYGPLSLDP 69

Query: 66  SAIVLHYGQEIFEGLKAYRWADGSIVSFRPEANAARLQSSARRLAIPELPEEVFIESLRQ 125
           +   LHY QEIFEGLKAYR  DGS+ SFRPEANAAR   SA R+A+P+LPE++F+ S+  
Sbjct: 70  ATAALHYAQEIFEGLKAYRHPDGSLASFRPEANAARFNKSAARMAMPDLPEDLFLRSIEL 129

Query: 126 LIAVDEKWVPPAGGEESLYLRPFVIATEPGLGVR-PSNEYRYLLIASPAGAYFKGGIKPV 184
           L+  D  WVP +  + SLYLRPF+IAT+ GLGV  PS  Y YLLIASP G+YF GG+KPV
Sbjct: 130 LLEHDGDWVP-SKPDFSLYLRPFMIATDVGLGVNNPSRSYVYLLIASPVGSYFSGGVKPV 188

Query: 185 SVWLSHEYVRASPGGTGAAKFGGNYAASLLAQAQAAEMGCDQVVWLDAIERRYVEEMGGM 244
           +VWLS +Y RA+PGGTGAAKF GNYAAS LAQAQA E GCDQVVWLDA E R+VEEMGGM
Sbjct: 189 TVWLSKDYTRAAPGGTGAAKFAGNYAASFLAQAQAVEKGCDQVVWLDAREHRWVEEMGGM 248

Query: 245 NLFFVFGSGGSARLVTPELSGSLLPGITRDSLLQLATDAGFAVEERKIDVDEWQKKAGAG 304
           NL+FVFG+G +ARL TP L+G+LLPGITR+SLL++A D G+  EE+ + ++EW++ A +G
Sbjct: 249 NLWFVFGTGENARLRTPPLTGTLLPGITRESLLRMAPDLGYEAEEKALSIEEWREAAESG 308

Query: 305 EITEVFACGTAAVITPVSHVKHHDGEFTIADGQPGEITMALRDTLTGIQRGTFADTHGWM 364
           EI+EVFACGTAAVITPV  VK  DGEF I DG PG +TM LR+ L G+Q G  AD +GW+
Sbjct: 309 EISEVFACGTAAVITPVGFVKSDDGEFRIGDGTPGPVTMRLREELVGLQTGQRADKYGWI 368

Query: 365 AR 366
            R
Sbjct: 369 TR 370


Lambda     K      H
   0.318    0.135    0.409 

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: 493
Number of extensions: 17
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: 368
Length of database: 371
Length adjustment: 30
Effective length of query: 338
Effective length of database: 341
Effective search space:   115258
Effective search space used:   115258
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate WP_017598163.1 D471_RS0108160 (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.3425.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.1e-127  410.4   0.0   2.4e-127  410.2   0.0    1.0  1  lcl|NCBI__GCF_000341125.1:WP_017598163.1  D471_RS0108160 branched-chain am


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000341125.1:WP_017598163.1  D471_RS0108160 branched-chain amino acid aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  410.2   0.0  2.4e-127  2.4e-127       1     312 [.      54     370 ..      54     371 .] 0.98

  Alignments for each domain:
  == domain 1  score: 410.2 bits;  conditional E-value: 2.4e-127
                                 TIGR01123   1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeel 69 
                                               W++a+l+++++l+ld+++a+lhY+qe+feGlkayR+ dG++ +fRp+ana+R+++sa r+++P+l+e+l
  lcl|NCBI__GCF_000341125.1:WP_017598163.1  54 WHDAKLEPYGPLSLDPATAALHYAQEIFEGLKAYRHPDGSLASFRPEANAARFNKSAARMAMPDLPEDL 122
                                               ********************************************************************* PP

                                 TIGR01123  70 flealkqlvkadkdwvpkakseasLYlRPfliatednlGvk.aakeylflvlasPvGaYfkgglapvsi 137
                                               fl++++ l++ d dwvp++  + sLYlRPf+iat+  lGv+ ++++y++l++asPvG+Yf gg++pv++
  lcl|NCBI__GCF_000341125.1:WP_017598163.1 123 FLRSIELLLEHDGDWVPSKP-DFSLYLRPFMIATDVGLGVNnPSRSYVYLLIASPVGSYFSGGVKPVTV 190
                                               *****************877.******************963788************************ PP

                                 TIGR01123 138 fveteyvRaapkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdg.. 204
                                               +++++y+Raap+GtGa+k++GnYaas+laq++a e+g+d+vv+ld+ e++ +ee+G++n+ ++ + g  
  lcl|NCBI__GCF_000341125.1:WP_017598163.1 191 WLSKDYTRAAPGGTGAAKFAGNYAASFLAQAQAVEKGCDQVVWLDAREHRWVEEMGGMNLWFVFGTGen 259
                                               ****************************************************************99965 PP

                                 TIGR01123 205 .elvttplsesiLegvtresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgel 270
                                                +l t+pl++ +L+g+tresll++a dlg+e+ee+ ++i+e+++a+e+Gei  vfacGtaavitPvg +
  lcl|NCBI__GCF_000341125.1:WP_017598163.1 260 aRLRTPPLTGTLLPGITRESLLRMAPDLGYEAEEKALSIEEWREAAESGEIseVFACGTAAVITPVGFV 328
                                               56789*********************************************99***************** PP

                                 TIGR01123 271 kiegkevevkseevGevtkklrdeltdiqyGkledkegWive 312
                                               k ++ e+++ ++ +G+vt++lr+el+++q+G+ +dk+gWi++
  lcl|NCBI__GCF_000341125.1:WP_017598163.1 329 KSDDGEFRIGDGTPGPVTMRLREELVGLQTGQRADKYGWITR 370
                                               ****************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (313 nodes)
Target sequences:                          1  (371 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: 13.19
//
[ok]

This GapMind analysis is from Apr 10 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