Alignments for a candidate for ilvE in Streptacidiphilus oryzae TH49

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvE in Streptacidiphilus oryzae TH49

Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_037572571.1 BS73_RS14690 branched-chain amino acid aminotransferase

Query= BRENDA::A0R066
         (368 letters)



>NCBI__GCF_000744815.1:WP_037572571.1
          Length = 359

 Score =  444 bits (1143), Expect = e-129
 Identities = 213/358 (59%), Positives = 269/358 (75%), Gaps = 4/358 (1%)

Query: 6   LEFTVSANTNPATDAVRESILANPGFGKYYTDHMVSIDYTVDEGWHNAQVIPYGPIQLDP 65
           ++  +  + +P   A RE+ LA PGFG+Y+TD+MV+I +T   GWH+AQ++PYGP+++DP
Sbjct: 1   MQIELKPSAHPLPAAEREARLAAPGFGRYFTDNMVTIRWTEGRGWHDAQLVPYGPLEMDP 60

Query: 66  SAIVLHYGQEIFEGLKAYRWADGSIVSFRPEANAARLQSSARRLAIPELPEEVFIESLRQ 125
           + + LHY QEIFEGLKAYR  DG +  FRPE NA R Q SAR LA+PELP E FIE+   
Sbjct: 61  ANMTLHYAQEIFEGLKAYRQPDGGVALFRPERNALRFQHSARTLAMPELPVETFIEACDA 120

Query: 126 LIAVDEKWVPPAGGEESLYLRPFVIATEPGLGVRPSNEYRYLLIASPAGAYFKGGIKPVS 185
           L+A D +WVPP GGE SLYLRPF+IA+E GLGV+P+NEY +L+IASPAG YF GG+KPVS
Sbjct: 121 LVAQDVEWVPPHGGEASLYLRPFMIASEVGLGVKPANEYLFLVIASPAGPYFPGGVKPVS 180

Query: 186 VWLSHEYVRASPGGTGAAKFGGNYAASLLAQAQAAEMGCDQVVWLDAIERRYVEEMGGMN 245
           +W+S + VRA PGG G AK GGNYAASLLAQA+AAE GC QV +LDA+ERR+VEE+GGMN
Sbjct: 181 IWISQDRVRAVPGGMGDAKTGGNYAASLLAQAEAAEQGCAQVAYLDAVERRWVEELGGMN 240

Query: 246 LFFVFGSGGSARLVTPELSGSLLPGITRDSLLQLATDAGFAVEERKIDVDEWQKKAGAGE 305
           L+FV+G     R+VTP L+GSLL G+TRDSLL LA D G+  EE +I VD+W++    G 
Sbjct: 241 LYFVYGD----RIVTPALTGSLLEGVTRDSLLTLARDLGYESEEARISVDQWREDTANGS 296

Query: 306 ITEVFACGTAAVITPVSHVKHHDGEFTIADGQPGEITMALRDTLTGIQRGTFADTHGW 363
           +TEVFACGTAAVITPV  VK     +T   G+PG +T+ LR+ L  +Q G   D HGW
Sbjct: 297 LTEVFACGTAAVITPVGEVKTKGAAWTQGSGEPGPVTLRLREALLSLQTGNAEDPHGW 354


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: 520
Number of extensions: 23
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: 368
Length of database: 359
Length adjustment: 29
Effective length of query: 339
Effective length of database: 330
Effective search space:   111870
Effective search space used:   111870
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_037572571.1 BS73_RS14690 (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.648816.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-132  426.9   0.0   2.4e-132  426.7   0.0    1.0  1  NCBI__GCF_000744815.1:WP_037572571.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000744815.1:WP_037572571.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  426.7   0.0  2.4e-132  2.4e-132       1     309 [.      45     354 ..      45     358 .. 0.99

  Alignments for each domain:
  == domain 1  score: 426.7 bits;  conditional E-value: 2.4e-132
                             TIGR01123   1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflea 73 
                                           W++a+l+++++le+d++ + lhY+qe+feGlkayR+ dG + lfRp++na R+++sa+ l++Pel+ e f+ea
  NCBI__GCF_000744815.1:WP_037572571.1  45 WHDAQLVPYGPLEMDPANMTLHYAQEIFEGLKAYRQPDGGVALFRPERNALRFQHSARTLAMPELPVETFIEA 117
                                           ************************************************************************* PP

                             TIGR01123  74 lkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsifveteyvRa 146
                                           +  lv++d +wvp++++easLYlRPf+ia e  lGvk+a+eylflv+asP+G+Yf gg++pvsi+++++ vRa
  NCBI__GCF_000744815.1:WP_037572571.1 118 CDALVAQDVEWVPPHGGEASLYLRPFMIASEVGLGVKPANEYLFLVIASPAGPYFPGGVKPVSIWISQDRVRA 190
                                           ************************************************************************* PP

                             TIGR01123 147 apkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttplsesiLegv 219
                                           +p+G+G +k+gGnYaasllaq++aaeqg+++v yld+ve++ +ee+G++n++++++d ++vt++l++s+Legv
  NCBI__GCF_000744815.1:WP_037572571.1 191 VPGGMGDAKTGGNYAASLLAQAEAAEQGCAQVAYLDAVERRWVEELGGMNLYFVYGD-RIVTPALTGSLLEGV 262
                                           *********************************************************.*************** PP

                             TIGR01123 220 tresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkiegkevevkseevGevtkk 290
                                           tr+sll+la+dlg+e ee +i++d++++ +++G++  vfacGtaavitPvge+k++g   +  s+e+G+vt +
  NCBI__GCF_000744815.1:WP_037572571.1 263 TRDSLLTLARDLGYESEEARISVDQWREDTANGSLteVFACGTAAVITPVGEVKTKGAAWTQGSGEPGPVTLR 335
                                           *********************************9999************************************ PP

                             TIGR01123 291 lrdeltdiqyGkledkegW 309
                                           lr++l+++q+G++ed++gW
  NCBI__GCF_000744815.1:WP_037572571.1 336 LREALLSLQTGNAEDPHGW 354
                                           ******************* PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (313 nodes)
Target sequences:                          1  (359 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: 13.78
//
[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:

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
changes to Amino acid biosynthesis since the original 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