GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Thermus aquaticus YT-1

Align branched-chain-amino-acid aminotransferase subunit (EC 2.6.1.42) (characterized)
to candidate WP_053767056.1 BVI061214_RS01840 branched-chain amino acid transaminase

Query= metacyc::MONOMER-11914
         (306 letters)



>NCBI__GCF_001280255.1:WP_053767056.1
          Length = 318

 Score =  318 bits (815), Expect = 1e-91
 Identities = 162/302 (53%), Positives = 204/302 (67%), Gaps = 2/302 (0%)

Query: 6   SGKIWLNGEMVEWEEATVHVLSHVVHYGSSVFEGIRCYRNSKGSAIFRLREHVKRLFDSA 65
           +G IW NG++V  EEA   VLSH +HYG+SVFEGIR Y   KG AIFRL+EHVKRL++SA
Sbjct: 15  AGLIWFNGKLVPQEEAKTSVLSHALHYGTSVFEGIRAYETPKGPAIFRLKEHVKRLYNSA 74

Query: 66  KIYRMDIPYTQEQICDAIVETVRENGLEECYIRPVVFRGYGEMGVHPV-NCPVDVAVAAW 124
           K+ RM+IPYT E++ +AI E VR NG + CYIRP+ + G   +GV+P+ N P +V VAAW
Sbjct: 75  KVLRMEIPYTPEEMEEAIKEVVRRNGYKSCYIRPLAWMGAKALGVNPLPNNPAEVMVAAW 134

Query: 125 EWGAYLGAEALEVGVDAGVSTWRRMAPNTMPNMAKAGGNYLNSQLAKMEAVRHGYDEAIM 184
           EWGAYLG EA+  G     S+W R   N MP  AK GGNY+NS LAKMEA+  G DEA++
Sbjct: 135 EWGAYLGEEAVRKGARLITSSWARFPANVMPGKAKVGGNYVNSALAKMEALAAGADEALL 194

Query: 185 LDYHGYISEGSGENIFLVSEGEIYTPPVSSSLLRGITRDSVIKIARTEGVTVHEEPITRE 244
           LD  GY++EGSGEN+F V +G IY    S + L GITRDSVI+IAR  G  V     TR+
Sbjct: 195 LDEEGYVAEGSGENLFFVRDGVIYALEHSVN-LEGITRDSVIRIARDLGYQVQVVRATRD 253

Query: 245 MLYIADEAFFTGTAAEITPIRSVDGIEIGAGRRGPVTKLLQDEFFRIIRAETEDSFGWLT 304
            LY+ADE F TGTAAE+TP+  +D   IG G  GPV   L++ +         +   WLT
Sbjct: 254 QLYMADEVFMTGTAAEVTPVSMIDWRPIGEGTAGPVALRLREVYLEAATGRRPEYEHWLT 313

Query: 305 YI 306
           Y+
Sbjct: 314 YV 315


Lambda     K      H
   0.320    0.136    0.414 

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: 354
Number of extensions: 18
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: 306
Length of database: 318
Length adjustment: 27
Effective length of query: 279
Effective length of database: 291
Effective search space:    81189
Effective search space used:    81189
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 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate WP_053767056.1 BVI061214_RS01840 (branched-chain amino acid transaminase)
to HMM TIGR01122 (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/TIGR01122.hmm
# target sequence database:        /tmp/gapView.1843479.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01122  [M=298]
Accession:   TIGR01122
Description: ilvE_I: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.8e-130  419.4   0.0   4.3e-130  419.2   0.0    1.0  1  NCBI__GCF_001280255.1:WP_053767056.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001280255.1:WP_053767056.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  419.2   0.0  4.3e-130  4.3e-130       1     298 []      19     315 ..      19     315 .. 0.99

  Alignments for each domain:
  == domain 1  score: 419.2 bits;  conditional E-value: 4.3e-130
                             TIGR01122   1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskeelvev 73 
                                           w++G+lv+ e+ak++vl+halhYGt+vfeGiRaYet+kg+aifrlkehv+Rly+sak+lr+eipy+ ee+ e+
  NCBI__GCF_001280255.1:WP_053767056.1  19 WFNGKLVPQEEAKTSVLSHALHYGTSVFEGIRAYETPKGPAIFRLKEHVKRLYNSAKVLRMEIPYTPEEMEEA 91 
                                           9************************************************************************ PP

                             TIGR01122  74 tkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavnsi 146
                                           +kev+r+n+ ks+YiRpl+++Ga+ lg++p  + + ev++aawewgaylgeea+ kG + ++ss++r   n++
  NCBI__GCF_001280255.1:WP_053767056.1  92 IKEVVRRNGYKSCYIRPLAWMGAKALGVNPLPNNPAEVMVAAWEWGAYLGEEAVRKGARLITSSWARFPANVM 164
                                           ******************************9999*************************************** PP

                             TIGR01122 147 ptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdavik 219
                                           p kak++gnY+ns+lak+eal+aG+dea+lLdeeGyvaeGsGen+f v+dgv++  +  + +L+gitrd+vi+
  NCBI__GCF_001280255.1:WP_053767056.1 165 PGKAKVGGNYVNSALAKMEALAAGADEALLLDEEGYVAEGSGENLFFVRDGVIYALEH-SVNLEGITRDSVIR 236
                                           *******************************************************999.89************ PP

                             TIGR01122 220 lakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlvegktekke 292
                                           +a++lg++v+  r +r++ly+aDevf+tGtaaevtP+  +D r igeg++Gpv  +l+e + +  +g+ +++e
  NCBI__GCF_001280255.1:WP_053767056.1 237 IARDLGYQVQVVRATRDQLYMADEVFMTGTAAEVTPVSMIDWRPIGEGTAGPVALRLREVYLEAATGRRPEYE 309
                                           ************************************************************************* PP

                             TIGR01122 293 ewltyv 298
                                           +wltyv
  NCBI__GCF_001280255.1:WP_053767056.1 310 HWLTYV 315
                                           ****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (318 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: 14.44
//
[ok]

This GapMind analysis is from Jul 25 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