Alignments for a candidate for ilvE in Thiomicrospira cyclica ALM1

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvE in Thiomicrospira cyclica ALM1

Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate WP_013835846.1 THICY_RS06625 branched-chain amino acid transaminase

Query= reanno::psRCH2:GFF445
         (307 letters)



>NCBI__GCF_000214825.1:WP_013835846.1
          Length = 309

 Score =  460 bits (1184), Expect = e-134
 Identities = 223/305 (73%), Positives = 258/305 (84%)

Query: 2   SMADRDGVIWYDGELVQWRDATTHVLTHTLHYGMGVFEGVRAYNTPDGTAIFRLQAHTDR 61
           +M+DRDG+IW DGE+V WR+A THVLTHTLHYGMGVFEGVRAY+   GTAIFRL+AHTDR
Sbjct: 3   TMSDRDGLIWKDGEMVPWREANTHVLTHTLHYGMGVFEGVRAYDADGGTAIFRLEAHTDR 62

Query: 62  LFDSAHIMNMPMPYSKEEINEATRAAVRENNLESAYIRPMVFYGSEGMGLRASGLKVHVI 121
           LF+SA IMNMPMP+ KE +N A RAAVREN L+SAYIRPMV+YGSEGMGLRA  LK HVI
Sbjct: 63  LFNSAKIMNMPMPFDKETLNAAQRAAVRENGLKSAYIRPMVYYGSEGMGLRADNLKTHVI 122

Query: 122 VAAWHWGAYMGDEALELGIKVRTSSFTRHHVNITMTRAKSNGAYINSMLALQEAISGGAD 181
           +AAW WGAYMG+E L  GIKV TSS+TRHH NITMT+AK+NGAY+NSMLALQEAI+ G  
Sbjct: 123 IAAWEWGAYMGEENLTKGIKVATSSYTRHHPNITMTKAKANGAYMNSMLALQEAIAHGCH 182

Query: 182 EALMLDPEGYVAEGSGENIFIIKDGVIYTPEVTACLNGITRGTVLTLAAEHGLKIVEKRI 241
           EAL+LD  G+VAEGSGEN F+IKDGVIYTP+++A L+GITR TV  +A E G ++VEKRI
Sbjct: 183 EALLLDSHGFVAEGSGENFFMIKDGVIYTPDLSAALDGITRKTVFQIAKELGYQVVEKRI 242

Query: 242 TRDEVYIADEAFFTGTAAEVTPIREVDGRAIGIGRRGPITEKLQKAYFDLVTGKTDAHAE 301
           TRDEVYIADEAFFTGTAAEVTPIRE+D R IG G RGPIT K+Q  YFD+V G++ AH  
Sbjct: 243 TRDEVYIADEAFFTGTAAEVTPIRELDNRPIGCGSRGPITAKIQAMYFDIVHGRSAAHEA 302

Query: 302 WRTLV 306
           W + V
Sbjct: 303 WLSRV 307


Lambda     K      H
   0.319    0.135    0.400 

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: 414
Number of extensions: 6
Number of successful extensions: 1
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: 307
Length of database: 309
Length adjustment: 27
Effective length of query: 280
Effective length of database: 282
Effective search space:    78960
Effective search space used:    78960
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_013835846.1 THICY_RS06625 (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.13947.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.9e-138  444.4   0.1     1e-137  444.2   0.1    1.0  1  lcl|NCBI__GCF_000214825.1:WP_013835846.1  THICY_RS06625 branched-chain ami


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000214825.1:WP_013835846.1  THICY_RS06625 branched-chain amino acid transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  444.2   0.1    1e-137    1e-137       1     298 []      12     307 ..      12     307 .. 0.99

  Alignments for each domain:
  == domain 1  score: 444.2 bits;  conditional E-value: 1e-137
                                 TIGR01122   1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskee 69 
                                               w dGe+v++++a++hvlth+lhYG+gvfeG+RaY++d g+aifrl+ h++Rl++saki+++++p+ ke+
  lcl|NCBI__GCF_000214825.1:WP_013835846.1  12 WKDGEMVPWREANTHVLTHTLHYGMGVFEGVRAYDADGGTAIFRLEAHTDRLFNSAKIMNMPMPFDKET 80 
                                               89******************************************************************* PP

                                 TIGR01122  70 lvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssf 138
                                               l+ +++ ++r+n+lksaYiRp+vy+G+e++gl++  +lk++viiaawewgay+gee l kGikv +ss+
  lcl|NCBI__GCF_000214825.1:WP_013835846.1  81 LNAAQRAAVRENGLKSAYIRPMVYYGSEGMGLRA-DNLKTHVIIAAWEWGAYMGEENLTKGIKVATSSY 148
                                               **********************************.899******************************* PP

                                 TIGR01122 139 rraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvses 207
                                               +r+++n+ +tkaka+g+Y+ns+la +ea+++G +ea+lLd++G+vaeGsGen+f++kdgv++tP++ ++
  lcl|NCBI__GCF_000214825.1:WP_013835846.1 149 TRHHPNITMTKAKANGAYMNSMLALQEAIAHGCHEALLLDSHGFVAEGSGENFFMIKDGVIYTPDL-SA 216
                                               ******************************************************************.88 PP

                                 TIGR01122 208 iLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkkl 276
                                               +L+gitr +v ++akelg++v+e+ri+r+e+y+aDe+f+tGtaaevtPire+D+r ig g+rGp+t k+
  lcl|NCBI__GCF_000214825.1:WP_013835846.1 217 ALDGITRKTVFQIAKELGYQVVEKRITRDEVYIADEAFFTGTAAEVTPIRELDNRPIGCGSRGPITAKI 285
                                               ********************************************************************* PP

                                 TIGR01122 277 qeaffdlvegktekkeewltyv 298
                                               q  +fd+v+g+  ++e wl+ v
  lcl|NCBI__GCF_000214825.1:WP_013835846.1 286 QAMYFDIVHGRSAAHEAWLSRV 307
                                               ******************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (309 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.59
//
[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