Alignments for a candidate for ilvE in Bacteroides thetaiotaomicron VPI-5482

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvE in Bacteroides thetaiotaomicron VPI-5482

Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate 353418 BT3892 branched-chain amino acid aminotransferase (NCBI ptt file)

Query= BRENDA::Q7BPX6
         (340 letters)



>FitnessBrowser__Btheta:353418
          Length = 339

 Score =  333 bits (855), Expect = 3e-96
 Identities = 173/338 (51%), Positives = 228/338 (67%), Gaps = 4/338 (1%)

Query: 5   LDWENLGFSYRNLPFRYIARFKDGKWSAGELTGDNQLHISESSPALHYGQQGFEGLKAYR 64
           +DW NL F Y    +     F++G W   E++ D  L++  ++  LHYGQ+ FEGLKA+R
Sbjct: 4   IDWANLSFGYMKTDYNVRINFRNGAWGELEVSSDEHLNLHMAATCLHYGQEAFEGLKAFR 63

Query: 65  TKDGSIQLFRPDQNAARLQKTARRLCMAEVSTEMFIDAVKQVVKANKDFVPPYGTGATLY 124
            KDG +++FR ++NAARLQ T + + MAE+ TE F +A+ +VVK N+ F+PPY TGA+LY
Sbjct: 64  GKDGKVRIFRLEENAARLQSTCQGILMAELPTERFKEAILKVVKLNERFIPPYETGASLY 123

Query: 125 LRPLLIGVGDVIGVKPADEYIFKVFAMPVGSYFKGGLAPSKFVISREYDRAAPLGTGGAK 184
           +RPLLIG    +GV PA+EY+F VF  PVG YFKGG + + +VI RE+DRAAP GTG  K
Sbjct: 124 IRPLLIGTSAQVGVHPAEEYMFVVFVTPVGPYFKGGFSTNPYVIIREFDRAAPHGTGIYK 183

Query: 185 VGGNYAASLQAEVGAKASGYADAIYLDPSTHTKIEEVGAANFFGITADNEFITPLSPSIL 244
           VGGNYAASL+A   A   GY+   YLD      I+E GAANFFGI  DN +ITP S SIL
Sbjct: 184 VGGNYAASLRANKKAHDLGYSCEFYLDAKEKKYIDECGAANFFGI-KDNTYITPKSSSIL 242

Query: 245 PSITKYSLLYLAEHRLGLKAIEGEVYAKDLGKFVEAGACGTAAIISPIGRIDDGED--SY 302
           PSIT  SL+ LAE  +G+K     +  ++L  F EAGACGTAA+ISPI RIDD E+  SY
Sbjct: 243 PSITNKSLMQLAED-MGIKVERRPIPEEELETFEEAGACGTAAVISPIQRIDDLENGKSY 301

Query: 303 IFHSETEVGPTVKRLYDELVGIQFGDVEAPEGWIVKVD 340
           +   + + GP   +LY++L GIQ+GD     GW+  V+
Sbjct: 302 VISKDGKPGPICTKLYNKLRGIQYGDEPDTHGWVTIVE 339


Lambda     K      H
   0.318    0.138    0.407 

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: 350
Number of extensions: 20
Number of successful extensions: 4
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: 340
Length of database: 339
Length adjustment: 28
Effective length of query: 312
Effective length of database: 311
Effective search space:    97032
Effective search space used:    97032
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 353418 BT3892 (branched-chain amino acid aminotransferase (NCBI ptt file))
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.21844.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   3.9e-114  366.8   0.0   4.5e-114  366.6   0.0    1.0  1  lcl|FitnessBrowser__Btheta:353418  BT3892 branched-chain amino acid


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:353418  BT3892 branched-chain amino acid aminotransferase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  366.6   0.0  4.5e-114  4.5e-114       1     312 [.      29     337 ..      29     338 .. 0.96

  Alignments for each domain:
  == domain 1  score: 366.6 bits;  conditional E-value: 4.5e-114
                          TIGR01123   1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflealkq 76 
                                        W e e+ s+++l+l+ +++ lhYgqe feGlka+R +dGk+ +fR ++na+Rl+++++ +l+ el++e f ea+ +
  lcl|FitnessBrowser__Btheta:353418  29 WGELEVSSDEHLNLHMAATCLHYGQEAFEGLKAFRGKDGKVRIFRLEENAARLQSTCQGILMAELPTERFKEAILK 104
                                        88999*********************************************************************** PP

                          TIGR01123  77 lvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsifveteyvRaapkGtG 152
                                        +vk++++++p+++++asLY+RP+li+t +++Gv++a+ey+f+v+++PvG+Yfkgg ++    +  e++Raap+GtG
  lcl|FitnessBrowser__Btheta:353418 105 VVKLNERFIPPYETGASLYIRPLLIGTSAQVGVHPAEEYMFVVFVTPVGPYFKGGFSTNPYVIIREFDRAAPHGTG 180
                                        *******************************************************999889999************ PP

                          TIGR01123 153 avkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttplsesiLegvtresllela 228
                                          kvgGnYaasl+a+kka++ g++   yld++ekk+i+e Gaan+f+i ++  + +tp+s siL+++t +sl++la
  lcl|FitnessBrowser__Btheta:353418 181 IYKVGGNYAASLRANKKAHDLGYSCEFYLDAKEKKYIDECGAANFFGIKDN--TYITPKSSSILPSITNKSLMQLA 254
                                        ************************************************885..9999******************* PP

                          TIGR01123 229 kdlgleveereiaidelkaaveaGeivfacGtaavitPvgelk..iegkevevkse.evGevtkklrdeltdiqyG 301
                                        +d+g++ve r i  +el+ + eaG    acGtaavi+P++++    +gk+++++++ ++G++ +kl+++l +iqyG
  lcl|FitnessBrowser__Btheta:353418 255 EDMGIKVERRPIPEEELETFEEAG----ACGTAAVISPIQRIDdlENGKSYVISKDgKPGPICTKLYNKLRGIQYG 326
                                        ************************....************99733477777765555******************* PP

                          TIGR01123 302 kledkegWive 312
                                        +  d++gW++ 
  lcl|FitnessBrowser__Btheta:353418 327 DEPDTHGWVTI 337
                                        ********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (313 nodes)
Target sequences:                          1  (339 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.69
//
[ok]

This GapMind analysis is from Apr 09 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