GapMind for catabolism of small carbon sources

 

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.carbon/TIGR01123.hmm
# target sequence database:        /tmp/gapView.29755.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.44
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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