GapMind for Amino acid biosynthesis

 

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

Align chorismate mutase (EC 5.4.99.5) (characterized)
to candidate 353460 BT3934 putative phospho-2-dehydro-3-deoxyheptonate aldolase/chorismate mutase (NCBI ptt file)

Query= reanno::Pedo557:CA265_RS11635
         (379 letters)



>FitnessBrowser__Btheta:353460
          Length = 353

 Score =  377 bits (968), Expect = e-109
 Identities = 181/342 (52%), Positives = 248/342 (72%), Gaps = 5/342 (1%)

Query: 20  PLIISGPCSAETEEQLLTTAHLLAATGKVSVLRAGIWKPRTRPGEFEGIGSIGLEWLKRA 79
           P++I+GPCSAETEEQ++ TA  LAA G+  + RAGIWKPRT+PG FEGIG  GL WLK  
Sbjct: 16  PIVIAGPCSAETEEQVMETAKQLAAKGQ-KIYRAGIWKPRTKPGGFEGIGVEGLAWLKEV 74

Query: 80  KAETGLPTAVEVANAKHVEEALAAGVDILWIGARSTVNPFTVQEIADALKGHDVPVLIKN 139
           K ETG+  + EVA AKHV E L AG+DILW+GAR+T NPF VQEIADALKG D+PVL+KN
Sbjct: 75  KKETGMYVSTEVATAKHVYECLKAGIDILWVGARTTANPFAVQEIADALKGVDIPVLVKN 134

Query: 140 PVNPDLQLWIGAIERINGAGITKIGAIHRGFSSFEKSSFRNEPMWELAIQLKTLCPELPI 199
           PVNPDL+LWIGA+ERI+ AG+ ++GAIHRGFSS++K  +RN P W + I+L+   P LPI
Sbjct: 135 PVNPDLELWIGALERIHNAGLKRLGAIHRGFSSYDKKIYRNLPQWHIPIELRRRLPNLPI 194

Query: 200 INDPSHICGNRELIPYISQKALDLDMQGLMIESHVDPSVAWTDAKQQVTPAALAELVDRL 259
             DPSHI G REL+  + Q+A+DL+  GL++ESH +P  AW+DA QQVTP  L  +++ L
Sbjct: 195 FCDPSHIGGKRELVAPLCQQAMDLNFDGLIVESHCNPDCAWSDASQQVTPDVLDYILNLL 254

Query: 260 TVREPEAPNEAFADKLADLRKSIDKIDDVLLQKLGERMAIVEKIGEFKRDNQVTILQVNR 319
            +R      E+    L+ LRK ID+ DD ++Q+L +RM +  +IG +K+++ +T+LQ  R
Sbjct: 255 VIRTETQTTES----LSQLRKQIDECDDNIIQELAKRMRVAREIGTYKKEHGITVLQAGR 310

Query: 320 WDAIIKKGHAFAKALKLDLNFTEKFLELVHGESIRKQTEIMN 361
           ++ I++K  A  +   +  +F +   E +H ES+R+Q EI+N
Sbjct: 311 YNEILEKRGAQGEQCGMSADFMKLIFEAIHEESVRQQIEIIN 352


Lambda     K      H
   0.317    0.134    0.389 

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: 363
Number of extensions: 10
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: 379
Length of database: 353
Length adjustment: 30
Effective length of query: 349
Effective length of database: 323
Effective search space:   112727
Effective search space used:   112727
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 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate 353460 BT3934 (putative phospho-2-dehydro-3-deoxyheptonate aldolase/chorismate mutase (NCBI ptt file))
to HMM PF01817 (CM_2)

# 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/PF01817.25.hmm
# target sequence database:        /tmp/gapView.2275.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       CM_2  [M=79]
Accession:   PF01817.25
Description: Chorismate mutase type II
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
    1.5e-27   82.1   3.2    2.4e-27   81.5   1.5    2.2  2  lcl|FitnessBrowser__Btheta:353460  BT3934 putative phospho-2-dehydr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:353460  BT3934 putative phospho-2-dehydro-3-deoxyheptonate aldolase/chorismate mutase (NCB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.16      0.16      40      53 ..      26      39 ..      23      51 .. 0.70
   2 !   81.5   1.5   2.4e-27   2.4e-27       1      78 [.     270     347 ..     270     348 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.16
                               CM_2 40 eReeevlerlrega 53
                                       e ee+v+e +++ a
  lcl|FitnessBrowser__Btheta:353460 26 ETEEQVMETAKQLA 39
                                       67999999999944 PP

  == domain 2  score: 81.5 bits;  conditional E-value: 2.4e-27
                               CM_2   1 RkeIdeiDrelleLlaeRmelakeiaeyKkenglpvldpeReeevlerlregaeelgldpeavekifreiisesra 76 
                                        Rk+Ide+D+++++ la+Rm++a+ei+ yKke+g++vl+  R +e+le++ ++ e++g+++++++ if++i++es++
  lcl|FitnessBrowser__Btheta:353460 270 RKQIDECDDNIIQELAKRMRVAREIGTYKKEHGITVLQAGRYNEILEKRGAQGEQCGMSADFMKLIFEAIHEESVR 345
                                        9***************************************************9*********************** PP

                               CM_2  77 lQ 78 
                                        +Q
  lcl|FitnessBrowser__Btheta:353460 346 QQ 347
                                        99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (79 nodes)
Target sequences:                          1  (353 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: 12.56
//
[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:

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