GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tpiA in Klebsiella michiganensis M5al

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate BWI76_RS27465 BWI76_RS27465 triose-phosphate isomerase

Query= BRENDA::P0A858
         (255 letters)



>FitnessBrowser__Koxy:BWI76_RS27465
          Length = 255

 Score =  466 bits (1199), Expect = e-136
 Identities = 237/255 (92%), Positives = 243/255 (95%)

Query: 1   MRHPLVMGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSHIM 60
           MRHPLVMGNWKLNGSRHMV+ELV+NLR ELAGV GCAVAIAPPEMYID+AK+ A GSHI 
Sbjct: 1   MRHPLVMGNWKLNGSRHMVNELVANLRTELAGVTGCAVAIAPPEMYIDLAKQAAAGSHIH 60

Query: 61  LGAQNVDLNLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQG 120
           LGAQNVDLNLSGAFTGETSA MLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQG
Sbjct: 61  LGAQNVDLNLSGAFTGETSAEMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQG 120

Query: 121 LTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSATP 180
           L PVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEG VIAYEPVWAIGTGKSATP
Sbjct: 121 LIPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGVVIAYEPVWAIGTGKSATP 180

Query: 181 AQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKAD 240
           AQAQAVHKFIRDHIAK DA +AEQVIIQYGGSVNA NAAELF QPDIDGALVGGASLKAD
Sbjct: 181 AQAQAVHKFIRDHIAKADAKVAEQVIIQYGGSVNAGNAAELFTQPDIDGALVGGASLKAD 240

Query: 241 AFAVIVKAAEAAKQA 255
           AFAVIVKAAEAAK+A
Sbjct: 241 AFAVIVKAAEAAKKA 255


Lambda     K      H
   0.316    0.130    0.366 

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: 310
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: 255
Length of database: 255
Length adjustment: 24
Effective length of query: 231
Effective length of database: 231
Effective search space:    53361
Effective search space used:    53361
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: 47 (22.7 bits)

Align candidate BWI76_RS27465 BWI76_RS27465 (triose-phosphate isomerase)
to HMM TIGR00419 (tpiA: triose-phosphate isomerase (EC 5.3.1.1))

# 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/TIGR00419.hmm
# target sequence database:        /tmp/gapView.9408.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00419  [M=228]
Accession:   TIGR00419
Description: tim: triose-phosphate isomerase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   1.6e-108  347.8   4.5   1.8e-108  347.6   4.5    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS27465  BWI76_RS27465 triose-phosphate i


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS27465  BWI76_RS27465 triose-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  347.6   4.5  1.8e-108  1.8e-108       1     228 []       5     240 ..       5     240 .. 0.99

  Alignments for each domain:
  == domain 1  score: 347.6 bits;  conditional E-value: 1.8e-108
                               TIGR00419   1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGaft 70 
                                             lv++n+Kln+s+++v+++va+l+ e+a+++g++va+app++++d +k+++  s+i+++Aqnvd++ sGaft
  lcl|FitnessBrowser__Koxy:BWI76_RS27465   5 LVMGNWKLNGSRHMVNELVANLRTELAGVTGCAVAIAPPEMYIDLAKQAAAgSHIHLGAQNVDLNLSGAFT 75 
                                             79***********************************************999******************* PP

                               TIGR00419  71 GeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleere.......aart 134
                                             Ge+sAemlkd+Ga++++igHsErR+++ke+deli+kk+a+lke+gl +v+C+get++e+e       +ar+
  lcl|FitnessBrowser__Koxy:BWI76_RS27465  76 GETSAEMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQGLIPVLCIGETEAENEagkteevCARQ 146
                                             *********************************************************************** PP

                               TIGR00419 135 innvattaaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaae 205
                                             i++v++t++aaA+e++v+A+EPv++iGtGk++++A+a++v+k++rdh++k++++vae+v+++yG+sv+a++
  lcl|FitnessBrowser__Koxy:BWI76_RS27465 147 IDAVLKTQGAAAFEGVVIAYEPVWAIGTGKSATPAQAQAVHKFIRDHIAKADAKVAEQVIIQYGGSVNAGN 217
                                             *********************************************************************** PP

                               TIGR00419 206 daelaaqldvdGvLlasavlkae 228
                                             +ael+ q+d+dG+L+++a+lka+
  lcl|FitnessBrowser__Koxy:BWI76_RS27465 218 AAELFTQPDIDGALVGGASLKAD 240
                                             *********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (255 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: 00:00:00.00
# Mc/sec: 5.93
//
[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