GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tpiA in Burkholderia phytofirmans PsJN

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate BPHYT_RS06610 BPHYT_RS06610 triosephosphate isomerase

Query= BRENDA::P0A858
         (255 letters)



>FitnessBrowser__BFirm:BPHYT_RS06610
          Length = 259

 Score =  216 bits (549), Expect = 5e-61
 Identities = 123/257 (47%), Positives = 156/257 (60%), Gaps = 6/257 (2%)

Query: 2   RHPLVMGNWKLNG---SRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSH 58
           R  LV+GNWK++G       + + V++   EL   A   V +  P  Y+  ++   EGS 
Sbjct: 5   RAKLVVGNWKMHGRLAENATLLQAVAHGAGELP--ADVRVGVCVPSPYLAQSQSLLEGSR 62

Query: 59  IMLGAQNVDLNLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKE 118
           ++ G Q+V     GA+TGE +A M+ D GA   I+GHSERR YH+ES EL+A K     E
Sbjct: 63  VVWGVQDVSAFTHGAYTGEVAAPMVVDFGATLAIVGHSERRAYHRESAELVAVKTQRALE 122

Query: 119 QGLTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSA 178
            GLTP++C+GET  E EAG TE+V   Q+D VL           V+AYEPVWAIGTGKSA
Sbjct: 123 AGLTPIVCVGETLEEREAGLTEQVVGTQLDEVLAKLSVQEAARLVVAYEPVWAIGTGKSA 182

Query: 179 TPAQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLK 238
           +  QAQAVH F+R  +A   A +A+ V + YGGSV   NA ELF QPDIDG L+GGASLK
Sbjct: 183 SSEQAQAVHAFLRARLAAKGAAVAD-VPLLYGGSVKPENAEELFRQPDIDGGLIGGASLK 241

Query: 239 ADAFAVIVKAAEAAKQA 255
              F  I KAA A   A
Sbjct: 242 DQDFLAICKAAAATSVA 258


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: 191
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: 255
Length of database: 259
Length adjustment: 24
Effective length of query: 231
Effective length of database: 235
Effective search space:    54285
Effective search space used:    54285
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 BPHYT_RS06610 BPHYT_RS06610 (triosephosphate 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.24386.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
    6.1e-63  198.7   0.6    7.1e-63  198.5   0.6    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS06610  BPHYT_RS06610 triosephosphate is


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS06610  BPHYT_RS06610 triosephosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.5   0.6   7.1e-63   7.1e-63       1     226 [.       8     241 ..       8     243 .. 0.93

  Alignments for each domain:
  == domain 1  score: 198.5 bits;  conditional E-value: 7.1e-63
                                TIGR00419   1 lviinfKlnesvgkvelevaklaeevas.eagvevavappfvdldvvkdeve.seiqvaAqnvdavksGa 68 
                                              lv++n+K+++ + + +++++ +a+   + +a+v v+v +p  +l   +  +e s++  + q+v a + Ga
  lcl|FitnessBrowser__BFirm:BPHYT_RS06610   8 LVVGNWKMHGRLAENATLLQAVAHGAGElPADVRVGVCVPSPYLAQSQSLLEgSRVVWGVQDVSAFTHGA 77 
                                              79*********************97665489*********************999*************** PP

                                TIGR00419  69 ftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleere.......a 131
                                              +tGe+ A m++d+Ga   ++gHsErR++++e+ el++ k  r+ e gl+++vCvgetleere       +
  lcl|FitnessBrowser__BFirm:BPHYT_RS06610  78 YTGEVAAPMVVDFGATLAIVGHSERRAYHRESAELVAVKTQRALEAGLTPIVCVGETLEEREaglteqvV 147
                                              **************************************************************77777766 PP

                                TIGR00419 132 artinnvattaaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasv 201
                                              +++++ v+ + ++      vvA+EPv++iGtGk++s  +a++v++++r  l+   + va +v +lyG+sv
  lcl|FitnessBrowser__BFirm:BPHYT_RS06610 148 GTQLDEVLAKLSVQEAARLVVAYEPVWAIGTGKSASSEQAQAVHAFLRARLAAKGAAVA-DVPLLYGGSV 216
                                              7777777777777779999*****************************88887777776.7********* PP

                                TIGR00419 202 taaedaelaaqldvdGvLlasavlk 226
                                              + +++ el+ q+d+dG L+++a+lk
  lcl|FitnessBrowser__BFirm:BPHYT_RS06610 217 KPENAEELFRQPDIDGGLIGGASLK 241
                                              ************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (259 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 7.04
//
[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