GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Paraburkholderia bryophila 376MFSha3.1

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate H281DRAFT_04564 H281DRAFT_04564 triosephosphate isomerase

Query= BRENDA::P0A858
         (255 letters)



>FitnessBrowser__Burk376:H281DRAFT_04564
          Length = 259

 Score =  221 bits (562), Expect = 2e-62
 Identities = 123/255 (48%), Positives = 155/255 (60%), Gaps = 2/255 (0%)

Query: 2   RHPLVMGNWKLNGSRHMVHELVSNLRKELAGV-AGCAVAIAPPEMYIDMAKREAEGSHIM 60
           R  LV+GNWK++G       L+  + K  A + A   V +  P  Y+  A+   EGS ++
Sbjct: 5   RAKLVVGNWKMHGCLADNAGLLQAVAKGAAELPADVRVGVCVPSPYLAQAQSLLEGSRVV 64

Query: 61  LGAQNVDLNLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQG 120
            G Q++     GA+TGE +A M+ D  A + I+GHSERR YH+ES EL+A K     E G
Sbjct: 65  WGVQDISAFTHGAYTGEVAAQMVADFSAAFAIVGHSERRAYHRESAELVAVKTQRALEAG 124

Query: 121 LTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSATP 180
           LTP++C+GET  E EAG TE+V   Q+D VL    A      V+AYEPVWAIGTGKSAT 
Sbjct: 125 LTPIVCVGETLEEREAGSTEQVVGAQLDEVLAKLSAEEAAHIVVAYEPVWAIGTGKSATS 184

Query: 181 AQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKAD 240
            QAQAVH F+R  +A   A +A  V + YGGSV   NA ELF+Q DIDG L+GGASLK  
Sbjct: 185 EQAQAVHAFLRSRLAAKGAGVA-NVTLLYGGSVKPDNAEELFSQQDIDGGLIGGASLKDK 243

Query: 241 AFAVIVKAAEAAKQA 255
            F  I KAA A   A
Sbjct: 244 DFLAICKAAAATTAA 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: 203
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 H281DRAFT_04564 H281DRAFT_04564 (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.carbon/TIGR00419.hmm
# target sequence database:        /tmp/gapView.9497.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
    1.4e-62  197.5   2.9    1.7e-62  197.2   2.9    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_04564  H281DRAFT_04564 triosephosphate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_04564  H281DRAFT_04564 triosephosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.2   2.9   1.7e-62   1.7e-62       1     227 [.       8     242 ..       8     243 .. 0.94

  Alignments for each domain:
  == domain 1  score: 197.2 bits;  conditional E-value: 1.7e-62
                                    TIGR00419   1 lviinfKlnesvgkvelevaklaeevas.eagvevavappfvdldvvkdeve.seiqvaAqnvdav 64 
                                                  lv++n+K+++ + + + +++ +a+  a+ +a+v v+v +p  +l  ++  +e s++  + q++ a 
  lcl|FitnessBrowser__Burk376:H281DRAFT_04564   8 LVVGNWKMHGCLADNAGLLQAVAKGAAElPADVRVGVCVPSPYLAQAQSLLEgSRVVWGVQDISAF 73 
                                                  79**********************8887579*********************999*********** PP

                                    TIGR00419  65 ksGaftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleere 130
                                                  + Ga+tGe+ A+m++d+ a++ ++gHsErR++++e+ el++ k  r+ e gl+++vCvgetleere
  lcl|FitnessBrowser__Burk376:H281DRAFT_04564  74 THGAYTGEVAAQMVADFSAAFAIVGHSERRAYHRESAELVAVKTQRALEAGLTPIVCVGETLEERE 139
                                                  ****************************************************************** PP

                                    TIGR00419 131 .......aartinnvattaaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskev 189
                                                         ++ +++ v+ + +a      vvA+EPv++iGtGk+++  +a++v++++r  l+   + v
  lcl|FitnessBrowser__Burk376:H281DRAFT_04564 140 agsteqvVGAQLDEVLAKLSAEEAAHIVVAYEPVWAIGTGKSATSEQAQAVHAFLRSRLAAKGAGV 205
                                                  666666666667777777777779999*****************************9999999999 PP

                                    TIGR00419 190 aesvrvlyGasvtaaedaelaaqldvdGvLlasavlka 227
                                                  a +v +lyG+sv+  ++ el+ q d+dG L+++a+lk 
  lcl|FitnessBrowser__Burk376:H281DRAFT_04564 206 A-NVTLLYGGSVKPDNAEELFSQQDIDGGLIGGASLKD 242
                                                  8.599*******************************95 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 8.48
//
[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