GapMind for catabolism of small carbon sources

 

Aligments for a candidate for tpi in Synechococcus elongatus PCC 7942

Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate Synpcc7942_1261 Synpcc7942_1261 triosephosphate isomerase

Query= SwissProt::P00943
         (253 letters)



>lcl|FitnessBrowser__SynE:Synpcc7942_1261 Synpcc7942_1261
           triosephosphate isomerase
          Length = 263

 Score =  240 bits (612), Expect = 2e-68
 Identities = 127/248 (51%), Positives = 173/248 (69%), Gaps = 11/248 (4%)

Query: 1   MRKPIIAGNWKMHKTLAEAVQFVEDVKGHVPPADEVISVV-CAPFLFLDRLVQAADGTDL 59
           +R+ IIAGNWKM+KT AEA++F++     +    E   VV CAPF  L  L +   G+ +
Sbjct: 22  VRRIIIAGNWKMYKTQAEALEFLQAFLPQLSETPESRKVVLCAPFTTLSSLSKTLHGSRV 81

Query: 60  KIGAQTMHFADQGAYTGEVSPVMLKDLGVTYVILGHSERRQMFAETDETVNKKVLAAFTR 119
           ++GAQ +H+A +GA+TGE+S  ML ++GV YV++GHSERRQ F ETDETVN+++LAA + 
Sbjct: 82  RVGAQNIHWAKEGAFTGEISGAMLTEIGVRYVVVGHSERRQYFGETDETVNQRLLAAQSF 141

Query: 120 GLIPIICCGESLEEREAGQTNAVVASQVEKALAGLTPEQVKQAVIAYEPIWAIGTGKSST 179
           GL+PI+C GES ++R+AG+T AV++ Q+E+ L G     +   VIAYEPIWAIGTG +  
Sbjct: 142 GLLPILCVGESKQQRDAGETEAVISRQLERGLVGADQTNL---VIAYEPIWAIGTGDTCA 198

Query: 180 PEDANSVCGHIRSVVSRLFGPEAAEAIRIQYGGSVKPDNIRDFLAQQQIDGPLVGGASLE 239
            E+AN V G IRS +     P       IQYGGSVKP+NI + +AQ +IDG LVGGASLE
Sbjct: 199 AEEANRVIGLIRSQLKDTDVP-------IQYGGSVKPENIDEIMAQPEIDGALVGGASLE 251

Query: 240 PASFLQLV 247
             SF ++V
Sbjct: 252 AESFARIV 259


Lambda     K      H
   0.318    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: 212
Number of extensions: 11
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: 253
Length of database: 263
Length adjustment: 24
Effective length of query: 229
Effective length of database: 239
Effective search space:    54731
Effective search space used:    54731
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: 47 (22.7 bits)

Align candidate Synpcc7942_1261 Synpcc7942_1261 (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.27726.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    5.5e-54  169.4   0.0    6.6e-54  169.1   0.0    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_1261  Synpcc7942_1261 triosephosphate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_1261  Synpcc7942_1261 triosephosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.1   0.0   6.6e-54   6.6e-54       1     228 []      26     253 ..      26     253 .. 0.92

  Alignments for each domain:
  == domain 1  score: 169.1 bits;  conditional E-value: 6.6e-54
                                 TIGR00419   1 lviinfKlnesvgkvelevaklaeevase.agvevavappfvdldvvkdeve.seiqvaAqnvdavksG 67 
                                               ++ +n+K+  +  +  + ++    +++++ +  +v++  pf  l+ +++ ++ s+++v+Aqn++  k G
  lcl|FitnessBrowser__SynE:Synpcc7942_1261  26 IIAGNWKMYKTQAEALEFLQAFLPQLSETpESRKVVLCAPFTTLSSLSKTLHgSRVRVGAQNIHWAKEG 94 
                                               6899***888999999999999999998626789******************9**************** PP

                                 TIGR00419  68 aftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartin 136
                                               aftGeis +ml ++G+++v++gHsErR ++ e+de +++++  ++  gl +++Cvge++++r+a++t  
  lcl|FitnessBrowser__SynE:Synpcc7942_1261  95 AFTGEISGAMLTEIGVRYVVVGHSERRQYFGETDETVNQRLLAAQSFGLLPILCVGESKQQRDAGETEA 163
                                               *****************************************************************9988 PP

                                 TIGR00419 137 nvattaaaaA....lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasv 201
                                               ++ ++ +        ++ v+A+EP+++iGtG + +  ea+ v + +r  lk        +v ++yG+sv
  lcl|FitnessBrowser__SynE:Synpcc7942_1261 164 VISRQLERGLvgadQTNLVIAYEPIWAIGTGDTCAAEEANRVIGLIRSQLK------DTDVPIQYGGSV 226
                                               888775432222358999*****************************4444......5799******** PP

                                 TIGR00419 202 taaedaelaaqldvdGvLlasavlkae 228
                                               + ++  e +aq+++dG+L+++a+l ae
  lcl|FitnessBrowser__SynE:Synpcc7942_1261 227 KPENIDEIMAQPEIDGALVGGASLEAE 253
                                               ************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (263 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: 7.74
//
[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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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