GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Phaeobacter inhibens BS107

Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate GFF2032 PGA1_c20650 triosephosphate isomerase TpiA

Query= SwissProt::Q8L1Z5
         (254 letters)



>FitnessBrowser__Phaeo:GFF2032
          Length = 250

 Score =  246 bits (629), Expect = 2e-70
 Identities = 131/243 (53%), Positives = 163/243 (67%), Gaps = 4/243 (1%)

Query: 6   RPFIAGNWKMNGTGESLGELRAIAAGISSDLGRLFEALICVPATLLSRAFDILGGENILL 65
           R   AGNWKMNGT  +L EL  +A    S      E LIC PATLL RA ++     + +
Sbjct: 3   RKLAAGNWKMNGTASALTELGNLAYSCKSAKA---EVLICPPATLLYRAANVCVDSKVSI 59

Query: 66  GGQNCHFDDYGPYTGDISAFMLKEAGASHVIIGHSERRTVYQESDAIVRAKVQAAWRAGL 125
           G Q+CH   YG +TGD+SA ML +AGA+ VI+GHSERR  + E+D  VRAK + A  AGL
Sbjct: 60  GAQDCHDATYGAHTGDLSAEMLHDAGATAVILGHSERRADHDETDETVRAKAKTAIAAGL 119

Query: 126 VALICVGETLEERKSNKVLDVLTRQLEGSLPDGATAENIIIAYEPVWAVGTGNTATSADV 185
            A+ICVGETL +R++ K LDV+  QL GSLPD A+   +++AYEPVWA+GTG   T   +
Sbjct: 120 TAIICVGETLNDREAGKTLDVVRAQLAGSLPDDASGTTVVVAYEPVWAIGTGKVPTVEQI 179

Query: 186 AEVHAFIHHKMHSRFGDEGAK-IRLLYGGSVKPSNAFELLSTAHVNGALIGGASLKAIDF 244
           AEVH  +   +  RFG E A  IRLLYGGSVK SNA E+ + AHV+GAL+GGASLKA DF
Sbjct: 180 AEVHNDMRASLVKRFGGETANAIRLLYGGSVKASNAKEIFAVAHVDGALVGGASLKAADF 239

Query: 245 LTI 247
             I
Sbjct: 240 API 242


Lambda     K      H
   0.320    0.137    0.403 

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: 232
Number of extensions: 7
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: 254
Length of database: 250
Length adjustment: 24
Effective length of query: 230
Effective length of database: 226
Effective search space:    51980
Effective search space used:    51980
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 46 (22.3 bits)

Align candidate GFF2032 PGA1_c20650 (triosephosphate isomerase TpiA)
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.25074.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
    1.5e-58  184.3   4.0    1.7e-58  184.1   4.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF2032  PGA1_c20650 triosephosphate isom


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF2032  PGA1_c20650 triosephosphate isomerase TpiA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.1   4.0   1.7e-58   1.7e-58       3     227 ..       7     236 ..       5     237 .. 0.91

  Alignments for each domain:
  == domain 1  score: 184.1 bits;  conditional E-value: 1.7e-58
                          TIGR00419   3 iinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkd.eveseiqvaAqnvdavksGaftGeisAem 77 
                                         +n+K+n++ +   +e+ +la    s a+ ev + pp   l ++++  v+s+++++Aq+++  + Ga+tG++sAem
  lcl|FitnessBrowser__Phaeo:GFF2032   7 AGNWKMNGTASAL-TELGNLAYSCKS-AKAEVLICPPATLLYRAANvCVDSKVSIGAQDCHDATYGAHTGDLSAEM 80 
                                        69******99876.689999998755.66788888888877776661577************************** PP

                          TIGR00419  78 lkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaaaaA.....le 148
                                        l+d+Ga  v++gHsErR+ + e+de + +k  ++ + gl++++Cvgetl++rea++t+++v  + a         +
  lcl|FitnessBrowser__Phaeo:GFF2032  81 LHDAGATAVILGHSERRADHDETDETVRAKAKTAIAAGLTAIICVGETLNDREAGKTLDVVRAQLAGSLpddasGT 156
                                        *************************************************************999876444555589 PP

                          TIGR00419 149 pdvvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvrvlyGasvtaaedaelaaqldvdGvLlasa 223
                                         +vvA+EPv++iGtGk+ +  +  +v++ +r  l k    e a+ +r+lyG+sv+a++++e +a   vdG+L+++a
  lcl|FitnessBrowser__Phaeo:GFF2032 157 TVVVAYEPVWAIGTGKVPTVEQIAEVHNDMRASLVKrFGGETANAIRLLYGGSVKASNAKEIFAVAHVDGALVGGA 232
                                        99*****************************98877699************************************* PP

                          TIGR00419 224 vlka 227
                                        +lka
  lcl|FitnessBrowser__Phaeo:GFF2032 233 SLKA 236
                                        ***8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (250 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: 7.78
//
[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