Alignments for a candidate for tpi in Phaeobacter inhibens BS107

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.1610.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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 8.24
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources