Aligments for a candidate for tpi in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Aligments for a candidate for tpi in Dinoroseobacter shibae DFL-12

Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate 3608685 Dshi_2078 Triose-phosphate isomerase (RefSeq)

Query= SwissProt::Q8L1Z5
         (254 letters)



>lcl|FitnessBrowser__Dino:3608685 Dshi_2078 Triose-phosphate
           isomerase (RefSeq)
          Length = 247

 Score =  231 bits (590), Expect = 8e-66
 Identities = 123/243 (50%), Positives = 160/243 (65%), Gaps = 4/243 (1%)

Query: 6   RPFIAGNWKMNGTGESLGELRAIAAGISSDLGRLFEALICVPATLLSRAFDILGGENILL 65
           R   AGNWKMNG   +L E  AI A  ++D     E L+C PATLL+       G  + +
Sbjct: 3   RKLAAGNWKMNGLRAALAEAEAITAAAAADGP---EVLLCPPATLLAPMAAQAEGTALQI 59

Query: 66  GGQNCHFDDYGPYTGDISAFMLKEAGASHVIIGHSERRTVYQESDAIVRAKVQAAWRAGL 125
           GGQ CH    G +TG +SA ML++AGAS+VI+GHSERR    E DA VRA+  AAW+AGL
Sbjct: 60  GGQYCHPAPSGAHTGHVSAPMLRDAGASYVIVGHSERRQDDGERDADVRAQTLAAWQAGL 119

Query: 126 VALICVGETLEERKSNKVLDVLTRQLEGSLPDGATAENIIIAYEPVWAVGTGNTATSADV 185
            A++CVGET  ER +   L ++  QL GS+PD AT  N+++AYEPVWA+GTG   +   +
Sbjct: 120 TAIVCVGETEAERDAANTLAIIGGQLAGSIPDTATGANLVVAYEPVWAIGTGRVPSVDQI 179

Query: 186 AEVHAFIHHKMHSRFGD-EGAKIRLLYGGSVKPSNAFELLSTAHVNGALIGGASLKAIDF 244
            EVH FI  ++  RFG+  G  +RLLYGGSVKP  A E+ + ++V+GAL+GGASLKA DF
Sbjct: 180 GEVHDFIRARLEQRFGEGVGRSVRLLYGGSVKPGIAAEIFAVSNVDGALVGGASLKAADF 239

Query: 245 LTI 247
             I
Sbjct: 240 TGI 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: 247
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: 254
Length of database: 247
Length adjustment: 24
Effective length of query: 230
Effective length of database: 223
Effective search space:    51290
Effective search space used:    51290
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 3608685 Dshi_2078 (Triose-phosphate isomerase (RefSeq))
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.17082.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-51  161.4   0.4    1.7e-51  161.2   0.4    1.0  1  lcl|FitnessBrowser__Dino:3608685  Dshi_2078 Triose-phosphate isome


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3608685  Dshi_2078 Triose-phosphate isomerase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.2   0.4   1.7e-51   1.7e-51       3     227 ..       7     236 ..       5     237 .. 0.90

  Alignments for each domain:
  == domain 1  score: 161.2 bits;  conditional E-value: 1.7e-51
                         TIGR00419   3 iinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftGeisAeml 78 
                                        +n+K+n+ +   ++  a +    a  +g ev + pp   l  ++ ++e + +q++ q ++   sGa+tG++sA ml
  lcl|FitnessBrowser__Dino:3608685   7 AGNWKMNGLRAALAEAEA-I-TAAAAADGPEVLLCPPATLLAPMAAQAEgTALQIGGQYCHPAPSGAHTGHVSAPML 81 
                                       68*****99888776433.3.3456778999999999999988888888799************************* PP

                         TIGR00419  79 kdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaaaaA.....lepd 150
                                       +d+Ga +v++gHsErR    e d  + ++   + + gl+++vCvget++er+aa+t+  +  + a          + 
  lcl|FitnessBrowser__Dino:3608685  82 RDAGASYVIVGHSERRQDDGERDADVRAQTLAAWQAGLTAIVCVGETEAERDAANTLAIIGGQLAGSIpdtatGANL 158
                                       ****************998888877999999999***********************99988766433344447789 PP

                         TIGR00419 151 vvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvrvlyGasvtaaedaelaaqldvdGvLlasavlk 226
                                       vvA+EPv++iGtG++ s  +  +v++++r  l++   + v +svr+lyG+sv+ + +ae +a  +vdG+L+++a+lk
  lcl|FitnessBrowser__Dino:3608685 159 VVAYEPVWAIGTGRVPSVDQIGEVHDFIRARLEQrFGEGVGRSVRLLYGGSVKPGIAAEIFAVSNVDGALVGGASLK 235
                                       ********************************9989999************************************** PP

                         TIGR00419 227 a 227
                                       a
  lcl|FitnessBrowser__Dino:3608685 236 A 236
                                       8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (247 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 5.83
//
[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, 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

GapMind for catabolism of small carbon sources