GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Pseudomonas fluorescens FW300-N2E2

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate Pf6N2E2_3356 Triosephosphate isomerase (EC 5.3.1.1)

Query= BRENDA::P0A858
         (255 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3356
          Length = 247

 Score =  229 bits (584), Expect = 4e-65
 Identities = 122/246 (49%), Positives = 161/246 (65%), Gaps = 2/246 (0%)

Query: 5   LVMGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSHIMLGAQ 64
           +V GNWK++G+R  V EL+  LR  LA  +G  VA+ PP +YI+      +G  I +GAQ
Sbjct: 1   MVAGNWKMHGTRASVAELIKGLR-HLALPSGVDVAVFPPCLYINQVVDGLKGKSISVGAQ 59

Query: 65  NVDL-NLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQGLTP 123
           N  + ++ GA TGE + + L D G   ++IGHSERR    E D+ + +KF+  +  GL P
Sbjct: 60  NSAVESMQGALTGEIAPSQLVDAGCSLVLIGHSERRQIMGEQDKALIRKFSAAQACGLIP 119

Query: 124 VLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSATPAQA 183
           VLC+GET  + EAGKT EV  RQ+  +++  G  AF  AVIAYEPVWAIGTG +A+P QA
Sbjct: 120 VLCVGETREQREAGKTLEVVGRQLGGIIEELGVDAFAKAVIAYEPVWAIGTGLTASPQQA 179

Query: 184 QAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKADAFA 243
           Q VH  IR  +A  ++ +A  V + YGGSV A+NAAELF  PDIDG L+GGASL AD F 
Sbjct: 180 QDVHAAIRAQLAAENSEVARGVRLLYGGSVKAANAAELFGMPDIDGGLIGGASLNADEFG 239

Query: 244 VIVKAA 249
            I +AA
Sbjct: 240 AICRAA 245


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: 176
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: 255
Length of database: 247
Length adjustment: 24
Effective length of query: 231
Effective length of database: 223
Effective search space:    51513
Effective search space used:    51513
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: 46 (22.3 bits)

Align candidate Pf6N2E2_3356 (Triosephosphate isomerase (EC 5.3.1.1))
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.18056.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
    7.5e-67  211.5   0.8    8.6e-67  211.3   0.8    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3356  Triosephosphate isomerase (EC 5.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3356  Triosephosphate isomerase (EC 5.3.1.1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.3   0.8   8.6e-67   8.6e-67       1     228 []       1     236 [.       1     236 [. 0.94

  Alignments for each domain:
  == domain 1  score: 211.3 bits;  conditional E-value: 8.6e-67
                                      TIGR00419   1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvda 63 
                                                    +v +n+K+++++ +v++++  l+ ++a ++gv vav pp ++++ v+d ++   i+v+Aqn  +
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3356   1 MVAGNWKMHGTRASVAELIKGLR-HLALPSGVDVAVFPPCLYINQVVDGLKgKSISVGAQNSAV 63 
                                                    699******************98.69*************************999*******988 PP

                                      TIGR00419  64 vk.sGaftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetl 126
                                                     + +Ga tGei    l+d+G+  vligHsErR ++ e d+ +  k++ +++ gl +v+Cvget 
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3356  64 ESmQGALTGEIAPSQLVDAGCSLVLIGHSERRQIMGEQDKALIRKFSAAQACGLIPVLCVGETR 127
                                                    6538************************************************************ PP

                                      TIGR00419 127 eereaartinnvattaaaaA.......lepdvvAvEPveliGtGkpvskAeaevveksvrdhlk 183
                                                    e+rea++t+++v ++ + +        + ++v+A+EPv++iGtG ++s+ +a+ v++ +r  l+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3356 128 EQREAGKTLEVVGRQLGGIIeelgvdaFAKAVIAYEPVWAIGTGLTASPQQAQDVHAAIRAQLA 191
                                                    ****88888877766655544444444************************************* PP

                                      TIGR00419 184 kvskevaesvrvlyGasvtaaedaelaaqldvdGvLlasavlkae 228
                                                      + eva+ vr+lyG+sv+aa++ael+  +d+dG L+++a+l a+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3356 192 AENSEVARGVRLLYGGSVKAANAAELFGMPDIDGGLIGGASLNAD 236
                                                    ******************************************997 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 9.27
//
[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