GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Pseudomonas fluorescens FW300-N2C3

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate AO356_07440 AO356_07440 triosephosphate isomerase

Query= BRENDA::P0A858
         (255 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_07440
          Length = 251

 Score =  239 bits (610), Expect = 4e-68
 Identities = 126/250 (50%), Positives = 168/250 (67%), Gaps = 2/250 (0%)

Query: 1   MRHPLVMGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSHIM 60
           MR P+V GNWK++G+R  V EL++ LR  LA  +G  VA+ PP +YI+      +G  I 
Sbjct: 1   MRRPMVAGNWKMHGTRASVAELINGLR-HLALPSGVDVAVFPPCLYINQVIDGLKGKSIS 59

Query: 61  LGAQNVDL-NLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQ 119
           +GAQN  + ++ GA TGE + + L D G   +++GHSERR    E D+ + +KFA  +  
Sbjct: 60  VGAQNSAVESMQGALTGEIAPSQLVDAGCSLVLVGHSERRQIMGEQDKTLIRKFAAAQAC 119

Query: 120 GLTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSAT 179
           GL PVLC+GET A+ EAGKT EV  RQ+ ++++  G  AF  AVIAYEPVWAIGTG +A+
Sbjct: 120 GLIPVLCVGETLAQREAGKTLEVVGRQLGSIIEDLGVGAFAKAVIAYEPVWAIGTGLTAS 179

Query: 180 PAQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKA 239
           P QAQ VH  IR  +A+ ++ +A  V + YGGSV A+NAAELF  PDIDG L+GGASL A
Sbjct: 180 PQQAQDVHAAIRAQLAEENSEVARGVRLLYGGSVKAANAAELFGMPDIDGGLIGGASLNA 239

Query: 240 DAFAVIVKAA 249
           D F  I +AA
Sbjct: 240 DEFGAICRAA 249


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: 175
Number of extensions: 6
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: 251
Length adjustment: 24
Effective length of query: 231
Effective length of database: 227
Effective search space:    52437
Effective search space used:    52437
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 AO356_07440 AO356_07440 (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.31980.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
    3.1e-67  212.7   0.9    3.6e-67  212.5   0.9    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07440  AO356_07440 triosephosphate isom


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07440  AO356_07440 triosephosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.5   0.9   3.6e-67   3.6e-67       1     228 []       5     240 ..       5     240 .. 0.94

  Alignments for each domain:
  == domain 1  score: 212.5 bits;  conditional E-value: 3.6e-67
                                       TIGR00419   1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvd 62 
                                                     +v +n+K+++++ +v+++++ l+ ++a ++gv vav pp ++++ v d ++   i+v+Aqn  
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07440   5 MVAGNWKMHGTRASVAELINGLR-HLALPSGVDVAVFPPCLYINQVIDGLKgKSISVGAQNSA 66 
                                                     699******************98.69*************************999*******98 PP

                                       TIGR00419  63 avk.sGaftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvge 124
                                                     + + +Ga tGei    l+d+G+  vl+gHsErR ++ e d+ +  k+a +++ gl +v+Cvge
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07440  67 VESmQGALTGEIAPSQLVDAGCSLVLVGHSERRQIMGEQDKTLIRKFAAAQACGLIPVLCVGE 129
                                                     86538********************************************************** PP

                                       TIGR00419 125 tleereaartinnvattaaaaA.......lepdvvAvEPveliGtGkpvskAeaevveksvrd 180
                                                     tl++rea++t+++v ++ + +        + ++v+A+EPv++iGtG ++s+ +a+ v++ +r 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07440 130 TLAQREAGKTLEVVGRQLGSIIedlgvgaFAKAVIAYEPVWAIGTGLTASPQQAQDVHAAIRA 192
                                                     ******77777777766665555555555********************************** PP

                                       TIGR00419 181 hlkkvskevaesvrvlyGasvtaaedaelaaqldvdGvLlasavlkae 228
                                                      l++ + eva+ vr+lyG+sv+aa++ael+  +d+dG L+++a+l a+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07440 193 QLAEENSEVARGVRLLYGGSVKAANAAELFGMPDIDGGLIGGASLNAD 240
                                                     *********************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (251 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 6.51
//
[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