GapMind for catabolism of small carbon sources

 

Aligments for a candidate for tpi in Shewanella loihica PV-4

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate 5210390 Shew_2831 Triose-phosphate isomerase (RefSeq)

Query= BRENDA::P0A858
         (255 letters)



>lcl|FitnessBrowser__PV4:5210390 Shew_2831 Triose-phosphate
           isomerase (RefSeq)
          Length = 260

 Score =  243 bits (621), Expect = 2e-69
 Identities = 118/259 (45%), Positives = 172/259 (66%), Gaps = 8/259 (3%)

Query: 1   MRHPLVMGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAE----- 55
           +R P+V GNWK+NG+  +  EL +    +L   +   V + PP ++++  +++ +     
Sbjct: 3   LRRPMVAGNWKMNGTAQLAQELFTKFATKLQNDSA-EVVLCPPSIFLESVRQQLDANKEA 61

Query: 56  --GSHIMLGAQNVDLNLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKF 113
             G  + +GAQN+  +  GA+TGE S  MLKD G +Y+IIGHSERR  + E+ +++A+KF
Sbjct: 62  LNGCLVRMGAQNLSQHDFGAYTGEVSGQMLKDSGCRYVIIGHSERRRMYGETSDIVAEKF 121

Query: 114 AVLKEQGLTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIG 173
           A  ++ GLTP+LC+GE+    EA +T EV A ++D V++  G  AF+ A+IAYEP+WA+G
Sbjct: 122 AAAQKHGLTPILCVGESGPAREARRTFEVIAEELDVVIEKNGTMAFDNAIIAYEPLWAVG 181

Query: 174 TGKSATPAQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVG 233
           TGKSATP QAQ VH FIR  +++V   I E + I YGGSV  SNAA+LFAQPD+DG L+G
Sbjct: 182 TGKSATPEQAQEVHAFIRKRLSEVSPYIGENIRILYGGSVTPSNAADLFAQPDVDGGLIG 241

Query: 234 GASLKADAFAVIVKAAEAA 252
           GASL +  F  +   A +A
Sbjct: 242 GASLNSTEFLSLCSIAMSA 260


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: 198
Number of extensions: 8
Number of successful extensions: 2
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: 260
Length adjustment: 24
Effective length of query: 231
Effective length of database: 236
Effective search space:    54516
Effective search space used:    54516
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: 47 (22.7 bits)

Align candidate 5210390 Shew_2831 (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.23229.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
    2.8e-69  219.4   0.0    3.4e-69  219.2   0.0    1.1  1  lcl|FitnessBrowser__PV4:5210390  Shew_2831 Triose-phosphate isome


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5210390  Shew_2831 Triose-phosphate isomerase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.2   0.0   3.4e-69   3.4e-69       1     226 [.       7     246 ..       7     248 .. 0.93

  Alignments for each domain:
  == domain 1  score: 219.2 bits;  conditional E-value: 3.4e-69
                        TIGR00419   1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdevese........iqvaAqnvdavksGaft 70 
                                      +v +n+K+n++ +  +++ +k a ++ + +  ev++ pp ++l+ v+++++++        ++++Aqn+  +++Ga+t
  lcl|FitnessBrowser__PV4:5210390   7 MVAGNWKMNGTAQLAQELFTKFATKLQN-DSAEVVLCPPSIFLESVRQQLDANkealngclVRMGAQNLSQHDFGAYT 83 
                                      699**********************976.66899***********9988763323444444899************** PP

                        TIGR00419  71 GeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleere.......aartinnvatt 141
                                      Ge+s +mlkd G+++v+igHsErR +  e+++++++k+a +++ gl++++Cvge+   re        a+++++v ++
  lcl|FitnessBrowser__PV4:5210390  84 GEVSGQMLKDSGCRYVIIGHSERRRMYGETSDIVAEKFAAAQKHGLTPILCVGESGPAREarrtfevIAEELDVVIEK 161
                                      ************************99999999***********************9999988888888999999999* PP

                        TIGR00419 142 aaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaaqldvdGvL 219
                                      ++++A++++++A+EP +++GtGk++++ +a++v++++r  l++vs+ + e++r+lyG+svt +++a+l+aq+dvdG L
  lcl|FitnessBrowser__PV4:5210390 162 NGTMAFDNAIIAYEPLWAVGTGKSATPEQAQEVHAFIRKRLSEVSPYIGENIRILYGGSVTPSNAADLFAQPDVDGGL 239
                                      ****************************************************************************** PP

                        TIGR00419 220 lasavlk 226
                                      +++a+l 
  lcl|FitnessBrowser__PV4:5210390 240 IGGASLN 246
                                      ****996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (260 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: 9.90
//
[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 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