GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Desulfovibrio vulgaris Miyazaki F

Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate 8499579 DvMF_0348 Triose-phosphate isomerase (RefSeq)

Query= SwissProt::Q5SJR1
         (250 letters)



>FitnessBrowser__Miya:8499579
          Length = 251

 Score =  197 bits (502), Expect = 1e-55
 Identities = 113/247 (45%), Positives = 144/247 (58%), Gaps = 6/247 (2%)

Query: 5   LVAGNWKMHKTPSEARVWFAELKRLLP---PLQSEAAVLPAFPIL-PVAKEVLAETQVGY 60
           L+A NWKM+KT  EAR   A L  L     P   E  + P F  L PVA  +   T    
Sbjct: 4   LMAANWKMYKTAGEARTTAASLAALTADTLPDDREVVIFPQFTALSPVADALRHATGYSV 63

Query: 61  GAQDVSAHKEGAYTGEVSARMLSDLGCRYAIVGHSERRRYHGETDALVAEKAKRLLEEGI 120
           G QDV    EGAYTGE+S  ML D GC + + GHSERR   GE+D LV  K    +  G+
Sbjct: 64  GGQDVYPAAEGAYTGEISPGMLMDCGCAWVLTGHSERRHVIGESDELVGAKTAFSINAGL 123

Query: 121 TPILCVGEPLEVREKGEAVPYTLRQLRGSLEGVEPPG-PEALVIAYEPVWAIGTGKNATP 179
             +LC+GE +E RE G       RQL   L GV+    P A+ +AYEPVWAIGTGK A P
Sbjct: 124 KVVLCIGETIEEREAGRLGEVLERQLETGLAGVKGDAVPAAIAVAYEPVWAIGTGKVAGP 183

Query: 180 EDAEAMHQAIRKALSERYGEAFASRVRILYGGSVNPKNFADLLSMPNVDGGLVGGASLEL 239
            +    H  +R+ L  R+GE   + VRILYGGSV P+N  +++++ NVDG LVGGASL+ 
Sbjct: 184 PEIVEAHALVRQLLVARFGEGGVA-VRILYGGSVKPENAREIIALDNVDGVLVGGASLQA 242

Query: 240 ESFLALL 246
           +SF  ++
Sbjct: 243 DSFSRII 249


Lambda     K      H
   0.317    0.135    0.393 

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: 205
Number of extensions: 11
Number of successful extensions: 4
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: 250
Length of database: 251
Length adjustment: 24
Effective length of query: 226
Effective length of database: 227
Effective search space:    51302
Effective search space used:    51302
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 8499579 DvMF_0348 (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.7549.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    1.2e-54  171.6   0.2    1.3e-54  171.4   0.2    1.0  1  lcl|FitnessBrowser__Miya:8499579  DvMF_0348 Triose-phosphate isome


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8499579  DvMF_0348 Triose-phosphate isomerase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.4   0.2   1.3e-54   1.3e-54       2     228 .]       5     243 ..       4     243 .. 0.90

  Alignments for each domain:
  == domain 1  score: 171.4 bits;  conditional E-value: 1.3e-54
                         TIGR00419   2 viinfKlnesvgkvelevaklaeevas..eagvevavappfvdldvvkdeve..seiqvaAqnvdavksGaftGeis 74 
                                       +  n+K+  + g+  +  a+la+  a+  +++ ev++ p+f  l+ v+d+++  +  +v+ q+v     Ga+tGeis
  lcl|FitnessBrowser__Miya:8499579   5 MAANWKMYKTAGEARTTAASLAALTADtlPDDREVVIFPQFTALSPVADALRhaTGYSVGGQDVYPAAEGAYTGEIS 81 
                                       678***999**************998844589*******************9666789******************* PP

                         TIGR00419  75 AemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaaa.aA.... 146
                                         ml d+G+++vl gHsErR ++ e+del+++k a   + glk+v+C+get eerea+r  +++ ++ ++  A    
  lcl|FitnessBrowser__Miya:8499579  82 PGMLMDCGCAWVLTGHSERRHVIGESDELVGAKTAFSINAGLKVVLCIGETIEEREAGRLGEVLERQLETgLAgvkg 158
                                       ********************************************************998877776653321234444 PP

                         TIGR00419 147 ...lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaaqldvdGvLl 220
                                               vA+EPv++iGtGk++ + e  + ++ vr+ l     e    vr+lyG+sv+ +++ e +a  +vdGvL+
  lcl|FitnessBrowser__Miya:8499579 159 davPAAIAVAYEPVWAIGTGKVAGPPEIVEAHALVRQLLVARFGEGGVAVRILYGGSVKPENAREIIALDNVDGVLV 235
                                       5434455699**************************9999988999999**************************** PP

                         TIGR00419 221 asavlkae 228
                                       ++a+l+a+
  lcl|FitnessBrowser__Miya:8499579 236 GGASLQAD 243
                                       *****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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 9.38
//
[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