Alignments for a candidate for tpiA in Desulfovibrio vulgaris Miyazaki F

GapMind for Amino acid biosynthesis

Alignments for a candidate for tpiA 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.aa/TIGR00419.hmm
# target sequence database:        /tmp/gapView.18802.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 6.76
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis