GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Thiohalospira halophila HL 3

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_093429068.1 BM272_RS12175 triose-phosphate isomerase

Query= BRENDA::P0A858
         (255 letters)



>NCBI__GCF_900112605.1:WP_093429068.1
          Length = 250

 Score =  255 bits (651), Expect = 7e-73
 Identities = 129/249 (51%), Positives = 164/249 (65%)

Query: 1   MRHPLVMGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSHIM 60
           MR PLV GNWK+NG R     L++ ++  +  V    VA+  P +Y+   +R+ E S I 
Sbjct: 1   MRQPLVAGNWKMNGDRATNEALLNGIKAGIGDVEQSEVAVCAPFVYLADVQRQLEASPIR 60

Query: 61  LGAQNVDLNLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQG 120
            G+Q+V     GAFTGE S  MLKD G  Y I+GHSERR+ H E ++ +A+KFA  +E G
Sbjct: 61  WGSQDVSAEPKGAFTGEVSVTMLKDFGCHYAIVGHSERRSLHGEDNDTVARKFAAAREGG 120

Query: 121 LTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSATP 180
           + P+LC+GET AE EA  TE+V   Q+DAV+   G AA    VIAYEPVWAIGTG +ATP
Sbjct: 121 IRPILCVGETLAEREADTTEQVVGAQLDAVMDAVGPAALADGVIAYEPVWAIGTGHTATP 180

Query: 181 AQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKAD 240
            QAQA+H FIR  +A  DA  A+ + I YGGS+  +NAAEL AQ DIDG L+GGASL AD
Sbjct: 181 EQAQAMHAFIRQRVADRDAATADALRILYGGSMKGANAAELMAQSDIDGGLIGGASLDAD 240

Query: 241 AFAVIVKAA 249
            F  I +AA
Sbjct: 241 EFLTICRAA 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: 188
Number of extensions: 6
Number of successful extensions: 1
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: 250
Length adjustment: 24
Effective length of query: 231
Effective length of database: 226
Effective search space:    52206
Effective search space used:    52206
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 WP_093429068.1 BM272_RS12175 (triose-phosphate 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.3742760.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.1e-71  227.3   0.4    1.2e-71  227.1   0.4    1.0  1  NCBI__GCF_900112605.1:WP_093429068.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900112605.1:WP_093429068.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.1   0.4   1.2e-71   1.2e-71       1     228 []       5     240 ..       5     240 .. 0.99

  Alignments for each domain:
  == domain 1  score: 227.1 bits;  conditional E-value: 1.2e-71
                             TIGR00419   1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftGe 72 
                                           lv +n+K+n+ + + e +++ +++ + ++++ evav  pfv+l  v++++e s i+ + q+v a  +GaftGe
  NCBI__GCF_900112605.1:WP_093429068.1   5 LVAGNWKMNGDRATNEALLNGIKAGIGDVEQSEVAVCAPFVYLADVQRQLEaSPIRWGSQDVSAEPKGAFTGE 77 
                                           799************************************************999******************* PP

                             TIGR00419  73 isAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleere.......aartinnv 138
                                           +s  mlkd+G+++ ++gHsErRsl+ e ++ ++ k+a ++e g+++++Cvgetl+ere       ++ ++++v
  NCBI__GCF_900112605.1:WP_093429068.1  78 VSVTMLKDFGCHYAIVGHSERRSLHGEDNDTVARKFAAAREGGIRPILCVGETLAEREadtteqvVGAQLDAV 150
                                           **********************************************************99999999******* PP

                             TIGR00419 139 attaaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaa 211
                                           ++  + aAl + v+A+EPv++iGtG ++++ +a+++++++r+ ++  ++  a+  r+lyG+s+++a++ael+a
  NCBI__GCF_900112605.1:WP_093429068.1 151 MDAVGPAALADGVIAYEPVWAIGTGHTATPEQAQAMHAFIRQRVADRDAATADALRILYGGSMKGANAAELMA 223
                                           ************************************************************************* PP

                             TIGR00419 212 qldvdGvLlasavlkae 228
                                           q d+dG L+++a+l a+
  NCBI__GCF_900112605.1:WP_093429068.1 224 QSDIDGGLIGGASLDAD 240
                                           **************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (250 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: 20.10
//
[ok]

This GapMind analysis is from Sep 24 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