GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Gallaecimonas xiamenensis 3-C-1

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_008485428.1 B3C1_RS13285 triose-phosphate isomerase

Query= BRENDA::P0A858
         (255 letters)



>NCBI__GCF_000299915.1:WP_008485428.1
          Length = 250

 Score =  263 bits (671), Expect = 3e-75
 Identities = 130/249 (52%), Positives = 173/249 (69%)

Query: 1   MRHPLVMGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSHIM 60
           MR PLVMGNWKL+GS+  V +L+  L  +   V G  +A+ PP +++  A+R    S I 
Sbjct: 1   MRRPLVMGNWKLHGSKASVEKLLVELMVKANEVEGVEIAVCPPLVFVGQAERLLRYSQIA 60

Query: 61  LGAQNVDLNLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQG 120
           LGAQN+D+N  GAFTGE +A ML + G +Y+++GHSERR  H E+D+L+A+KF  +K  G
Sbjct: 61  LGAQNIDVNRQGAFTGEVAADMLGEFGVRYVLVGHSERRAMHHENDDLVARKFEAVKAAG 120

Query: 121 LTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSATP 180
           L PVLC+GET+AE   G+T++V   Q+ AV+K  G  AF+ AV+AYEPVWAIG+G++A+P
Sbjct: 121 LIPVLCVGETQAERNNGETKDVIGHQLQAVVKRCGRKAFDNAVVAYEPVWAIGSGQAASP 180

Query: 181 AQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKAD 240
             AQ VH+FIR  +A  D   A+ + I YGGSV ASNA  LF   D+DGALVGGASL A 
Sbjct: 181 VDAQKVHEFIRAQVAAQDPASAQALRILYGGSVKASNAQALFMMDDVDGALVGGASLDAQ 240

Query: 241 AFAVIVKAA 249
            F+ I  AA
Sbjct: 241 EFSGIFNAA 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: 183
Number of extensions: 3
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_008485428.1 B3C1_RS13285 (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.2767896.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.9e-74  235.7   2.4    3.3e-74  235.5   2.4    1.0  1  NCBI__GCF_000299915.1:WP_008485428.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000299915.1:WP_008485428.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.5   2.4   3.3e-74   3.3e-74       1     227 [.       5     239 ..       5     240 .. 0.98

  Alignments for each domain:
  == domain 1  score: 235.5 bits;  conditional E-value: 3.3e-74
                             TIGR00419   1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftGe 72 
                                           lv++n+Kl++s  +ve+++ +l  +  +++gve+av pp v++  +++ ++ s+i ++Aqn+d++++GaftGe
  NCBI__GCF_000299915.1:WP_008485428.1   5 LVMGNWKLHGSKASVEKLLVELMVKANEVEGVEIAVCPPLVFVGQAERLLRySQIALGAQNIDVNRQGAFTGE 77 
                                           79*********************************************************************** PP

                             TIGR00419  73 isAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleere.......aartinnv 138
                                           + A+ml ++G+++vl+gHsErR++++e d+l++ k+  +k+ gl +v+Cvget++er+        ++++++v
  NCBI__GCF_000299915.1:WP_008485428.1  78 VAADMLGEFGVRYVLVGHSERRAMHHENDDLVARKFEAVKAAGLIPVLCVGETQAERNngetkdvIGHQLQAV 150
                                           ********************************************************99888888888999999 PP

                             TIGR00419 139 attaaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaa 211
                                            +  +  A++++vvA+EPv++iG+G+++s+ +a+ v++++r  ++  ++  a+  r+lyG+sv+a++++ l++
  NCBI__GCF_000299915.1:WP_008485428.1 151 VKRCGRKAFDNAVVAYEPVWAIGSGQAASPVDAQKVHEFIRAQVAAQDPASAQALRILYGGSVKASNAQALFM 223
                                           99999999***************************************************************** PP

                             TIGR00419 212 qldvdGvLlasavlka 227
                                             dvdG+L+++a+l a
  NCBI__GCF_000299915.1:WP_008485428.1 224 MDDVDGALVGGASLDA 239
                                           *************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: 14.30
//
[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