GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Galbibacter marinus ck-I2-15

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_008991764.1 I215_RS09580 triose-phosphate isomerase

Query= BRENDA::Q10657
         (247 letters)



>NCBI__GCF_000300875.1:WP_008991764.1
          Length = 249

 Score =  219 bits (559), Expect = 3e-62
 Identities = 119/247 (48%), Positives = 162/247 (65%), Gaps = 4/247 (1%)

Query: 3   RKFFVGGNWKMNGDYASVDGIVTFLNASADNSSVDVVVAPPAPYLAYAKSKLK-AGVLVA 61
           R+  V GNWKMN D A    +++ L     N+ V V +AP    L  A   LK   V V 
Sbjct: 2   REKIVAGNWKMNNDLAETQALISDLRKVLTNTDVKVKIAPTYVNLYPAYETLKDTAVEVV 61

Query: 62  AQNCYKVPKGAFTGEISPAMIKDLGLEWVILGHSERRHVFGESDALIAEKTVHALEAGIK 121
           AQN ++   GA+TGE+S  M+K +G++ VILGHSERR  FGE DAL+A+K   A++AG+ 
Sbjct: 62  AQNMHQAKSGAYTGEVSADMLKSIGIQTVILGHSERRAYFGEDDALLAQKVSAAVDAGLN 121

Query: 122 VVFCIGEKLEEREAGHTKDVNFRQLQAIVDK--GVSWENIVIAYEPVWAIGTGKTASGEQ 179
           V+FC GE+LE+R++    D+   QL++ +      +W+ IV+AYEPVWAIGTG+TAS EQ
Sbjct: 122 VIFCFGEELEDRKSDKHFDLVASQLKSGLFHLPASAWKQIVLAYEPVWAIGTGETASPEQ 181

Query: 180 AQEVHEWIRAFLKEKVSPAVADATRIIYGGSVTADNAAELGKKPDIDGFLVGGASLK-PD 238
           AQE+HE+IR  +  +   ++AD   I+YGGSV   NA E+  KPD+DG L+GGASL   D
Sbjct: 182 AQEMHEFIRKTVAGQYDASLADGVSILYGGSVKPANATEIFSKPDVDGGLIGGASLNAED 241

Query: 239 FVKIINA 245
           FV I+NA
Sbjct: 242 FVAIVNA 248


Lambda     K      H
   0.317    0.134    0.396 

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: 180
Number of extensions: 8
Number of successful extensions: 3
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: 247
Length of database: 249
Length adjustment: 24
Effective length of query: 223
Effective length of database: 225
Effective search space:    50175
Effective search space used:    50175
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_008991764.1 I215_RS09580 (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.524900.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.7e-66  210.3   0.1      2e-66  210.1   0.1    1.0  1  NCBI__GCF_000300875.1:WP_008991764.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000300875.1:WP_008991764.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.1   0.1     2e-66     2e-66       1     228 []       5     240 ..       5     240 .. 0.93

  Alignments for each domain:
  == domain 1  score: 210.1 bits;  conditional E-value: 2e-66
                             TIGR00419   1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftGe 72 
                                           +v +n+K+n+ + + + ++++l++ +  +++v+v +ap +v l  + + ++ + ++v+Aqn++  ksGa+tGe
  NCBI__GCF_000300875.1:WP_008991764.1   5 IVAGNWKMNNDLAETQALISDLRKVL-TNTDVKVKIAPTYVNLYPAYETLKdTAVEVVAQNMHQAKSGAYTGE 76 
                                           699*******************9766.56899******************9899******************* PP

                             TIGR00419  73 isAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaa.. 143
                                           +sA+mlk +G++ v++gHsErR+++ e d l+++kv+ + + gl+++ C ge le+r++ ++++ va + +  
  NCBI__GCF_000300875.1:WP_008991764.1  77 VSADMLKSIGIQTVILGHSERRAYFGEDDALLAQKVSAAVDAGLNVIFCFGEELEDRKSDKHFDLVASQLKsg 149
                                           **********************************************************777777777665522 PP

                             TIGR00419 144 .....aaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvrvlyGasvtaaedaela 210
                                                a A+++ v+A+EPv++iGtG ++s+ +a+++++++r  ++   ++ +a+ v++lyG+sv+ a+++e +
  NCBI__GCF_000300875.1:WP_008991764.1 150 lfhlpASAWKQIVLAYEPVWAIGTGETASPEQAQEMHEFIRKTVAGqYDASLADGVSILYGGSVKPANATEIF 222
                                           33333788*********************************9999879************************* PP

                             TIGR00419 211 aqldvdGvLlasavlkae 228
                                            ++dvdG L+++a+l ae
  NCBI__GCF_000300875.1:WP_008991764.1 223 SKPDVDGGLIGGASLNAE 240
                                           ***************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (249 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: 14.19
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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