GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Halococcus hamelinensis 100A6

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_007692221.1 C447_RS06860 triose-phosphate isomerase

Query= BRENDA::Q12UK2
         (221 letters)



>NCBI__GCF_000336675.1:WP_007692221.1
          Length = 215

 Score =  217 bits (553), Expect = 1e-61
 Identities = 116/214 (54%), Positives = 148/214 (69%), Gaps = 5/214 (2%)

Query: 5   IVLNLKTYLEGTGEGAVRIARACKEVGEASGIEIAIAPQFCDIYRVASQVDVPVYSQHLD 64
           +++NLK Y        V IA    +V + SG+ IA+APQ   + RVA +  V  ++QH+ 
Sbjct: 3   VLVNLKAY----AADPVEIATVAHDVADESGVRIAVAPQTAHLERVA-ETGVETWAQHVS 57

Query: 65  GVGAGSFTGHAFAKCIKDAGAVGTLINHSECRLKLADIEASVTAAKGEGLRTIICTNNIA 124
            V  GS TG A A+ + DAG VGTLINHSE RLKLAD++ +V AA+  GL T++C NN  
Sbjct: 58  PVEHGSHTGSALAEAVADAGVVGTLINHSEKRLKLADVDGAVNAAERAGLETVVCANNPD 117

Query: 125 TTAAAAALGPDYVAVEPPELIGSGIPVSKADPEVVTGSVAAVERIDPAVKVLCGAGISKG 184
              AAAALGPD VAVEPPELIG  + VS+ADP++V  +VAA E +D +V VLCGAG+S G
Sbjct: 118 QVGAAAALGPDAVAVEPPELIGGDVSVSQADPDIVEDAVAAAEAVDDSVDVLCGAGVSTG 177

Query: 185 EDLKAAIELGSVGVLLASGIVKAKDPKAALEDLV 218
           EDL AA +LG+ GVLLASG+ KA DP+AAL  LV
Sbjct: 178 EDLDAAGDLGAEGVLLASGVAKADDPRAALTSLV 211


Lambda     K      H
   0.316    0.134    0.378 

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: 175
Number of extensions: 4
Number of successful extensions: 2
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: 221
Length of database: 215
Length adjustment: 22
Effective length of query: 199
Effective length of database: 193
Effective search space:    38407
Effective search space used:    38407
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: 45 (21.9 bits)

Align candidate WP_007692221.1 C447_RS06860 (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.3245479.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.9e-53  167.6  10.4    2.3e-53  167.4  10.4    1.1  1  NCBI__GCF_000336675.1:WP_007692221.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000336675.1:WP_007692221.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.4  10.4   2.3e-53   2.3e-53      16     228 .]      14     201 ..       2     201 .. 0.95

  Alignments for each domain:
  == domain 1  score: 167.4 bits;  conditional E-value: 2.3e-53
                             TIGR00419  16 elevaklaeevaseagvevavappfvdldvvkdeveseiqvaAqnvdavksGaftGeisAemlkdlGakgvli 88 
                                             e+a++a++va+e+gv +avap+  +l++v++     ++  Aq+v  v+ G++tG+ +Ae+++d+G+ g+li
  NCBI__GCF_000336675.1:WP_007692221.1  14 PVEIATVAHDVADESGVRIAVAPQTAHLERVAET---GVETWAQHVSPVEHGSHTGSALAEAVADAGVVGTLI 83 
                                           5689*************************99875...468********************************* PP

                             TIGR00419  89 gHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaaaaAlepdvvAvEPveliG 161
                                           +HsE+R  lk+ad  ++  v+ +   gl++vvC              nn  +  aaaAl pd vAvEP+eliG
  NCBI__GCF_000336675.1:WP_007692221.1  84 NHSEKR--LKLAD--VDGAVNAAERAGLETVVCA-------------NNPDQVGAAAALGPDAVAVEPPELIG 139
                                           ******..*****..*******************.............9999999******************* PP

                             TIGR00419 162 tGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaaqldvdGvLlasavlkae 228
                                             ++vs+A+++ ve+ v      +++ v +sv vl+Ga+v+++ed ++a +l+++GvLlas+v ka+
  NCBI__GCF_000336675.1:WP_007692221.1 140 GDVSVSQADPDIVEDAVA-----AAEAVDDSVDVLCGAGVSTGEDLDAAGDLGAEGVLLASGVAKAD 201
                                           ******************.....9*****************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (215 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: 15.93
//
[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