GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Kocuria flava HO-9041

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_058858668.1 AS188_RS09635 triose-phosphate isomerase

Query= BRENDA::P9WG43
         (261 letters)



>NCBI__GCF_001482365.1:WP_058858668.1
          Length = 271

 Score =  324 bits (830), Expect = 1e-93
 Identities = 162/252 (64%), Positives = 196/252 (77%), Gaps = 2/252 (0%)

Query: 3   RKPLIAGNWKMNLNHYEAIALVQKIAFSLPDKYYD--RVDVAVIPPFTDLRSVQTLVDGD 60
           R PLIAGNWKMN++H + IAL+QK+A++L D  +D  RV+VAV PPFTDLRSVQ+LV+ D
Sbjct: 11  RTPLIAGNWKMNMDHVQGIALLQKLAWTLDDAKHDHDRVEVAVFPPFTDLRSVQSLVEAD 70

Query: 61  KLRLTYGAQDLSPHDSGAYTGDVSGAFLAKLGCSYVVVGHSERRTYHNEDDALVAAKAAT 120
            LR+ YGAQDLS  DSGAYTGDVSG FLA+LGC+YV+VGHSERRT H E DAL AAK A 
Sbjct: 71  GLRVRYGAQDLSDKDSGAYTGDVSGQFLARLGCTYVLVGHSERRTLHGETDALCAAKIAA 130

Query: 121 ALKHGLTPIVCIGEHLDVREAGNHVAHNIEQLRGSLAGLLAEQIGSVVIAYEPVWAIGTG 180
           A +HGL P++C+GE L+VR+AG HV H +EQLRG++AGL AE++  +V+AYEPVWAIGTG
Sbjct: 131 AHRHGLVPVLCVGEGLEVRQAGEHVGHTLEQLRGAVAGLDAERVAELVVAYEPVWAIGTG 190

Query: 181 RVASAADAQEVCAAIRKELASLASPRIADTVRVLYGGSVNAKNVGDIVAQDDVDGGLVGG 240
            VA   DAQE+ AAIR ELA L   R A   R+LYGGS  A N   ++   DVDG LVGG
Sbjct: 191 EVAGPEDAQEMAAAIRAELADLHDARTAARTRILYGGSAKAANAAALLKGRDVDGLLVGG 250

Query: 241 ASLDGEHFATLA 252
           ASLD E FA++A
Sbjct: 251 ASLDAEEFASIA 262


Lambda     K      H
   0.318    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: 242
Number of extensions: 8
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: 261
Length of database: 271
Length adjustment: 25
Effective length of query: 236
Effective length of database: 246
Effective search space:    58056
Effective search space used:    58056
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 (21.7 bits)
S2: 47 (22.7 bits)

Align candidate WP_058858668.1 AS188_RS09635 (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.2009082.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    4.3e-55  173.0   0.1    4.9e-55  172.8   0.1    1.0  1  NCBI__GCF_001482365.1:WP_058858668.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001482365.1:WP_058858668.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.8   0.1   4.9e-55   4.9e-55       1     228 []      14     256 ..      14     256 .. 0.91

  Alignments for each domain:
  == domain 1  score: 172.8 bits;  conditional E-value: 4.9e-55
                             TIGR00419   1 lviinfKlnesvgkvelevaklaeev....aseagvevavappfvdldvvkdeve...seiqvaAqnvdavks 66 
                                           l+ +n+K+n    +   +++kla  +     +++ vevav ppf dl+ v+  ve    +++ +Aq++  ++s
  NCBI__GCF_001482365.1:WP_058858668.1  14 LIAGNWKMNMDHVQGIALLQKLAWTLddakHDHDRVEVAVFPPFTDLRSVQSLVEadgLRVRYGAQDLSDKDS 86 
                                           6899***9999999888999988766221145678*****************999523357789********* PP

                             TIGR00419  67 GaftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnva 139
                                           Ga+tG++s + l+ lG+ +vl+gHsErR+l+ e+d l ++k+a ++  gl +v+Cvge le r+a++++   +
  NCBI__GCF_001482365.1:WP_058858668.1  87 GAYTGDVSGQFLARLGCTYVLVGHSERRTLHGETDALCAAKIAAAHRHGLVPVLCVGEGLEVRQAGEHVGHTL 159
                                           ******************************************************************9998777 PP

                             TIGR00419 140 tt.aaaaA......lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvrvlyGasvtaa 204
                                           ++ ++a+A        + vvA+EPv++iGtG ++ + +a+++ + +r  l+   ++  a  +r+lyG+s +aa
  NCBI__GCF_001482365.1:WP_058858668.1 160 EQlRGAVAgldaerVAELVVAYEPVWAIGTGEVAGPEDAQEMAAAIRAELADlHDARTAARTRILYGGSAKAA 232
                                           663677789999999999*********************************9899****************** PP

                             TIGR00419 205 edaelaaqldvdGvLlasavlkae 228
                                           ++a l    dvdG+L+++a+l ae
  NCBI__GCF_001482365.1:WP_058858668.1 233 NAAALLKGRDVDGLLVGGASLDAE 256
                                           *********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (271 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: 13.51
//
[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