GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Acidithiobacillus ferrooxidans ATCC 23270

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_215905524.1 AFE_RS12080 triose-phosphate isomerase

Query= BRENDA::P0A858
         (255 letters)



>NCBI__GCF_000021485.1:WP_215905524.1
          Length = 253

 Score =  218 bits (554), Expect = 1e-61
 Identities = 124/250 (49%), Positives = 158/250 (63%), Gaps = 3/250 (1%)

Query: 5   LVMGNWKLNG-SRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSHIMLGA 63
           +V GNWK+NG S   VH   + L   L  +    V I PP   +    +EA+ S +  G 
Sbjct: 1   MVAGNWKMNGLSGDAVHLTQAILHAGLEPMRP-EVVIFPPFTLLHAVSQEAKSSALRWGG 59

Query: 64  QNVDLNLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQGLTP 123
           QN+    SGA+TGE S AML+D+G +Y++IGHSERR    ESD  I +K       GL P
Sbjct: 60  QNLFWEASGAYTGEISGAMLRDMGCRYVLIGHSERRQIFAESDAQIVQKIKAALLSGLIP 119

Query: 124 VLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFE-GAVIAYEPVWAIGTGKSATPAQ 182
           V+C+GETEAE   G T+ V  RQ++AVL      A +   +IAYEPVWAIGTG SA+P Q
Sbjct: 120 VVCVGETEAERAQGLTDAVLRRQLEAVLPLLNLEASQPNLIIAYEPVWAIGTGLSASPEQ 179

Query: 183 AQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKADAF 242
           AQAVH FIR+  A   A +A ++++ YGGSV  +NAA LF Q DIDGALVGGASL+A  F
Sbjct: 180 AQAVHVFIRELAAAYSAQLARRLLLLYGGSVKGNNAAALFDQADIDGALVGGASLQAGEF 239

Query: 243 AVIVKAAEAA 252
             I +AAE+A
Sbjct: 240 IQICRAAESA 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: 185
Number of extensions: 5
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: 255
Length of database: 253
Length adjustment: 24
Effective length of query: 231
Effective length of database: 229
Effective search space:    52899
Effective search space used:    52899
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: 47 (22.7 bits)

Align candidate WP_215905524.1 AFE_RS12080 (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.2550914.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
      2e-60  190.4   0.0    2.3e-60  190.3   0.0    1.0  1  NCBI__GCF_000021485.1:WP_215905524.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000021485.1:WP_215905524.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.3   0.0   2.3e-60   2.3e-60       1     227 [.       1     236 [.       1     237 [. 0.93

  Alignments for each domain:
  == domain 1  score: 190.3 bits;  conditional E-value: 2.3e-60
                             TIGR00419   1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftGe 72 
                                           +v +n+K+n+  g+   + + + +   ++   ev++ ppf  l+ v++e++ s ++ + qn+    sGa+tGe
  NCBI__GCF_000021485.1:WP_215905524.1   1 MVAGNWKMNGLSGDAVHLTQAILHAGLEPMRPEVVIFPPFTLLHAVSQEAKsSALRWGGQNLFWEASGAYTGE 73 
                                           699*******988877777777777779999*******************9889******************* PP

                             TIGR00419  73 isAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleere.......aartinnv 138
                                           is +ml+d+G+++vligHsErR +++e+d  i +k+  +   gl +vvCvget++er          r++++v
  NCBI__GCF_000021485.1:WP_215905524.1  74 ISGAMLRDMGCRYVLIGHSERRQIFAESDAQIVQKIKAALLSGLIPVVCVGETEAERAqgltdavLRRQLEAV 146
                                           *********************************************************9888887777899999 PP

                             TIGR00419 139 attaaaaAlepd.vvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaela 210
                                           +   +  A +p+ ++A+EPv++iGtG ++s+ +a++v+ ++r+  +  s+++a+   +lyG+sv+++++a l+
  NCBI__GCF_000021485.1:WP_215905524.1 147 LPLLNLEASQPNlIIAYEPVWAIGTGLSASPEQAQAVHVFIRELAAAYSAQLARRLLLLYGGSVKGNNAAALF 219
                                           988888887665278***************************888889************************* PP

                             TIGR00419 211 aqldvdGvLlasavlka 227
                                            q d+dG+L+++a+l+a
  NCBI__GCF_000021485.1:WP_215905524.1 220 DQADIDGALVGGASLQA 236
                                           ***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (253 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: 16.92
//
[ok]

This GapMind analysis is from Apr 09 2024. 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