Alignments for a candidate for tpi in Magnetospirillum magneticum AMB-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for tpi in Magnetospirillum magneticum AMB-1

Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate WP_011384224.1 AMB_RS09205 triose-phosphate isomerase

Query= SwissProt::Q8L1Z5
         (254 letters)



>NCBI__GCF_000009985.1:WP_011384224.1
          Length = 251

 Score =  227 bits (578), Expect = 2e-64
 Identities = 119/248 (47%), Positives = 159/248 (64%), Gaps = 7/248 (2%)

Query: 6   RPFIAGNWKMNGTGESLGELRAIAAGISSDLGRLF---EALICVPATLLSRAFDILGGEN 62
           R  IAGNWKMNG      +  A+A G++  L       + L+C P TL++   D L G  
Sbjct: 5   RKLIAGNWKMNGLK---ADGLALAKGLADKLASASPNCDMLVCPPFTLIAPVADALAGSK 61

Query: 63  ILLGGQNCHFDDYGPYTGDISAFMLKEAGASHVIIGHSERRTVYQESDAIVRAKVQAAWR 122
           + +GGQ+CH    G +TGD S  ML + G  + I+GHSERRT + E+D +V+AK  AA  
Sbjct: 62  LAVGGQDCHAKTSGAHTGDTSPAMLADLGCKYAIVGHSERRTDHAETDNVVKAKAAAALS 121

Query: 123 AGLVALICVGETLEERKSNKVLDVLTRQLEGSLPDGATAENIIIAYEPVWAVGTGNTATS 182
           AGLVA++C+GETL +R + + ++V   QL GSLP+GA A N +IAYEPVWA+GTG  AT 
Sbjct: 122 AGLVAIVCIGETLAQRDAGQTIEVNRSQLNGSLPEGANAANTVIAYEPVWAIGTGRVATP 181

Query: 183 ADVAEVHAFIHHKMHSRFG-DEGAKIRLLYGGSVKPSNAFELLSTAHVNGALIGGASLKA 241
           A   EVHA I  ++    G +E  K+R+LYGGS+KP NA ELL+   V+G LIGGA+LK 
Sbjct: 182 AQAQEVHAAIRAELARLVGAEEAGKMRILYGGSMKPDNAKELLALPDVDGGLIGGAALKV 241

Query: 242 IDFLTICD 249
            DF  I +
Sbjct: 242 ADFWAIAE 249


Lambda     K      H
   0.320    0.137    0.403 

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: 224
Number of extensions: 11
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: 254
Length of database: 251
Length adjustment: 24
Effective length of query: 230
Effective length of database: 227
Effective search space:    52210
Effective search space used:    52210
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 46 (22.3 bits)

Align candidate WP_011384224.1 AMB_RS09205 (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.19583.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
      1e-64  204.5   0.8    1.3e-64  204.2   0.8    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011384224.1  AMB_RS09205 triose-phosphate iso


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011384224.1  AMB_RS09205 triose-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.2   0.8   1.3e-64   1.3e-64       1     226 [.       7     240 ..       7     242 .. 0.94

  Alignments for each domain:
  == domain 1  score: 204.2 bits;  conditional E-value: 1.3e-64
                                 TIGR00419   1 lviinfKlnesvgkvelevaklaeevasea.gvevavappfvdldvvkdeve.seiqvaAqnvdavksG 67 
                                               l+ +n+K+n+   +   +   la+++as + ++ + v ppf  +  v+d++  s++ v+ q+++a++sG
  lcl|NCBI__GCF_000009985.1:WP_011384224.1   7 LIAGNWKMNGLKADGLALAKGLADKLASASpNCDMLVCPPFTLIAPVADALAgSKLAVGGQDCHAKTSG 75 
                                               689*******99988888888******98648*******************99**************** PP

                                 TIGR00419  68 aftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartin 136
                                               a+tG++s +ml+dlG+k+ ++gHsErR+ ++e+d+++++k a +   gl ++vC+getl++r+a++ti+
  lcl|NCBI__GCF_000009985.1:WP_011384224.1  76 AHTGDTSPAMLADLGCKYAIVGHSERRTDHAETDNVVKAKAAAALSAGLVAIVCIGETLAQRDAGQTIE 144
                                               ********************************************************************9 PP

                                 TIGR00419 137 nvattaaaaA.....lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvrvlyGa 199
                                               +   + +          + v+A+EPv++iGtG+++++A+a++v++ +r  l++ v +e a ++r+lyG+
  lcl|NCBI__GCF_000009985.1:WP_011384224.1 145 VNRSQLNGSLpeganAANTVIAYEPVWAIGTGRVATPAQAQEVHAAIRAELARlVGAEEAGKMRILYGG 213
                                               7766644322344448899**********************************99************** PP

                                 TIGR00419 200 svtaaedaelaaqldvdGvLlasavlk 226
                                               s++  +++el a +dvdG L+++a lk
  lcl|NCBI__GCF_000009985.1:WP_011384224.1 214 SMKPDNAKELLALPDVDGGLIGGAALK 240
                                               *************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (251 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: 6.69
//
[ok]

This GapMind analysis is from Sep 17 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources