Alignments for a candidate for tpi in Mesorhizobium ciceri WSM1271

GapMind for catabolism of small carbon sources

Alignments for a candidate for tpi in Mesorhizobium ciceri WSM1271

Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate YP_004143121.1 Mesci_3956 triosephosphate isomerase

Query= SwissProt::Q8L1Z5
         (254 letters)



>NCBI__GCF_000185905.1:YP_004143121.1
          Length = 255

 Score =  304 bits (779), Expect = 1e-87
 Identities = 154/254 (60%), Positives = 185/254 (72%)

Query: 1   MSPNIRPFIAGNWKMNGTGESLGELRAIAAGISSDLGRLFEALICVPATLLSRAFDILGG 60
           M+P IRP +AGNWKMNGT  SL ELR I  G  S L    EAL+CVPATLL+ A +IL  
Sbjct: 1   MTPGIRPLVAGNWKMNGTSASLNELRMIGNGFMSGLDAETEALVCVPATLLAHAAEILSR 60

Query: 61  ENILLGGQNCHFDDYGPYTGDISAFMLKEAGASHVIIGHSERRTVYQESDAIVRAKVQAA 120
             +  GG++CH  + G YTG ISA ML++AGASHVI+GHSE R    E DA V+AK  AA
Sbjct: 61  TPVHAGGEDCHTKESGAYTGCISAEMLRDAGASHVIVGHSECREQRGEDDATVQAKASAA 120

Query: 121 WRAGLVALICVGETLEERKSNKVLDVLTRQLEGSLPDGATAENIIIAYEPVWAVGTGNTA 180
           WRAGLVA+ICVGET E+R++   LDVL+RQ+EGS+P  AT  N IIAYEPVWA+GTG T 
Sbjct: 121 WRAGLVAIICVGETHEQREAGATLDVLSRQVEGSVPPSATPSNTIIAYEPVWAIGTGLTP 180

Query: 181 TSADVAEVHAFIHHKMHSRFGDEGAKIRLLYGGSVKPSNAFELLSTAHVNGALIGGASLK 240
           T+ADVA  HA I  K+  + G   AK+R+LYGGSVKPSNA ELL   +V+GAL+GGASLK
Sbjct: 181 TAADVAAAHAHIREKLSEKLGGVAAKVRILYGGSVKPSNAVELLGVRNVDGALVGGASLK 240

Query: 241 AIDFLTICDVYRKL 254
           A DFL I + YR +
Sbjct: 241 AADFLGIAEAYRNI 254


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: 261
Number of extensions: 9
Number of successful extensions: 1
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: 255
Length adjustment: 24
Effective length of query: 230
Effective length of database: 231
Effective search space:    53130
Effective search space used:    53130
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: 47 (22.7 bits)

Align candidate YP_004143121.1 Mesci_3956 (triosephosphate 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.4213.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.1e-51  161.9   2.2    1.3e-51  161.6   2.2    1.0  1  lcl|NCBI__GCF_000185905.1:YP_004143121.1  Mesci_3956 triosephosphate isome


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000185905.1:YP_004143121.1  Mesci_3956 triosephosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.6   2.2   1.3e-51   1.3e-51       1     227 [.       8     241 ..       8     242 .. 0.89

  Alignments for each domain:
  == domain 1  score: 161.6 bits;  conditional E-value: 1.3e-51
                                 TIGR00419   1 lviinfKlnesvgkvelevaklae.evas.eagvevavappfvdldvvkdeve.seiqvaAqnvdavks 66 
                                               lv +n+K+n++  + ++ +  + +  +++  a+ e  v +p   l  +++ ++ + ++ +  ++++++s
  lcl|NCBI__GCF_000185905.1:YP_004143121.1   8 LVAGNWKMNGTSASLNE-LRMIGNgFMSGlDAETEALVCVPATLLAHAAEILSrTPVHAGGEDCHTKES 75 
                                               799*******9877665.555655255552345566788888888888888874566666799****** PP

                                 TIGR00419  67 GaftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaarti 135
                                               Ga+tG isAeml+d+Ga +v++gHsE R    e d  +++k + +   gl +++Cvget e+rea+ t+
  lcl|NCBI__GCF_000185905.1:YP_004143121.1  76 GAYTGCISAEMLRDAGASHVIVGHSECREQRGEDDATVQAKASAAWRAGLVAIICVGETHEQREAGATL 144
                                               ********************************************************************* PP

                                 TIGR00419 136 nnvattaaaaA.....lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGa 199
                                               +++ ++ +         ++ ++A+EPv++iGtG + + A+  + ++ +r+ l++    va +vr+lyG+
  lcl|NCBI__GCF_000185905.1:YP_004143121.1 145 DVLSRQVEGSVppsatPSNTIIAYEPVWAIGTGLTPTAADVAAAHAHIREKLSEKLGGVAAKVRILYGG 213
                                               ***9997754445545899************************************************** PP

                                 TIGR00419 200 svtaaedaelaaqldvdGvLlasavlka 227
                                               sv+ ++++el    +vdG+L+++a+lka
  lcl|NCBI__GCF_000185905.1:YP_004143121.1 214 SVKPSNAVELLGVRNVDGALVGGASLKA 241
                                               ***************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (255 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: 9.34
//
[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:

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
the source code
instructions for running GapMind on your computer

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