Alignments for a candidate for tpiA in Xanthobacter autotrophicus Py2

GapMind for Amino acid biosynthesis

Alignments for a candidate for tpiA in Xanthobacter autotrophicus Py2

Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate WP_012116350.1 XAUT_RS22185 triose-phosphate isomerase

Query= SwissProt::Q8L1Z5
         (254 letters)



>NCBI__GCF_000017645.1:WP_012116350.1
          Length = 254

 Score =  276 bits (707), Expect = 2e-79
 Identities = 140/247 (56%), Positives = 173/247 (70%)

Query: 1   MSPNIRPFIAGNWKMNGTGESLGELRAIAAGISSDLGRLFEALICVPATLLSRAFDILGG 60
           M  + R  IAGNWKMNG   SL E+ A+AAG   DL    + L+C PATLL  A + L G
Sbjct: 1   MPASRRVLIAGNWKMNGLKSSLAEIEALAAGYDGDLKAKLDLLVCPPATLLISAAERLAG 60

Query: 61  ENILLGGQNCHFDDYGPYTGDISAFMLKEAGASHVIIGHSERRTVYQESDAIVRAKVQAA 120
             + LGGQNCH    G +TG ISA MLK+AG + VI+GHSERRT   ESDA+V AKV+AA
Sbjct: 61  SGVQLGGQNCHPAPAGAHTGGISAEMLKDAGVTSVIVGHSERRTNLSESDAVVMAKVKAA 120

Query: 121 WRAGLVALICVGETLEERKSNKVLDVLTRQLEGSLPDGATAENIIIAYEPVWAVGTGNTA 180
           W  GL+ ++CVGET EER + + + V+TRQ+  SLP+G TA N++IAYEPVWA+GTG T 
Sbjct: 121 WCFGLLPIVCVGETAEERDAGEAVGVVTRQVHQSLPEGCTASNLVIAYEPVWAIGTGRTP 180

Query: 181 TSADVAEVHAFIHHKMHSRFGDEGAKIRLLYGGSVKPSNAFELLSTAHVNGALIGGASLK 240
           T  DVA +H  I   + S+FG E   IR+LYGGSVKP NA  L++ A V+GAL+GGASLK
Sbjct: 181 TPEDVANIHGTIRSVLRSQFGAEADGIRILYGGSVKPDNAATLMAVADVDGALVGGASLK 240

Query: 241 AIDFLTI 247
           A DFL I
Sbjct: 241 AADFLAI 247


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: 236
Number of extensions: 7
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: 254
Length adjustment: 24
Effective length of query: 230
Effective length of database: 230
Effective search space:    52900
Effective search space used:    52900
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 WP_012116350.1 XAUT_RS22185 (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.aa/TIGR00419.hmm
# target sequence database:        /tmp/gapView.23784.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    5.1e-56  176.0   0.4    6.1e-56  175.8   0.4    1.0  1  lcl|NCBI__GCF_000017645.1:WP_012116350.1  XAUT_RS22185 triose-phosphate is


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000017645.1:WP_012116350.1  XAUT_RS22185 triose-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.8   0.4   6.1e-56   6.1e-56       1     227 [.       8     241 ..       8     242 .. 0.90

  Alignments for each domain:
  == domain 1  score: 175.8 bits;  conditional E-value: 6.1e-56
                                 TIGR00419   1 lviinfKlnesvgkvelevaklae..evaseagvevavappfvdldvvkdeve.seiqvaAqnvdavks 66 
                                               l+ +n+K+n+  ++ +++   la+  +   +a+  + v pp   l  +++++  s +q++ qn++   +
  lcl|NCBI__GCF_000017645.1:WP_012116350.1   8 LIAGNWKMNGLKSSLAEI-EALAAgyDGDLKAKLDLLVCPPATLLISAAERLAgSGVQLGGQNCHPAPA 75 
                                               689****99988777654.44554244455778889999998888777777777*************** PP

                                 TIGR00419  67 GaftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaarti 135
                                               Ga+tG isAemlkd+G+  v++gHsErR+ l e+d ++ +kv  +   gl ++vCvget eer+a++ +
  lcl|NCBI__GCF_000017645.1:WP_012116350.1  76 GAHTGGISAEMLKDAGVTSVIVGHSERRTNLSESDAVVMAKVKAAWCFGLLPIVCVGETAEERDAGEAV 144
                                               ********************************************************************* PP

                                 TIGR00419 136 nnvattaaaaA.....lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGa 199
                                                +v+++           ++ v+A+EPv++iGtG++ ++ +   +++++r  l+      a+ +r+lyG+
  lcl|NCBI__GCF_000017645.1:WP_012116350.1 145 GVVTRQVHQSLpegctASNLVIAYEPVWAIGTGRTPTPEDVANIHGTIRSVLRSQFGAEADGIRILYGG 213
                                               ***9987665556666999******************************99999888889********* PP

                                 TIGR00419 200 svtaaedaelaaqldvdGvLlasavlka 227
                                               sv+  ++a l+a  dvdG+L+++a+lka
  lcl|NCBI__GCF_000017645.1:WP_012116350.1 214 SVKPDNAATLMAVADVDGALVGGASLKA 241
                                               ***************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (254 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: 5.99
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis