Alignments for a candidate for tpi in Phaeacidiphilus oryzae TH49

GapMind for catabolism of small carbon sources

Alignments for a candidate for tpi in Phaeacidiphilus oryzae TH49

Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate WP_037579273.1 BS73_RS12430 triose-phosphate isomerase

Query= SwissProt::Q9Z520
         (258 letters)



>NCBI__GCF_000744815.1:WP_037579273.1
          Length = 261

 Score =  402 bits (1034), Expect = e-117
 Identities = 195/258 (75%), Positives = 223/258 (86%)

Query: 1   MTTRTPLMAGNWKMNLNHLEAIAHVQKLAFALADKDYDAVEVAVLAPFTDLRSVQTLVDG 60
           MT RTPLMAGNWKMNLNHLEAIAHVQKLAFAL DKD++ VEVAVL PFTDLRSVQTLVDG
Sbjct: 1   MTARTPLMAGNWKMNLNHLEAIAHVQKLAFALHDKDFEQVEVAVLPPFTDLRSVQTLVDG 60

Query: 61  DKLKIKYGAQDISAHDGGAYTGEISGPMLAKLKCTYVAVGHSERRQYHAETDEIVNAKVK 120
           D+LKI+YGAQD+SAHD GAYTGEISGPML+K KC Y  VGHSERRQYH E +   N KVK
Sbjct: 61  DRLKIRYGAQDVSAHDSGAYTGEISGPMLSKFKCAYALVGHSERRQYHGENETTCNEKVK 120

Query: 121 AAYKHGLTPILCVGEELDVREAGNHVEHTLAQVEGGLKDLAAEQAESVVIAYEPVWAIGT 180
           AAY++G+ P+LCVGE L++R++G HV  TLAQV+G L  + AEQ ES+VIAYEPVWAIGT
Sbjct: 121 AAYRNGIVPLLCVGEGLEIRKSGGHVAFTLAQVDGALAGVPAEQVESLVIAYEPVWAIGT 180

Query: 181 GKVCGADDAQEVCAAIRGKLAELYSQELADKVRIQYGGSVKSGNVAEIMAKPDIDGALVG 240
           G+V   +DAQEVC AIR +LAELYS + AD+VR+ YGGSVKSGNVA IMA+PD+DGALVG
Sbjct: 181 GEVATPEDAQEVCGAIRRRLAELYSPQTADRVRVLYGGSVKSGNVASIMAQPDVDGALVG 240

Query: 241 GASLDSDEFVKIVRFRDQ 258
           GASLD +EFVKIVR+RDQ
Sbjct: 241 GASLDPEEFVKIVRYRDQ 258


Lambda     K      H
   0.316    0.133    0.381 

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: 308
Number of extensions: 5
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: 258
Length of database: 261
Length adjustment: 24
Effective length of query: 234
Effective length of database: 237
Effective search space:    55458
Effective search space used:    55458
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_037579273.1 BS73_RS12430 (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.3212628.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.8e-55  173.6   0.0    3.2e-55  173.4   0.0    1.0  1  NCBI__GCF_000744815.1:WP_037579273.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000744815.1:WP_037579273.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.4   0.0   3.2e-55   3.2e-55       2     228 .]       8     247 ..       7     247 .. 0.91

  Alignments for each domain:
  == domain 1  score: 173.4 bits;  conditional E-value: 3.2e-55
                             TIGR00419   2 viinfKlnesvgkvelevaklaeevasea..gvevavappfvdldvvkdeve...seiqvaAqnvdavksGaf 69 
                                           + +n+K+n    +    v+kla  + +++  +vevav ppf dl+ v+  v+    +i+ +Aq+v a++sGa+
  NCBI__GCF_000744815.1:WP_037579273.1   8 MAGNWKMNLNHLEAIAHVQKLAFALHDKDfeQVEVAVLPPFTDLRSVQTLVDgdrLKIRYGAQDVSAHDSGAY 80 
                                           679*****99999999******9999876337889999*********9988753357999************* PP

                             TIGR00419  70 tGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartin.nvatt 141
                                           tGeis  ml  + +++ l+gHsErR ++ e +   ++kv  +   g+ +++Cvge le r+++ ++  ++a+ 
  NCBI__GCF_000744815.1:WP_037579273.1  81 TGEISGPMLSKFKCAYALVGHSERRQYHGENETTCNEKVKAAYRNGIVPLLCVGEGLEIRKSGGHVAfTLAQV 153
                                           **********************************************************999776665145555 PP

                             TIGR00419 142 aaaaA......lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvrvlyGasvtaaeda 207
                                            +a A       e+ v+A+EPv++iGtG ++++ +a++v + +r  l++  s++ a+ vrvlyG+sv++++ a
  NCBI__GCF_000744815.1:WP_037579273.1 154 DGALAgvpaeqVESLVIAYEPVWAIGTGEVATPEDAQEVCGAIRRRLAElYSPQTADRVRVLYGGSVKSGNVA 226
                                           6677777788899***********************************999********************** PP

                             TIGR00419 208 elaaqldvdGvLlasavlkae 228
                                             +aq+dvdG+L+++a+l +e
  NCBI__GCF_000744815.1:WP_037579273.1 227 SIMAQPDVDGALVGGASLDPE 247
                                           *****************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (261 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: 13.06
//
[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:

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 2024 update 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