Alignments for a candidate for tpi in Bacteroides thetaiotaomicron VPI-5482

GapMind for catabolism of small carbon sources

Alignments for a candidate for tpi in Bacteroides thetaiotaomicron VPI-5482

Align Triosephosphate isomerase; TIM; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate 353455 BT3929 triosephosphate isomerase (NCBI ptt file)

Query= SwissProt::P29613
         (247 letters)



>FitnessBrowser__Btheta:353455
          Length = 252

 Score =  224 bits (572), Expect = 1e-63
 Identities = 122/248 (49%), Positives = 166/248 (66%), Gaps = 5/248 (2%)

Query: 3   RKFCVGGNWKMNGDQKSIAEIAKTLSSAALD--PNTEVVIGCPAIYLMYARNLLPC-ELG 59
           RK  V GNWKMN   +    +AK L+ A  +  PN +V+I  P I+L     L+   ++G
Sbjct: 2   RKNIVAGNWKMNKTLQEGIALAKELNEALANEKPNCDVIICTPFIHLASVTPLVDAAKIG 61

Query: 60  LAGQNAYKVAKGAFTGEISPAMLKDIGADWVILGHSERRAIFGESDALIAEKAEHALAEG 119
           +  +N    A GA+TGE+S  M+   GA +VILGHSERRA +GE+ A++ EK + ALA G
Sbjct: 62  VGAENCADKASGAYTGEVSAEMVASTGAKYVILGHSERRAYYGETVAILEEKVKLALANG 121

Query: 120 LKVIACIGETLEEREAGKTNEVVARQM-CAYAQKIKDWKNVVVAYEPVWAIGTGQTATPD 178
           L  I CIGE LEEREA K NEVVA QM   ++   +D+  +++AYEPVWAIGTG+TA+P+
Sbjct: 122 LTPIFCIGEVLEEREANKQNEVVAAQMESVFSLSAEDFSKIILAYEPVWAIGTGKTASPE 181

Query: 179 QAQEVHAFLRQWLSDNISKEVSASLRIQYGGSVTAANAKELAKKPDIDGFLVGGASLK-P 237
           QAQE+HAF+R  ++D   KE++ +  I YGGS   +NAKEL   PD+DG L+GGA+LK  
Sbjct: 182 QAQEIHAFIRSIVADKYGKEIADNTSILYGGSCKPSNAKELFSNPDVDGGLIGGAALKVS 241

Query: 238 EFVDIINA 245
           +F  II+A
Sbjct: 242 DFKGIIDA 249


Lambda     K      H
   0.316    0.132    0.388 

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: 196
Number of extensions: 9
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: 247
Length of database: 252
Length adjustment: 24
Effective length of query: 223
Effective length of database: 228
Effective search space:    50844
Effective search space used:    50844
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: 46 (22.3 bits)

Align candidate 353455 BT3929 (triosephosphate isomerase (NCBI ptt file))
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.3626.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-66  210.9   2.2    1.3e-66  210.7   2.2    1.0  1  lcl|FitnessBrowser__Btheta:353455  BT3929 triosephosphate isomerase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:353455  BT3929 triosephosphate isomerase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.7   2.2   1.3e-66   1.3e-66       1     226 [.       5     239 ..       5     241 .. 0.96

  Alignments for each domain:
  == domain 1  score: 210.7 bits;  conditional E-value: 1.3e-66
                          TIGR00419   1 lviinfKlnesvgkvelevaklaeevasea.gvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftGeis 74 
                                        +v +n+K+n ++++   +  +l+e +a+e+ ++ v +  pf++l  v+  v+ ++i v+A n+  + sGa+tGe+s
  lcl|FitnessBrowser__Btheta:353455   5 IVAGNWKMNKTLQEGIALAKELNEALANEKpNCDVIICTPFIHLASVTPLVDaAKIGVGAENCADKASGAYTGEVS 80 
                                        699***********************987548******************99899********************* PP

                          TIGR00419  75 AemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaaaaA.... 146
                                        Aem++ +Gak+v++gHsErR++  e+  ++e+kv  + + gl+++ C+ge leerea ++ ++va + + +     
  lcl|FitnessBrowser__Btheta:353455  81 AEMVASTGAKYVILGHSERRAYYGETVAILEEKVKLALANGLTPIFCIGEVLEEREANKQNEVVAAQMESVFslsa 156
                                        ****************************************************************999887766777 PP

                          TIGR00419 147 ..lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvrvlyGasvtaaedaelaaqldvdGvL 219
                                          +++ ++A+EPv++iGtGk++s+ +a+++++++r  ++    ke+a+++++lyG+s + ++++el+ ++dvdG L
  lcl|FitnessBrowser__Btheta:353455 157 edFSKIILAYEPVWAIGTGKTASPEQAQEIHAFIRSIVADkYGKEIADNTSILYGGSCKPSNAKELFSNPDVDGGL 232
                                        88*********************************99987799********************************* PP

                          TIGR00419 220 lasavlk 226
                                        +++a lk
  lcl|FitnessBrowser__Btheta:353455 233 IGGAALK 239
                                        *****99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (252 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: 7.68
//
[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
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