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.23192.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 6.07
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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:

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:

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:

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:

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