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

GapMind for catabolism of small carbon sources

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

Align imidazolonepropionase (EC 3.5.2.7) (characterized)
to candidate 352219 BT2692 imidazolonepropionase (NCBI ptt file)

Query= BRENDA::P42084
         (421 letters)



>FitnessBrowser__Btheta:352219
          Length = 417

 Score =  330 bits (845), Expect = 6e-95
 Identities = 179/412 (43%), Positives = 261/412 (63%), Gaps = 7/412 (1%)

Query: 6   DTILINIGQLLTMESSGPRAGKSMQDLHVIEDAVVGIHEQKIVFAGQKGAE---AGYEAD 62
           + ++I   +++T   +  R G  M  L +IE+  V + +  I + G+   E     Y+  
Sbjct: 3   ENLIIFNARIVTPTGTSARKGAEMGQLRIIENGTVEVTKGIITYVGESRGEDRDGYYQHY 62

Query: 63  EIIDCSGRLVTPGLVDPHTHLVFGGSREKEMNLKLQGISYLDILAQGGGILSTVKDTRAA 122
              +  G  + PG VD HTH VFGG R +E + +L+G SY+ I+ +GGGI STVK TR  
Sbjct: 63  WHYNARGHCLLPGFVDSHTHFVFGGERSEEFSWRLKGESYMSIMERGGGIASTVKATRQM 122

Query: 123 SEEELLQKAHFHLQRMLSYGTTTAEVKSGYGLEKETELKQLRVAKKLH--ESQPVDLVST 180
           +  +L   A   L++M + G TT E KSGYGL++ETEL QL++ + L+  E + +D+VST
Sbjct: 123 NFLKLRSAAEGFLKKMSAMGVTTVEGKSGYGLDRETELLQLKIMRSLNNDEHKRIDIVST 182

Query: 181 FMGAHAIPPEYQNDPDDFLDQML-SLLPEIKEQELASFADIFTETGVFTVSQSRRYLQKA 239
           F+GAHA+P EY+   D+++D ++  +LP I+E ELA   D+F E GVF+V QSRR LQ A
Sbjct: 183 FLGAHALPEEYKGRGDEYIDFLIREMLPVIRENELAECCDVFCEQGVFSVEQSRRLLQAA 242

Query: 240 AEAGFGLKIHADEIDPLGGAELAGKLKAVSADHLVGTSDEGIKKLAEAGTIAVLLPGTTF 299
            E GF LK+HADEI   GGAELA +L A+SADHL+  SD GI+ +A+AG +A LLP T F
Sbjct: 243 KEQGFLLKLHADEIVSFGGAELAAELGALSADHLLQASDAGIRAMADAGVVATLLPLTAF 302

Query: 300 YLGKSTYARARAMIDEGVCVSLATDFNPGSSPTENIQLIMSIAALHLKMTAEEIWHAVTV 359
            L K  YAR R MID G  V+LATD NPGS  + +I L +++A +++K++ EE   A+T+
Sbjct: 303 AL-KEPYARGREMIDAGCAVALATDLNPGSCFSGSIPLTIALACIYMKLSIEETITALTL 361

Query: 360 NAAYAIGKGEEAGQLKAGRSADLVIWQAPNYMYIPYHYGVNHVHQVMKNGTI 411
           N A A+ + +  G ++ G+  D VI  + NY  +PY+ G+N V   +K G +
Sbjct: 362 NGAAALHRADRIGSIEVGKQGDFVILNSDNYHILPYYVGMNCVIMTIKGGML 413


Lambda     K      H
   0.316    0.134    0.378 

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: 435
Number of extensions: 12
Number of successful extensions: 4
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: 421
Length of database: 417
Length adjustment: 32
Effective length of query: 389
Effective length of database: 385
Effective search space:   149765
Effective search space used:   149765
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: 50 (23.9 bits)

Align candidate 352219 BT2692 (imidazolonepropionase (NCBI ptt file))
to HMM TIGR01224 (hutI: imidazolonepropionase (EC 3.5.2.7))

# 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/TIGR01224.hmm
# target sequence database:        /tmp/gapView.25682.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01224  [M=377]
Accession:   TIGR01224
Description: hutI: imidazolonepropionase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   3.8e-135  436.5   0.0   4.4e-135  436.3   0.0    1.0  1  lcl|FitnessBrowser__Btheta:352219  BT2692 imidazolonepropionase (NC


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:352219  BT2692 imidazolonepropionase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  436.3   0.0  4.4e-135  4.4e-135       1     375 [.      32     411 ..      32     413 .. 0.97

  Alignments for each domain:
  == domain 1  score: 436.3 bits;  conditional E-value: 4.4e-135
                          TIGR01224   1 iedaailveegkiaaigqka..alpge.eaakiidleGklvvPGlvDpHtHlvfagdRvkefelklqGasYleila 73 
                                        ie++++ v++g i+++g+    +  g+ +   + ++ G+  +PG+vD+HtH vf+g+R++ef  +l+G sY+ i++
  lcl|FitnessBrowser__Btheta:352219  32 IENGTVEVTKGIITYVGESRgeDRDGYyQHYWHYNARGHCLLPGFVDSHTHFVFGGERSEEFSWRLKGESYMSIME 107
                                        58999************9886655554467778899**************************************** PP

                          TIGR01224  74 eGgGilstvratraAseeellkeaeerlkkllrsGtttlEvKsGYGLdleaElkmLrvikalke..elpvdvvttf 147
                                        +GgGi stv+atr+ +  +l+  ae  lkk+ + G+tt+E KsGYGLd e+El +L+++++l++  ++++d+v+tf
  lcl|FitnessBrowser__Btheta:352219 108 RGGGIASTVKATRQMNFLKLRSAAEGFLKKMSAMGVTTVEGKSGYGLDRETELLQLKIMRSLNNdeHKRIDIVSTF 183
                                        ************************************************************997522789******* PP

                          TIGR01224 148 lgaHavPkevqededeyvdaileelipkvaeeklaeavDvFcekgvFsveqsrrilkaaqeaGlavklHaeelkal 223
                                        lgaHa+P+e++++ dey+d ++ e++p ++e++lae +DvFce+gvFsveqsrr+l+aa+e+G+ +klHa+e+ + 
  lcl|FitnessBrowser__Btheta:352219 184 LGAHALPEEYKGRGDEYIDFLIREMLPVIRENELAECCDVFCEQGVFSVEQSRRLLQAAKEQGFLLKLHADEIVSF 259
                                        **************************************************************************** PP

                          TIGR01224 224 ggaelaaklgavsadHleeasdedikalaeagtvavlLPgtaflLreaapparklidekvivalatDlnPgsspll 299
                                        ggaelaa+lga+sadHl++asd++i+a+a+ag+va+lLP taf+L+e +++ r++id++  valatDlnPgs+   
  lcl|FitnessBrowser__Btheta:352219 260 GGAELAAELGALSADHLLQASDAGIRAMADAGVVATLLPLTAFALKEPYARGREMIDAGCAVALATDLNPGSCFSG 335
                                        **************************************************************************** PP

                          TIGR01224 300 slqlilslavtllkltaeealaaatvnaAqalglgeekGtleeGkdadlvvlsaesyeeiaYrlgvnvveaviknG 375
                                        s++l ++la+  +kl+ ee+++a t+n A+al ++++ G++e Gk++d+v+l+ ++y+ ++Y +g+n v ++ik G
  lcl|FitnessBrowser__Btheta:352219 336 SIPLTIALACIYMKLSIEETITALTLNGAAALHRADRIGSIEVGKQGDFVILNSDNYHILPYYVGMNCVIMTIKGG 411
                                        *************************************************************************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (377 nodes)
Target sequences:                          1  (417 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.27
//
[ok]

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

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Protein sequences (fasta format)
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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