GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutI in Klebsiella michiganensis M5al

Align Imidazolonepropionase (EC 3.5.2.7) (characterized)
to candidate BWI76_RS08720 BWI76_RS08720 imidazolonepropionase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_317
         (401 letters)



>FitnessBrowser__Koxy:BWI76_RS08720
          Length = 405

 Score =  426 bits (1095), Expect = e-124
 Identities = 222/397 (55%), Positives = 282/397 (71%), Gaps = 7/397 (1%)

Query: 2   KTLWQHCHVATM---AQGVYSIIEDAAIVTSGAHIEWIGPRGELPAGEYPAVNDLNGAWV 58
           + +W++  +AT+   +   Y +++  A++     IE I P GE PAG+     DL G  +
Sbjct: 8   RVIWRNARLATLDPRSSQPYGLLDHHALLVRNGRIEAIVPEGEAPAGQSI---DLGGRLL 64

Query: 59  TPGLIDCHTHTVFGGNRSGEFEQRLQGVSYADIAASGGGIASTVRATRAASEDELFASAA 118
           TPGLIDCHTH VFGG+R+ E+EQRL GVSY  I+A+GGGI +TVRATR +SE EL A A 
Sbjct: 65  TPGLIDCHTHLVFGGSRAQEWEQRLNGVSYQTISANGGGINATVRATRDSSEAELLALAR 124

Query: 119 KRLKSLMRDGVTSIEIKSGYGLDLANERKMLRVARRLGAELPVSVRSTCLAAHALPPEYK 178
           +RL  L+R+GVT++EIKSGYGLDLANERKMLRV ++L A   V V  T L+AHA PPEYK
Sbjct: 125 QRLARLLREGVTTLEIKSGYGLDLANERKMLRVVQQLAATHAVEVSPTLLSAHATPPEYK 184

Query: 179 DRADDYIDHICADMLPALAAEGLVDAVDAFCEYLAFSPAQVERVFITAQALGLPVKLHAE 238
              D YI+ +C  +LP L  EGL ++VDAFCE + FSP Q ER++ TAQALG+PVK H E
Sbjct: 185 GDPDGYINLVCETILPTLWEEGLFESVDAFCENVGFSPTQTERIYSTAQALGIPVKGHVE 244

Query: 239 QLSSLHGSSLAARYHALSADHLEFMTEDDAIAMAKSGTVAVLLPGAFYFLRETQLPPMEA 298
           QLSSL G+ L +RYH LSADH+E++T +   AM++SGTVAVLLPGAFYFL ET+ PP+E 
Sbjct: 245 QLSSLGGAELVSRYHGLSADHIEYLTPEGVAAMSRSGTVAVLLPGAFYFLNETRRPPVEL 304

Query: 299 LRKHGVKIAIASDLNPGTSPALSLRLMLNMACTCFRMTPEEALAGATIHAATALGMADTH 358
           LR++ V +A+A+D NPGTSP  SL L +NMAC  F +TPEEA AG T HAA ALG   +H
Sbjct: 305 LREYQVPMAVATDYNPGTSPFASLHLAMNMACVKFGLTPEEAWAGVTRHAAQALGRQASH 364

Query: 359 GSLEVGKVADFVAWQIDRPADLCYWLG-GDLEKRVVR 394
           G L  G VADF  W  + P ++ Y  G   L +RVVR
Sbjct: 365 GQLAPGFVADFAIWDAEHPVEMVYEPGRSPLWQRVVR 401


Lambda     K      H
   0.320    0.133    0.399 

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: 470
Number of extensions: 18
Number of successful extensions: 2
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: 401
Length of database: 405
Length adjustment: 31
Effective length of query: 370
Effective length of database: 374
Effective search space:   138380
Effective search space used:   138380
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: 50 (23.9 bits)

Align candidate BWI76_RS08720 BWI76_RS08720 (imidazolonepropionase)
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.24750.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   5.3e-144  465.6   0.0     6e-144  465.4   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS08720  BWI76_RS08720 imidazolonepropion


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS08720  BWI76_RS08720 imidazolonepropionase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  465.4   0.0    6e-144    6e-144       3     377 .]      32     404 ..      30     404 .. 0.99

  Alignments for each domain:
  == domain 1  score: 465.4 bits;  conditional E-value: 6e-144
                               TIGR01224   3 daailveegkiaaigqkaalpgeeaakiidleGklvvPGlvDpHtHlvfagdRvkefelklqGasYleila 73 
                                             ++a+lv++g+i ai ++ ++p+    + idl+G+l +PGl+D+HtHlvf+g+R++e+e++l+G+sY++i a
  lcl|FitnessBrowser__Koxy:BWI76_RS08720  32 HHALLVRNGRIEAIVPEGEAPA---GQSIDLGGRLLTPGLIDCHTHLVFGGSRAQEWEQRLNGVSYQTISA 99 
                                             689*************999998...899******************************************* PP

                               TIGR01224  74 eGgGilstvratraAseeellkeaeerlkkllrsGtttlEvKsGYGLdleaElkmLrvikalkeelpvdvv 144
                                             +GgGi  tvratr+ se+ell+ a++rl++llr+G+ttlE+KsGYGLdl +E kmLrv+++l++++ v+v+
  lcl|FitnessBrowser__Koxy:BWI76_RS08720 100 NGGGINATVRATRDSSEAELLALARQRLARLLREGVTTLEIKSGYGLDLANERKMLRVVQQLAATHAVEVS 170
                                             *********************************************************************** PP

                               TIGR01224 145 ttflgaHavPkevqededeyvdaileelipkvaeeklaeavDvFcekgvFsveqsrrilkaaqeaGlavkl 215
                                             +t+l aHa P+e+++d+d y++ ++e+++p   ee l e+vD+Fce+ +Fs+ q++ri++ aq+ G++vk 
  lcl|FitnessBrowser__Koxy:BWI76_RS08720 171 PTLLSAHATPPEYKGDPDGYINLVCETILPTLWEEGLFESVDAFCENVGFSPTQTERIYSTAQALGIPVKG 241
                                             *********************************************************************** PP

                               TIGR01224 216 HaeelkalggaelaaklgavsadHleeasdedikalaeagtvavlLPgtaflLr.eaapparklidekviv 285
                                             H e+l++lggael ++ +++sadH+e++++e+++a+  +gtvavlLPg++++L+ +  pp + l++++v++
  lcl|FitnessBrowser__Koxy:BWI76_RS08720 242 HVEQLSSLGGAELVSRYHGLSADHIEYLTPEGVAAMSRSGTVAVLLPGAFYFLNeTRRPPVELLREYQVPM 312
                                             ******************************************************8889************* PP

                               TIGR01224 286 alatDlnPgsspllslqlilslavtllkltaeealaaatvnaAqalglgeekGtleeGkdadlvvlsaesy 356
                                             a+atD nPg+sp++sl+l++++a++++ lt+eea+a++t +aAqalg+++++G+l+ G  ad+++++ae++
  lcl|FitnessBrowser__Koxy:BWI76_RS08720 313 AVATDYNPGTSPFASLHLAMNMACVKFGLTPEEAWAGVTRHAAQALGRQASHGQLAPGFVADFAIWDAEHP 383
                                             *********************************************************************** PP

                               TIGR01224 357 eeiaYrlgvnvveaviknGev 377
                                              e+ Y+ g + + +++++Ge+
  lcl|FitnessBrowser__Koxy:BWI76_RS08720 384 VEMVYEPGRSPLWQRVVRGEI 404
                                             ****************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (377 nodes)
Target sequences:                          1  (405 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.21
//
[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