Aligments for a candidate for hutI in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Aligments 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.8422.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.46
//
[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, or view the source code.

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