Alignments for a candidate for hutI in Lysobacter daejeonensis GH1-9

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutI in Lysobacter daejeonensis GH1-9

Align Imidazolonepropionase (EC 3.5.2.7) (characterized)
to candidate WP_036137730.1 N800_RS09760 imidazolonepropionase

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



>NCBI__GCF_000768355.1:WP_036137730.1
          Length = 409

 Score =  449 bits (1154), Expect = e-131
 Identities = 232/381 (60%), Positives = 280/381 (73%), Gaps = 4/381 (1%)

Query: 18  YSIIEDAAIVTSGAHIEWIGPRGELPAGEYPAVNDLNGA--WVTPGLIDCHTHTVFGGNR 75
           Y  I D A+      + ++GPR  LP        ++  A  W+TPGL+DCHTH VF G+R
Sbjct: 27  YGEITDGALGWRDGVLTFVGPRNALPDSPDRLAREVIEARGWITPGLVDCHTHLVFAGDR 86

Query: 76  SGEFEQRLQGVSYADIAASGGGIASTVRATRAASEDELFASAAKRLKSLMRDGVTSIEIK 135
           + EFE RLQG SY  IA +GGGI STVRATR ASEDEL   +  R ++L+ DG T++EIK
Sbjct: 87  AREFELRLQGASYEAIARAGGGILSTVRATREASEDELLRQSLPRARALLADGATTLEIK 146

Query: 136 SGYGLDLANERKMLRVARRLGAELPVSVRSTCLAAHALPPEYKDRADDYIDHICADMLPA 195
           SGYGLD  +ERKMLRVARR+G  L V+VR+T LAAHALPPEYK+RADDYID  C D LP 
Sbjct: 147 SGYGLDFDSERKMLRVARRVGEVLGVTVRTTYLAAHALPPEYKERADDYIDAAC-DWLPR 205

Query: 196 LAAEGLVDAVDAFCEYLAFSPAQVERVFITAQALGLPVKLHAEQLSSLHGSSLAARYHAL 255
           L AEGLVDAVDAFCE + F+PAQ  R+F  A+ALGLPVKLHA+QLS L G++LAA +  L
Sbjct: 206 LHAEGLVDAVDAFCEGIGFTPAQTRRMFEAARALGLPVKLHADQLSDLGGAALAAEFSGL 265

Query: 256 SADHLEFMTEDDAIAMAKSGTVAVLLPGAFYFLRETQLPPMEALRKHGVKIAIASDLNPG 315
           SADH+E+ +ED   AMA  GTVAVLLPGAF+ LRET+LPP++A R HGV +A+A+D NPG
Sbjct: 266 SADHVEYTSEDSVRAMAAHGTVAVLLPGAFHVLRETKLPPLDAFRVHGVPMAVATDCNPG 325

Query: 316 TSPALSLRLMLNMACTCFRMTPEEALAGATIHAATALGMADTHGSLEVGKVADFVAWQID 375
           TSP LS+R  + +ACT FR+TPEEAL GAT+HAA ALG+ D  G L VG  ADFV WQ+ 
Sbjct: 326 TSPLLSMRQAMQLACTHFRLTPEEALRGATVHAAHALGLTD-RGVLRVGARADFVQWQVG 384

Query: 376 RPADLCYWLGGDLEKRVVRHG 396
            PA+LCYWLGG L   V   G
Sbjct: 385 HPAELCYWLGGRLADAVYAGG 405


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: 492
Number of extensions: 14
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: 401
Length of database: 409
Length adjustment: 31
Effective length of query: 370
Effective length of database: 378
Effective search space:   139860
Effective search space used:   139860
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 WP_036137730.1 N800_RS09760 (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.4176189.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.6e-141  455.9   0.0   5.3e-141  455.7   0.0    1.0  1  NCBI__GCF_000768355.1:WP_036137730.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000768355.1:WP_036137730.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  455.7   0.0  5.3e-141  5.3e-141       3     375 ..      32     405 ..      30     407 .. 0.96

  Alignments for each domain:
  == domain 1  score: 455.7 bits;  conditional E-value: 5.3e-141
                             TIGR01224   3 daailveegkiaaigqkaalpge...eaakiidleGklvvPGlvDpHtHlvfagdRvkefelklqGasYleil 72 
                                           d+a+  ++g ++++g+++alp      a ++i++ G  ++PGlvD+HtHlvfagdR++efel+lqGasY+ i+
  NCBI__GCF_000768355.1:WP_036137730.1  32 DGALGWRDGVLTFVGPRNALPDSpdrLAREVIEARG-WITPGLVDCHTHLVFAGDRAREFELRLQGASYEAIA 103
                                           77888899**********887765435677777776.689********************************* PP

                             TIGR01224  73 aeGgGilstvratraAseeellkeaeerlkkllrsGtttlEvKsGYGLdleaElkmLrvikalkeelpvdvvt 145
                                           ++GgGilstvratr+Ase+ell++  +r++ ll+ G+ttlE+KsGYGLd+++E kmLrv++++ e l v v t
  NCBI__GCF_000768355.1:WP_036137730.1 104 RAGGGILSTVRATREASEDELLRQSLPRARALLADGATTLEIKSGYGLDFDSERKMLRVARRVGEVLGVTVRT 176
                                           ************************************************************************* PP

                             TIGR01224 146 tflgaHavPkevqededeyvdaileelipkvaeeklaeavDvFcekgvFsveqsrrilkaaqeaGlavklHae 218
                                           t+l+aHa+P+e++e+ d+y+da ++  +p+ + e l++avD+Fce  +F+++q+rr+++aa++ Gl+vklHa+
  NCBI__GCF_000768355.1:WP_036137730.1 177 TYLAAHALPPEYKERADDYIDAACD-WLPRLHAEGLVDAVDAFCEGIGFTPAQTRRMFEAARALGLPVKLHAD 248
                                           ************************9.99********************************************* PP

                             TIGR01224 219 elkalggaelaaklgavsadHleeasdedikalaeagtvavlLPgtaflLr.eaapparklidekvivalatD 290
                                           +l+ lgga+laa++ ++sadH+e++s++ ++a+a+ gtvavlLPg++++Lr ++ pp ++++ ++v++a+atD
  NCBI__GCF_000768355.1:WP_036137730.1 249 QLSDLGGAALAAEFSGLSADHVEYTSEDSVRAMAAHGTVAVLLPGAFHVLReTKLPPLDAFRVHGVPMAVATD 321
                                           ***************************************************8889****************** PP

                             TIGR01224 291 lnPgsspllslqlilslavtllkltaeealaaatvnaAqalglgeekGtleeGkdadlvvlsaesyeeiaYrl 363
                                            nPg+splls++ +++la+t+++lt+eeal++atv+aA+algl++ +G l+ G +ad+v +++ +++e+ Y+l
  NCBI__GCF_000768355.1:WP_036137730.1 322 CNPGTSPLLSMRQAMQLACTHFRLTPEEALRGATVHAAHALGLTD-RGVLRVGARADFVQWQVGHPAELCYWL 393
                                           ********************************************9.*************************** PP

                             TIGR01224 364 gvnvveaviknG 375
                                           g+   +av+  G
  NCBI__GCF_000768355.1:WP_036137730.1 394 GGRLADAVYAGG 405
                                           ***999999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (377 nodes)
Target sequences:                          1  (409 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: 00:00:00.00
# Mc/sec: 20.58
//
[ok]

This GapMind analysis is from Sep 24 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 2024 update 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