Alignments for a candidate for hutI in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutI in Shewanella loihica PV-4

Align Imidazolonepropionase (EC 3.5.2.7) (characterized)
to candidate 5211347 Shew_3759 imidazolonepropionase (RefSeq)

Query= reanno::MR1:199292
         (408 letters)



>FitnessBrowser__PV4:5211347
          Length = 408

 Score =  724 bits (1868), Expect = 0.0
 Identities = 356/408 (87%), Positives = 380/408 (93%)

Query: 1   MSWDQVWIDVNVATMDPSISAPYGAITHAAIAVKDGKIAWLGPRSELPAFDVLSIPVYRG 60
           MSWDQVWIDVN+ATMDP ISAPYGAIT AAIAVK+GKIAW+GPRSELP FDVLS PVYRG
Sbjct: 1   MSWDQVWIDVNIATMDPEISAPYGAITDAAIAVKEGKIAWMGPRSELPEFDVLSTPVYRG 60

Query: 61  KGGWITPGLIDAHTHLVFAGNRANEFELRLKGATYEEIARAGGGIISTVNACREADEAAL 120
           KGGW+TPGLIDAHTHLVFAGNRANEFELRL+GA+YEEIARAGGGIISTV ACREA EA L
Sbjct: 61  KGGWLTPGLIDAHTHLVFAGNRANEFELRLQGASYEEIARAGGGIISTVKACREASEAEL 120

Query: 121 FELGRQRLNALAKEGVTTVEIKSGYGLDTETELKILRVARELGKHHHVDVKTTFLGAHAV 180
           FELGRQRLNALAKEGVTTVEIKSGYGLDTETELK+LRVARELGKHHHVDVKTTFLGAHA+
Sbjct: 121 FELGRQRLNALAKEGVTTVEIKSGYGLDTETELKLLRVARELGKHHHVDVKTTFLGAHAI 180

Query: 181 PPEYKGNSDGYVDLIINKMLPAVIKENLADAVDVFCENIAFNLEQTERVLSAAKAAGLQV 240
           PPEYK NSD YVDL+I++ML AVI ENLADAVDVFCENIAF+LEQTERVLS AKAAGL +
Sbjct: 181 PPEYKDNSDAYVDLVIDEMLTAVINENLADAVDVFCENIAFSLEQTERVLSTAKAAGLDI 240

Query: 241 KLHAEQLSNMGGSELAARLGAKSVDHIEYLDEAGVKALSESGTCAVLLPGAFYFLRETQK 300
           KLHAEQLSN+GGS +AA+LGAKSVDHIEYLDE GVKALSESGTCA LLPGAFYFLRETQ 
Sbjct: 241 KLHAEQLSNLGGSAMAAKLGAKSVDHIEYLDEVGVKALSESGTCATLLPGAFYFLRETQM 300

Query: 301 PPIDLLRQYGVPMVLASDFNPGSFPICSTLLMLNMGCTLFRLTPEEALAGLTLNAAKALG 360
           PPIDLLRQY VPMVLASD+NPGS P+CS+LLMLNMGCTLFRLTPEEALAG+T NAAKALG
Sbjct: 301 PPIDLLRQYEVPMVLASDYNPGSSPLCSSLLMLNMGCTLFRLTPEEALAGMTRNAAKALG 360

Query: 361 IEDKVGSLVVGKQADFCLWNIATPAQLAYSYGVNPCKDVVKNGKLVHQ 408
           +ED VG L  G QADFCLW+I TPA LAYSYGV+ CK+VVKNGKLVHQ
Sbjct: 361 VEDSVGVLKPGMQADFCLWDITTPAALAYSYGVDVCKEVVKNGKLVHQ 408


Lambda     K      H
   0.319    0.136    0.402 

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: 659
Number of extensions: 13
Number of successful extensions: 1
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: 408
Length of database: 408
Length adjustment: 31
Effective length of query: 377
Effective length of database: 377
Effective search space:   142129
Effective search space used:   142129
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate 5211347 Shew_3759 (imidazolonepropionase (RefSeq))
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.3276.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   9.1e-150  484.6   0.0     1e-149  484.4   0.0    1.0  1  lcl|FitnessBrowser__PV4:5211347  Shew_3759 imidazolonepropionase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5211347  Shew_3759 imidazolonepropionase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  484.4   0.0    1e-149    1e-149       2     376 ..      27     404 ..      26     405 .. 0.98

  Alignments for each domain:
  == domain 1  score: 484.4 bits;  conditional E-value: 1e-149
                        TIGR01224   2 edaailveegkiaaigqkaalpgeeaak..iidleGklvvPGlvDpHtHlvfagdRvkefelklqGasYleilaeGgG 77 
                                       daai+v+egkia++g++++lp  + +   +   +G+  +PGl+D+HtHlvfag+R++efel+lqGasY+ei+++GgG
  lcl|FitnessBrowser__PV4:5211347  27 TDAAIAVKEGKIAWMGPRSELPEFDVLStpVYRGKGGWLTPGLIDAHTHLVFAGNRANEFELRLQGASYEEIARAGGG 104
                                      689*******************9975551156667899**************************************** PP

                        TIGR01224  78 ilstvratraAseeellkeaeerlkkllrsGtttlEvKsGYGLdleaElkmLrvikalkeelpvdvvttflgaHavPk 155
                                      i+stv+a r+Ase+el++  ++rl+ l ++G+tt+E+KsGYGLd+e+Elk+Lrv+++l ++++vdv+ttflgaHa+P+
  lcl|FitnessBrowser__PV4:5211347 105 IISTVKACREASEAELFELGRQRLNALAKEGVTTVEIKSGYGLDTETELKLLRVARELGKHHHVDVKTTFLGAHAIPP 182
                                      ****************************************************************************** PP

                        TIGR01224 156 evqededeyvdaileelipkvaeeklaeavDvFcekgvFsveqsrrilkaaqeaGlavklHaeelkalggaelaaklg 233
                                      e+++++d+yvd +++e++ +v +e+la+avDvFce+ +Fs eq++r+l+ a++aGl +klHae+l++lgg+++aaklg
  lcl|FitnessBrowser__PV4:5211347 183 EYKDNSDAYVDLVIDEMLTAVINENLADAVDVFCENIAFSLEQTERVLSTAKAAGLDIKLHAEQLSNLGGSAMAAKLG 260
                                      ****************************************************************************** PP

                        TIGR01224 234 avsadHleeasdedikalaeagtvavlLPgtaflLr.eaapparklidekvivalatDlnPgsspllslqlilslavt 310
                                      a s+dH+e++++ ++kal e+gt a+lLPg++++Lr +++pp++ l++++v++ la+D nPgsspl s  l+l++++t
  lcl|FitnessBrowser__PV4:5211347 261 AKSVDHIEYLDEVGVKALSESGTCATLLPGAFYFLReTQMPPIDLLRQYEVPMVLASDYNPGSSPLCSSLLMLNMGCT 338
                                      ************************************999*************************************** PP

                        TIGR01224 311 llkltaeealaaatvnaAqalglgeekGtleeGkdadlvvlsaesyeeiaYrlgvnvveaviknGe 376
                                      l++lt+eeala++t naA+alg++++ G l+ G +ad+ +++++ ++ +aY +gv+v ++v+knG+
  lcl|FitnessBrowser__PV4:5211347 339 LFRLTPEEALAGMTRNAAKALGVEDSVGVLKPGMQADFCLWDITTPAALAYSYGVDVCKEVVKNGK 404
                                      *****************************************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (377 nodes)
Target sequences:                          1  (408 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: 00:00:00.01
# Mc/sec: 12.11
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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