Alignments for a candidate for hutI in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutI in Stenotrophomonas chelatiphaga DSM 21508

Align Imidazolonepropionase (EC 3.5.2.7) (characterized)
to candidate WP_057506767.1 ABB28_RS00625 imidazolonepropionase

Query= reanno::Korea:Ga0059261_3964
         (395 letters)



>NCBI__GCF_001431535.1:WP_057506767.1
          Length = 401

 Score =  460 bits (1184), Expect = e-134
 Identities = 245/395 (62%), Positives = 286/395 (72%), Gaps = 8/395 (2%)

Query: 6   DTLWRNARLATMTGDGLGIVEQGAIAATGGTISYIGPDSDAPDA--AEIVDCQGRWITPG 63
           DTLW N  L T+ GDGLG++    +A+  G I ++G          A  +D +GRWI+PG
Sbjct: 4   DTLWTNVHLMTLQGDGLGVIADAELASLDGRIVHVGAAGSGAQLQPATRIDGEGRWISPG 63

Query: 64  LVDCHTHLVHAGNRAREFEARLEGATYEEIARAGGGILSTVTATRAASEDELIASALPRL 123
           L+DCHTHLV+AGNRA EFE RL+G +Y +IARAGGGI+STV ATRAAS  EL+  + PRL
Sbjct: 64  LIDCHTHLVYAGNRANEFEQRLQGVSYADIARAGGGIVSTVRATRAASHAELVRQSRPRL 123

Query: 124 DQLIAEGVTTVEIKSGYGLTLDDELKMLRAARSLGEARNVHIRTTLLAAHAVPPEYKGDA 183
             + AEG+TT+EIKSGYGL LDDE K L+ AR LG   NVH+  T L AHAVPP  +  A
Sbjct: 124 LAMRAEGITTLEIKSGYGLALDDERKQLQVARQLGVDCNVHVVPTFLGAHAVPPGRQ--A 181

Query: 184 DGYVDLVCETIIPA--AIGHADAVDAFCEGIGFSPEQTDRVLAAAVAHGLPVKLHAEQLS 241
             Y+D VC+ +IPA  A G A+AVD FCE I FS  Q  +V  AA AHGL VK+HAEQLS
Sbjct: 182 QEYIDEVCKLMIPAIAAEGLAEAVDIFCEDIAFSTAQAAQVFEAARAHGLAVKIHAEQLS 241

Query: 242 NLHGAALAAHHNALSADHLEHLDEAGIAAMAASGTVATLLPGAFYFTREEHRPPIAALRA 301
           N HGA LAA H ALSADH+EHLD AGIAAMAA+GTVA LLPGAFYFTR+   PPI ALRA
Sbjct: 242 NQHGAELAARHGALSADHIEHLDAAGIAAMAAAGTVAVLLPGAFYFTRDTTLPPIEALRA 301

Query: 302 AGVPIALATDCNPGTSPMASILLAANMGATFFRLTVTECLRGITVNGARALGL--RTGTL 359
           AGVP+ALATD NPGTSP+ S LLA NMGAT FRLTV EC+ G T N ARALG   R G L
Sbjct: 302 AGVPLALATDSNPGTSPLTSPLLAMNMGATLFRLTVDECIAGFTRNAARALGRADRIGQL 361

Query: 360 EPGGPADLAIWNVTDLAELVYRIGANPLHSRIYAG 394
             G  ADLAIW++   A+LVYRIG NPLH+R+  G
Sbjct: 362 AVGMDADLAIWDIDAPADLVYRIGFNPLHARVVRG 396


Lambda     K      H
   0.318    0.134    0.396 

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: 510
Number of extensions: 26
Number of successful extensions: 5
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: 395
Length of database: 401
Length adjustment: 31
Effective length of query: 364
Effective length of database: 370
Effective search space:   134680
Effective search space used:   134680
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 WP_057506767.1 ABB28_RS00625 (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.3784.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-139  449.6   1.0   4.3e-139  449.5   1.0    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057506767.1  ABB28_RS00625 imidazolonepropion


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057506767.1  ABB28_RS00625 imidazolonepropionase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  449.5   1.0  4.3e-139  4.3e-139       4     376 ..      26     397 ..      23     398 .. 0.98

  Alignments for each domain:
  == domain 1  score: 449.5 bits;  conditional E-value: 4.3e-139
                                 TIGR01224   4 aailveegkiaaigqkaalpgeeaakiidleGklvvPGlvDpHtHlvfagdRvkefelklqGasYleil 72 
                                               a ++  +g+i+++g     +  + a+ id eG+ + PGl+D+HtHlv+ag+R++efe++lqG+sY++i+
  lcl|NCBI__GCF_001431535.1:WP_057506767.1  26 AELASLDGRIVHVGAAGSGAQLQPATRIDGEGRWISPGLIDCHTHLVYAGNRANEFEQRLQGVSYADIA 94 
                                               55666789*******998888899********************************************* PP

                                 TIGR01224  73 aeGgGilstvratraAseeellkeaeerlkkllrsGtttlEvKsGYGLdleaElkmLrvikalkeelpv 141
                                               ++GgGi+stvratraAs++el+++ ++rl  ++++G+ttlE+KsGYGL l++E k+L+v+++l  + +v
  lcl|NCBI__GCF_001431535.1:WP_057506767.1  95 RAGGGIVSTVRATRAASHAELVRQSRPRLLAMRAEGITTLEIKSGYGLALDDERKQLQVARQLGVDCNV 163
                                               ********************************************************************* PP

                                 TIGR01224 142 dvvttflgaHavPkevqededeyvdaileelipkvaeeklaeavDvFcekgvFsveqsrrilkaaqeaG 210
                                               +vv+tflgaHavP++ q++  ey+d++++ +ip++a e laeavD+Fce  +Fs +q+ ++++aa+++G
  lcl|NCBI__GCF_001431535.1:WP_057506767.1 164 HVVPTFLGAHAVPPGRQAQ--EYIDEVCKLMIPAIAAEGLAEAVDIFCEDIAFSTAQAAQVFEAARAHG 230
                                               ***************7777..************************************************ PP

                                 TIGR01224 211 lavklHaeelkalggaelaaklgavsadHleeasdedikalaeagtvavlLPgtaflLr.eaapparkl 278
                                               lavk+Hae+l++  gaelaa+ ga+sadH+e++++++i+a+a+agtvavlLPg++++ r ++ pp+++l
  lcl|NCBI__GCF_001431535.1:WP_057506767.1 231 LAVKIHAEQLSNQHGAELAARHGALSADHIEHLDAAGIAAMAAAGTVAVLLPGAFYFTRdTTLPPIEAL 299
                                               *********************************************************9999******** PP

                                 TIGR01224 279 idekvivalatDlnPgsspllslqlilslavtllkltaeealaaatvnaAqalglgeekGtleeGkdad 347
                                               ++++v++alatD nPg+spl+s  l++++++tl++lt +e +a+ t naA alg++++ G+l+ G dad
  lcl|NCBI__GCF_001431535.1:WP_057506767.1 300 RAAGVPLALATDSNPGTSPLTSPLLAMNMGATLFRLTVDECIAGFTRNAARALGRADRIGQLAVGMDAD 368
                                               ********************************************************************* PP

                                 TIGR01224 348 lvvlsaesyeeiaYrlgvnvveaviknGe 376
                                               l++++++ ++++ Yr+g n ++a++++G+
  lcl|NCBI__GCF_001431535.1:WP_057506767.1 369 LAIWDIDAPADLVYRIGFNPLHARVVRGQ 397
                                               **************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (377 nodes)
Target sequences:                          1  (401 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.58
//
[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 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