Alignments for a candidate for hutI in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutI in Cupriavidus basilensis 4G11

Align Imidazolonepropionase (EC 3.5.2.7) (characterized)
to candidate RR42_RS16905 RR42_RS16905 imidazolonepropionase

Query= reanno::Cup4G11:RR42_RS16905
         (420 letters)



>FitnessBrowser__Cup4G11:RR42_RS16905
          Length = 420

 Score =  833 bits (2153), Expect = 0.0
 Identities = 420/420 (100%), Positives = 420/420 (100%)

Query: 1   MSSSTESAKSADGVWHRCHLLPDGDPAKAIRDAALVVQQGRIVWLGMQAELPQAYAALPR 60
           MSSSTESAKSADGVWHRCHLLPDGDPAKAIRDAALVVQQGRIVWLGMQAELPQAYAALPR
Sbjct: 1   MSSSTESAKSADGVWHRCHLLPDGDPAKAIRDAALVVQQGRIVWLGMQAELPQAYAALPR 60

Query: 61  HDAGSAWITPGLVDCHTHLVYGGQRADEFAMRLAGAGYEEIARAGGGIVSTVRATRAADE 120
           HDAGSAWITPGLVDCHTHLVYGGQRADEFAMRLAGAGYEEIARAGGGIVSTVRATRAADE
Sbjct: 61  HDAGSAWITPGLVDCHTHLVYGGQRADEFAMRLAGAGYEEIARAGGGIVSTVRATRAADE 120

Query: 121 DTLFALAAARLAPLLAEGVTTLEIKSGYGLDLASERKQLRVARRLGDAFGVTVHTTFLGA 180
           DTLFALAAARLAPLLAEGVTTLEIKSGYGLDLASERKQLRVARRLGDAFGVTVHTTFLGA
Sbjct: 121 DTLFALAAARLAPLLAEGVTTLEIKSGYGLDLASERKQLRVARRLGDAFGVTVHTTFLGA 180

Query: 181 HALPPEYAGRADDYITLVCETMMPVLADEGLIDAVDAFCESVGFSLAQTERVFQAAERHG 240
           HALPPEYAGRADDYITLVCETMMPVLADEGLIDAVDAFCESVGFSLAQTERVFQAAERHG
Sbjct: 181 HALPPEYAGRADDYITLVCETMMPVLADEGLIDAVDAFCESVGFSLAQTERVFQAAERHG 240

Query: 241 LRVKLHAEQLSNLGGTALAARYRALSADHLEHLDEAGVVAMAGSGTVAVLLPGAYYFLRD 300
           LRVKLHAEQLSNLGGTALAARYRALSADHLEHLDEAGVVAMAGSGTVAVLLPGAYYFLRD
Sbjct: 241 LRVKLHAEQLSNLGGTALAARYRALSADHLEHLDEAGVVAMAGSGTVAVLLPGAYYFLRD 300

Query: 301 TNLPPIDLLRRHGVPMAISTDHNPGTSPVTSLLLMMNMACTLFRLTVPEVLAGVTTHAAR 360
           TNLPPIDLLRRHGVPMAISTDHNPGTSPVTSLLLMMNMACTLFRLTVPEVLAGVTTHAAR
Sbjct: 301 TNLPPIDLLRRHGVPMAISTDHNPGTSPVTSLLLMMNMACTLFRLTVPEVLAGVTTHAAR 360

Query: 361 ALGAADRHGLLAAGRAADFVLWNVDSPAELAYWFGRNPAAAVVRQGKVYPAATSVQGVRP 420
           ALGAADRHGLLAAGRAADFVLWNVDSPAELAYWFGRNPAAAVVRQGKVYPAATSVQGVRP
Sbjct: 361 ALGAADRHGLLAAGRAADFVLWNVDSPAELAYWFGRNPAAAVVRQGKVYPAATSVQGVRP 420


Lambda     K      H
   0.321    0.134    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: 795
Number of extensions: 23
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: 420
Length of database: 420
Length adjustment: 32
Effective length of query: 388
Effective length of database: 388
Effective search space:   150544
Effective search space used:   150544
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 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate RR42_RS16905 RR42_RS16905 (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.5431.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.8e-150  484.6   0.1     1e-149  484.4   0.1    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS16905  RR42_RS16905 imidazolonepropiona


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS16905  RR42_RS16905 imidazolonepropionase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  484.4   0.1    1e-149    1e-149       2     377 .]      31     408 ..      30     408 .. 0.99

  Alignments for each domain:
  == domain 1  score: 484.4 bits;  conditional E-value: 1e-149
                                 TIGR01224   2 edaailveegkiaaigqkaalpge.eaakiidleGklvvPGlvDpHtHlvfagdRvkefelklqGasYl 69 
                                                daa++v++g+i+++g +a+lp    a+  +d++   ++PGlvD+HtHlv++g+R++ef+++l+Ga Y+
  lcl|FitnessBrowser__Cup4G11:RR42_RS16905  31 RDAALVVQQGRIVWLGMQAELPQAyAALPRHDAGSAWITPGLVDCHTHLVYGGQRADEFAMRLAGAGYE 99 
                                               6899****************997647888999999********************************** PP

                                 TIGR01224  70 eilaeGgGilstvratraAseeellkeaeerlkkllrsGtttlEvKsGYGLdleaElkmLrvikalkee 138
                                               ei+++GgGi+stvratraA+e+ l++ a +rl+ ll++G+ttlE+KsGYGLdl +E k+Lrv+++l + 
  lcl|FitnessBrowser__Cup4G11:RR42_RS16905 100 EIARAGGGIVSTVRATRAADEDTLFALAAARLAPLLAEGVTTLEIKSGYGLDLASERKQLRVARRLGDA 168
                                               ********************************************************************* PP

                                 TIGR01224 139 lpvdvvttflgaHavPkevqededeyvdaileelipkvaeeklaeavDvFcekgvFsveqsrrilkaaq 207
                                               + v v ttflgaHa+P+e+ ++ d+y++ ++e+++p  a+e l++avD+Fce+ +Fs +q++r+++aa+
  lcl|FitnessBrowser__Cup4G11:RR42_RS16905 169 FGVTVHTTFLGAHALPPEYAGRADDYITLVCETMMPVLADEGLIDAVDAFCESVGFSLAQTERVFQAAE 237
                                               ********************************************************************* PP

                                 TIGR01224 208 eaGlavklHaeelkalggaelaaklgavsadHleeasdedikalaeagtvavlLPgtaflLr.eaappa 275
                                                +Gl+vklHae+l++lgg++laa+ +a+sadHle+++++++ a+a +gtvavlLPg++++Lr ++ pp+
  lcl|FitnessBrowser__Cup4G11:RR42_RS16905 238 RHGLRVKLHAEQLSNLGGTALAARYRALSADHLEHLDEAGVVAMAGSGTVAVLLPGAYYFLRdTNLPPI 306
                                               **************************************************************999**** PP

                                 TIGR01224 276 rklidekvivalatDlnPgsspllslqlilslavtllkltaeealaaatvnaAqalglgeekGtleeGk 344
                                               + l+ ++v++a++tD nPg+sp++sl l++++a+tl++lt +e+la++t +aA alg ++++G l++G+
  lcl|FitnessBrowser__Cup4G11:RR42_RS16905 307 DLLRRHGVPMAISTDHNPGTSPVTSLLLMMNMACTLFRLTVPEVLAGVTTHAARALGAADRHGLLAAGR 375
                                               ********************************************************************* PP

                                 TIGR01224 345 dadlvvlsaesyeeiaYrlgvnvveaviknGev 377
                                                ad+v+++++s++e+aY++g n  +av+ +G+v
  lcl|FitnessBrowser__Cup4G11:RR42_RS16905 376 AADFVLWNVDSPAELAYWFGRNPAAAVVRQGKV 408
                                               ******************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (377 nodes)
Target sequences:                          1  (420 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: 9.89
//
[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
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