Alignments for a candidate for hutI in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutI in Acidovorax sp. GW101-3H11

Align Imidazolonepropionase (EC 3.5.2.7) (characterized)
to candidate Ac3H11_2550 Imidazolonepropionase (EC 3.5.2.7)

Query= reanno::acidovorax_3H11:Ac3H11_2550
         (429 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2550
          Length = 429

 Score =  860 bits (2223), Expect = 0.0
 Identities = 429/429 (100%), Positives = 429/429 (100%)

Query: 1   VGRQMQHMDNHGHPSGSAASQNADGVWHNLQPAPGLWVADVAVPEGQPACVVVQQGQMAW 60
           VGRQMQHMDNHGHPSGSAASQNADGVWHNLQPAPGLWVADVAVPEGQPACVVVQQGQMAW
Sbjct: 1   VGRQMQHMDNHGHPSGSAASQNADGVWHNLQPAPGLWVADVAVPEGQPACVVVQQGQMAW 60

Query: 61  VGPEAQLPAAYKALSRHDARGALATPGLVDCHTHLVYGGQRANEFAMRLAGATYEEVAQA 120
           VGPEAQLPAAYKALSRHDARGALATPGLVDCHTHLVYGGQRANEFAMRLAGATYEEVAQA
Sbjct: 61  VGPEAQLPAAYKALSRHDARGALATPGLVDCHTHLVYGGQRANEFAMRLAGATYEEVAQA 120

Query: 121 GGGIVSSVKATRAASEDELFAQAAPRLQALLDEGVCAIEIKSGYGLALEHERKQLRVARR 180
           GGGIVSSVKATRAASEDELFAQAAPRLQALLDEGVCAIEIKSGYGLALEHERKQLRVARR
Sbjct: 121 GGGIVSSVKATRAASEDELFAQAAPRLQALLDEGVCAIEIKSGYGLALEHERKQLRVARR 180

Query: 181 LGEVFGVTVRTTFLGAHALPSEYAGRSGDYTDLVCNEMLPALAAEGLVDAVDVFCERIAF 240
           LGEVFGVTVRTTFLGAHALPSEYAGRSGDYTDLVCNEMLPALAAEGLVDAVDVFCERIAF
Sbjct: 181 LGEVFGVTVRTTFLGAHALPSEYAGRSGDYTDLVCNEMLPALAAEGLVDAVDVFCERIAF 240

Query: 241 TLAETEQVFQAAQKLGIPVKLHAEQLSDMGGSALAARYGALSCDHIEHLSADGIAAMKAA 300
           TLAETEQVFQAAQKLGIPVKLHAEQLSDMGGSALAARYGALSCDHIEHLSADGIAAMKAA
Sbjct: 241 TLAETEQVFQAAQKLGIPVKLHAEQLSDMGGSALAARYGALSCDHIEHLSADGIAAMKAA 300

Query: 301 GTVAVLLPGAYYTLRDTHLPPIAQLREAGVPMAVSTDHNPGTSPALSLLLMANMACTLFR 360
           GTVAVLLPGAYYTLRDTHLPPIAQLREAGVPMAVSTDHNPGTSPALSLLLMANMACTLFR
Sbjct: 301 GTVAVLLPGAYYTLRDTHLPPIAQLREAGVPMAVSTDHNPGTSPALSLLLMANMACTLFR 360

Query: 361 LTVPEALAGITTHAARALGLQDSHGLIASGRPANFVLWPVGEAAELAYWFGQKPACTIVR 420
           LTVPEALAGITTHAARALGLQDSHGLIASGRPANFVLWPVGEAAELAYWFGQKPACTIVR
Sbjct: 361 LTVPEALAGITTHAARALGLQDSHGLIASGRPANFVLWPVGEAAELAYWFGQKPACTIVR 420

Query: 421 QGCIHGVMP 429
           QGCIHGVMP
Sbjct: 421 QGCIHGVMP 429


Lambda     K      H
   0.319    0.133    0.403 

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: 857
Number of extensions: 19
Number of successful extensions: 3
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: 429
Length of database: 429
Length adjustment: 32
Effective length of query: 397
Effective length of database: 397
Effective search space:   157609
Effective search space used:   157609
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: 51 (24.3 bits)

Align candidate Ac3H11_2550 (Imidazolonepropionase (EC 3.5.2.7))
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.30358.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-144  464.8   0.2   1.1e-143  464.6   0.2    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2550  Imidazolonepropionase (EC 3.5.2.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2550  Imidazolonepropionase (EC 3.5.2.7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  464.6   0.2  1.1e-143  1.1e-143       4     375 ..      49     422 ..      46     424 .. 0.98

  Alignments for each domain:
  == domain 1  score: 464.6 bits;  conditional E-value: 1.1e-143
                                        TIGR01224   4 aailveegkiaaigqkaalpge.eaakiidleGklvvPGlvDpHtHlvfagdRvkefelklq 64 
                                                      a ++v++g++a++g++a+lp+  +a+  +d+ G l++PGlvD+HtHlv++g+R++ef+++l+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2550  49 ACVVVQQGQMAWVGPEAQLPAAyKALSRHDARGALATPGLVDCHTHLVYGGQRANEFAMRLA 110
                                                      6899***************986599************************************* PP

                                        TIGR01224  65 GasYleilaeGgGilstvratraAseeellkeaeerlkkllrsGtttlEvKsGYGLdleaEl 126
                                                      Ga+Y+e++++GgGi+s v+atraAse+el+++a +rl+ ll +G+ ++E+KsGYGL le E 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2550 111 GATYEEVAQAGGGIVSSVKATRAASEDELFAQAAPRLQALLDEGVCAIEIKSGYGLALEHER 172
                                                      ************************************************************** PP

                                        TIGR01224 127 kmLrvikalkeelpvdvvttflgaHavPkevqededeyvdaileelipkvaeeklaeavDvF 188
                                                      k+Lrv+++l e + v v ttflgaHa+P e+ +++ +y+d +++e++p+ a e l++avDvF
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2550 173 KQLRVARRLGEVFGVTVRTTFLGAHALPSEYAGRSGDYTDLVCNEMLPALAAEGLVDAVDVF 234
                                                      ************************************************************** PP

                                        TIGR01224 189 cekgvFsveqsrrilkaaqeaGlavklHaeelkalggaelaaklgavsadHleeasdedika 250
                                                      ce+ +F+ ++++++++aaq+ G++vklHae+l+ +gg++laa+ ga+s dH+e++s+++i+a
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2550 235 CERIAFTLAETEQVFQAAQKLGIPVKLHAEQLSDMGGSALAARYGALSCDHIEHLSADGIAA 296
                                                      ************************************************************** PP

                                        TIGR01224 251 laeagtvavlLPgtaflLr.eaapparklidekvivalatDlnPgsspllslqlilslavtl 311
                                                      +++agtvavlLPg++++Lr ++ pp+ +l++++v++a++tD nPg+sp lsl l+ ++a+tl
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2550 297 MKAAGTVAVLLPGAYYTLRdTHLPPIAQLREAGVPMAVSTDHNPGTSPALSLLLMANMACTL 358
                                                      *******************9999*************************************** PP

                                        TIGR01224 312 lkltaeealaaatvnaAqalglgeekGtleeGkdadlvvlsaesyeeiaYrlgvnvveavik 373
                                                      ++lt +eala++t +aA algl++++G +++G+ a++v++ + + +e+aY++g +   +++ 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2550 359 FRLTVPEALAGITTHAARALGLQDSHGLIASGRPANFVLWPVGEAAELAYWFGQKPACTIVR 420
                                                      *****************************************************987777777 PP

                                        TIGR01224 374 nG 375
                                                      +G
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2550 421 QG 422
                                                      66 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (377 nodes)
Target sequences:                          1  (429 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: 7.62
//
[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