Alignments for a candidate for hutI in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutI in Paraburkholderia bryophila 376MFSha3.1

Align Imidazolonepropionase (EC 3.5.2.7) (characterized)
to candidate H281DRAFT_04869 H281DRAFT_04869 imidazolonepropionase

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



>FitnessBrowser__Burk376:H281DRAFT_04869
          Length = 409

 Score =  582 bits (1499), Expect = e-171
 Identities = 296/401 (73%), Positives = 328/401 (81%), Gaps = 1/401 (0%)

Query: 14  VWHRCHLLPDGDPAKAIRDAALVVQQGRIVWLGMQAELPQAYAALPRHDAGSAWITPGLV 73
           VWH+ +L P GDP   +RDAA+ V+ G IVWLG  A LP  YA  PR +   AW+TPGLV
Sbjct: 5   VWHQLNLCPQGDPEHTLRDAAIAVENGNIVWLGAAAGLPAEYADWPRENLHGAWVTPGLV 64

Query: 74  DCHTHLVYGGQRADEFAMRLAGAGYEEIARAGGGIVSTVRATRAADEDTLFALAAARLAP 133
           DCHTHLVYGGQRADEFA RLAG  YEEIAR GGGIVSTVRATRAA ED LF  +AARL P
Sbjct: 65  DCHTHLVYGGQRADEFAQRLAGVSYEEIARQGGGIVSTVRATRAATEDELFRQSAARLEP 124

Query: 134 LLAEGVTTLEIKSGYGLDLASERKQLRVARRLGDAFGVTVHTTFLGAHALPPEYAGRADD 193
           LLAEGVT +EIKSGYGLDL SERK LRVAR+LG+ + VTV+TTFLGAHALPPE+AGRAD 
Sbjct: 125 LLAEGVTAVEIKSGYGLDLDSERKMLRVARQLGERYPVTVYTTFLGAHALPPEFAGRADA 184

Query: 194 YITLVCETMMPVLADEGLIDAVDAFCESVGFSLAQTERVFQAAERHGLRVKLHAEQLSNL 253
           YI  VC TM+P LADEGL+DAVD FCE +GFSL Q+ERVF AA R+ L VK+HAEQLSN 
Sbjct: 185 YIDEVCNTMLPALADEGLVDAVDVFCERIGFSLEQSERVFNAAARYKLPVKMHAEQLSNG 244

Query: 254 GGTALAARYRALSADHLEHLDEAGVVAMAGSGTVAVLLPGAYYFLRDTNLPPIDLLRRHG 313
           GGTALAAR+RALSADHLE LDEAGV AM  +GTVAVLLPGAYYF+R+T LPP+DLLRR+ 
Sbjct: 245 GGTALAARHRALSADHLEFLDEAGVAAMNEAGTVAVLLPGAYYFIRETQLPPLDLLRRYE 304

Query: 314 VPMAISTDHNPGTSPVTSLLLMMNMACTLFRLTVPEVLAGVTTHAARALGAADRHGLLAA 373
           VP+AISTD NPGTSP TSLLLMMNMA TLFR+TVPEVL GVT+HAARALG ADRHG L  
Sbjct: 305 VPIAISTDSNPGTSPTTSLLLMMNMASTLFRMTVPEVLKGVTSHAARALGKADRHGSLEV 364

Query: 374 GRAADFVLWNVDSPAELAYWFGRNPAAAVVRQGK-VYPAAT 413
           GRAADF +W VDS AELAYW GR   A VVR G+ VY  +T
Sbjct: 365 GRAADFAVWAVDSLAELAYWIGRPLCARVVRAGETVYRPST 405


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: 599
Number of extensions: 20
Number of successful extensions: 2
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: 409
Length adjustment: 31
Effective length of query: 389
Effective length of database: 378
Effective search space:   147042
Effective search space used:   147042
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 H281DRAFT_04869 H281DRAFT_04869 (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.8510.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   4.1e-146  472.6   0.0   4.7e-146  472.4   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_04869  H281DRAFT_04869 imidazolonepropi


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_04869  H281DRAFT_04869 imidazolonepropionase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  472.4   0.0  4.7e-146  4.7e-146       3     376 ..      23     398 ..      21     399 .. 0.98

  Alignments for each domain:
  == domain 1  score: 472.4 bits;  conditional E-value: 4.7e-146
                                    TIGR01224   3 daailveegkiaaigqkaalpge.eaakiidleGklvvPGlvDpHtHlvfagdRvkefelklqGas 67 
                                                  daai+ve+g+i+++g  a lp+e  +    +l+G  v+PGlvD+HtHlv++g+R++ef+++l+G+s
  lcl|FitnessBrowser__Burk376:H281DRAFT_04869  23 DAAIAVENGNIVWLGAAAGLPAEyADWPRENLHGAWVTPGLVDCHTHLVYGGQRADEFAQRLAGVS 88 
                                                  89*******************98445567889********************************** PP

                                    TIGR01224  68 YleilaeGgGilstvratraAseeellkeaeerlkkllrsGtttlEvKsGYGLdleaElkmLrvik 133
                                                  Y+ei+++GgGi+stvratraA e+el+++  +rl+ ll++G+t++E+KsGYGLdl++E kmLrv++
  lcl|FitnessBrowser__Burk376:H281DRAFT_04869  89 YEEIARQGGGIVSTVRATRAATEDELFRQSAARLEPLLAEGVTAVEIKSGYGLDLDSERKMLRVAR 154
                                                  ****************************************************************** PP

                                    TIGR01224 134 alkeelpvdvvttflgaHavPkevqededeyvdaileelipkvaeeklaeavDvFcekgvFsveqs 199
                                                  +l e+ pv v ttflgaHa+P+e+ ++ d+y+d+++++++p+ a+e l++avDvFce+ +Fs eqs
  lcl|FitnessBrowser__Burk376:H281DRAFT_04869 155 QLGERYPVTVYTTFLGAHALPPEFAGRADAYIDEVCNTMLPALADEGLVDAVDVFCERIGFSLEQS 220
                                                  ****************************************************************** PP

                                    TIGR01224 200 rrilkaaqeaGlavklHaeelkalggaelaaklgavsadHleeasdedikalaeagtvavlLPgta 265
                                                  +r+++aa+   l+vk+Hae+l++ gg++laa+ +a+sadHle +++++++a+ eagtvavlLPg++
  lcl|FitnessBrowser__Burk376:H281DRAFT_04869 221 ERVFNAAARYKLPVKMHAEQLSNGGGTALAARHRALSADHLEFLDEAGVAAMNEAGTVAVLLPGAY 286
                                                  ****************************************************************** PP

                                    TIGR01224 266 flLr.eaapparklidekvivalatDlnPgsspllslqlilslavtllkltaeealaaatvnaAqa 330
                                                  +++r ++ pp + l+ ++v++a++tD nPg+sp++sl l++++a tl+++t +e+l+++t +aA a
  lcl|FitnessBrowser__Burk376:H281DRAFT_04869 287 YFIReTQLPPLDLLRRYEVPIAISTDSNPGTSPTTSLLLMMNMASTLFRMTVPEVLKGVTSHAARA 352
                                                  ****8999********************************************************** PP

                                    TIGR01224 331 lglgeekGtleeGkdadlvvlsaesyeeiaYrlgvnvveaviknGe 376
                                                  lg+++++G+le G+ ad++v+ ++s +e+aY++g    + v+ +Ge
  lcl|FitnessBrowser__Burk376:H281DRAFT_04869 353 LGKADRHGSLEVGRAADFAVWAVDSLAELAYWIGRPLCARVVRAGE 398
                                                  *****************************************99997 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.71
//
[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