Alignments for a candidate for hutI in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutI in Burkholderia phytofirmans PsJN

Align Imidazolonepropionase (EC 3.5.2.7) (characterized)
to candidate BPHYT_RS07575 BPHYT_RS07575 imidazolonepropionase

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



>FitnessBrowser__BFirm:BPHYT_RS07575
          Length = 407

 Score =  589 bits (1518), Expect = e-173
 Identities = 296/394 (75%), Positives = 328/394 (83%)

Query: 14  VWHRCHLLPDGDPAKAIRDAALVVQQGRIVWLGMQAELPQAYAALPRHDAGSAWITPGLV 73
           VWH   L P GDP   + DAA+ V+ G IVWLG  + LP  YAA PR D   AW+TPGLV
Sbjct: 5   VWHHLKLCPQGDPQNTLPDAAIAVENGTIVWLGAASSLPADYAAWPREDLHGAWVTPGLV 64

Query: 74  DCHTHLVYGGQRADEFAMRLAGAGYEEIARAGGGIVSTVRATRAADEDTLFALAAARLAP 133
           DCHTHLVYGGQRADEFA RLAG  YEEIAR GGGIVSTVRATRAADE +LF  +AARL P
Sbjct: 65  DCHTHLVYGGQRADEFAQRLAGVSYEEIARQGGGIVSTVRATRAADEASLFRQSAARLEP 124

Query: 134 LLAEGVTTLEIKSGYGLDLASERKQLRVARRLGDAFGVTVHTTFLGAHALPPEYAGRADD 193
           LLAEGVTT+EIKSGYGLDLASERK LRVAR+LG+ + VTV+TTFLGAHALPPE+AGRAD 
Sbjct: 125 LLAEGVTTVEIKSGYGLDLASERKMLRVARQLGERYPVTVYTTFLGAHALPPEFAGRADA 184

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

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

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

Query: 374 GRAADFVLWNVDSPAELAYWFGRNPAAAVVRQGK 407
           GRAADF +W+VDS AELAYW GR   A VVR G+
Sbjct: 365 GRAADFAVWSVDSLAELAYWIGRPLCARVVRAGE 398


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: 628
Number of extensions: 25
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: 407
Length adjustment: 31
Effective length of query: 389
Effective length of database: 376
Effective search space:   146264
Effective search space used:   146264
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 BPHYT_RS07575 BPHYT_RS07575 (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.12019.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   2.6e-148  479.8   0.0     3e-148  479.6   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS07575  BPHYT_RS07575 imidazolonepropion


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS07575  BPHYT_RS07575 imidazolonepropionase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  479.6   0.0    3e-148    3e-148       3     376 ..      23     398 ..      21     399 .. 0.98

  Alignments for each domain:
  == domain 1  score: 479.6 bits;  conditional E-value: 3e-148
                                TIGR01224   3 daailveegkiaaigqkaalpge.eaakiidleGklvvPGlvDpHtHlvfagdRvkefelklqGasYlei 71 
                                              daai+ve+g i+++g  + lp+   a    dl+G  v+PGlvD+HtHlv++g+R++ef+++l+G+sY+ei
  lcl|FitnessBrowser__BFirm:BPHYT_RS07575  23 DAAIAVENGTIVWLGAASSLPADyAAWPREDLHGAWVTPGLVDCHTHLVYGGQRADEFAQRLAGVSYEEI 92 
                                              89*******************974566789**************************************** PP

                                TIGR01224  72 laeGgGilstvratraAseeellkeaeerlkkllrsGtttlEvKsGYGLdleaElkmLrvikalkeelpv 141
                                              +++GgGi+stvratraA+e++l+++  +rl+ ll++G+tt+E+KsGYGLdl +E kmLrv+++l e+ pv
  lcl|FitnessBrowser__BFirm:BPHYT_RS07575  93 ARQGGGIVSTVRATRAADEASLFRQSAARLEPLLAEGVTTVEIKSGYGLDLASERKMLRVARQLGERYPV 162
                                              ********************************************************************** PP

                                TIGR01224 142 dvvttflgaHavPkevqededeyvdaileelipkvaeeklaeavDvFcekgvFsveqsrrilkaaqeaGl 211
                                               v ttflgaHa+P+e+ ++ d+y+d+++++++p+ a+e l++avDvFce+ +Fs eqs+r+++aa+   l
  lcl|FitnessBrowser__BFirm:BPHYT_RS07575 163 TVYTTFLGAHALPPEFAGRADAYIDEVCNTMLPALADEGLVDAVDVFCERIGFSLEQSERVFNAAERYKL 232
                                              ********************************************************************** PP

                                TIGR01224 212 avklHaeelkalggaelaaklgavsadHleeasdedikalaeagtvavlLPgtaflLr.eaapparklid 280
                                              +vk+Hae+l++ gg++laa+ +a+sadHle +++++++a++eagtvavlLPg+++++r ++ pp + l+ 
  lcl|FitnessBrowser__BFirm:BPHYT_RS07575 233 PVKMHAEQLSNGGGTALAARHRALSADHLEFLDEAGVAAMKEAGTVAVLLPGAYYFIReTQLPPLELLRR 302
                                              **********************************************************8999******** PP

                                TIGR01224 281 ekvivalatDlnPgsspllslqlilslavtllkltaeealaaatvnaAqalglgeekGtleeGkdadlvv 350
                                              ++v+va++tD nPg+sp +sl l++++a tl+++t +e+l+++t +aA alg+++++G+le+G+ ad++v
  lcl|FitnessBrowser__BFirm:BPHYT_RS07575 303 YQVPVAISTDSNPGTSPATSLLLMMNMATTLFRMTVPEVLQGVTSHAARALGKADRHGSLEAGRAADFAV 372
                                              ********************************************************************** PP

                                TIGR01224 351 lsaesyeeiaYrlgvnvveaviknGe 376
                                              +s++s +e+aY++g    + v+ +Ge
  lcl|FitnessBrowser__BFirm:BPHYT_RS07575 373 WSVDSLAELAYWIGRPLCARVVRAGE 398
                                              *********************99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (377 nodes)
Target sequences:                          1  (407 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: 11.68
//
[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