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.28797.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: 12.06
//
[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:

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:

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:

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:

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