GapMind for catabolism of small carbon sources

 

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

Align Histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate H281DRAFT_04873 H281DRAFT_04873 histidine ammonia-lyase

Query= reanno::BFirm:BPHYT_RS07555
         (506 letters)



>FitnessBrowser__Burk376:H281DRAFT_04873
          Length = 507

 Score =  951 bits (2459), Expect = 0.0
 Identities = 491/506 (97%), Positives = 499/506 (98%)

Query: 1   MTLKPGYLTLPQLRQIAREHVALQLDPASHAAIDACAQAVADIAAKGEPAYGINTGFGRL 60
           MTLKPG+LTLPQLRQIAREHV L+LDPASHAAIDACA+AVADIAAKGEPAYGINTGFGRL
Sbjct: 2   MTLKPGHLTLPQLRQIAREHVPLRLDPASHAAIDACAKAVADIAAKGEPAYGINTGFGRL 61

Query: 61  ASTHIPHDQLELLQRNLVLSHAVGVGEPMSRPVVRLLIALKLSSLGRGHSGIRREVMEAL 120
           ASTHIPHDQLELLQRNLVLSHAVGVGEPMSRPVVRLLIALKLSSLGRGHSGIRREVMEAL
Sbjct: 62  ASTHIPHDQLELLQRNLVLSHAVGVGEPMSRPVVRLLIALKLSSLGRGHSGIRREVMEAL 121

Query: 121 ITLYNADVLPVIPVKGSVGASGDLAPLAHMSATLLGVGEVFAKGERMPATEGLALVGLKP 180
           ITLYNADVLPVIPVKGSVGASGDLAPLAHMSA LLGVGEVFAKGER+PATEGL+LVGLKP
Sbjct: 122 ITLYNADVLPVIPVKGSVGASGDLAPLAHMSAVLLGVGEVFAKGERLPATEGLSLVGLKP 181

Query: 181 LTLQAKEGLALLNGTQASTALALYNMFAIEDLYRTALVSGALSVDAAMGSVKPFDARIHE 240
           LTLQAKEGLALLNGTQASTALALYNMFAIEDLYRTALV+GALSVDAA GSVKPFDARIHE
Sbjct: 182 LTLQAKEGLALLNGTQASTALALYNMFAIEDLYRTALVAGALSVDAAAGSVKPFDARIHE 241

Query: 241 LRGHQGQIDAAGAYRSLLQGSGINVSHADCDKVQDPYSLRCQPQVMGACLDQMRHAANVL 300
           LRGHQGQIDAA AYRSLLQGSGINVSHADCDKVQDPYSLRCQPQVMGACLDQMRHAA+VL
Sbjct: 242 LRGHQGQIDAASAYRSLLQGSGINVSHADCDKVQDPYSLRCQPQVMGACLDQMRHAADVL 301

Query: 301 LLEANAVSDNPLIFPDTGEVLSGGNFHAEPVAFAADNLALAAAEIGALAERRIALLIDAT 360
           LLEANAVSDNPLIFPDTGEVLSGGNFHAEPVAFAADNLALAAAEIGALAERRIALLIDAT
Sbjct: 302 LLEANAVSDNPLIFPDTGEVLSGGNFHAEPVAFAADNLALAAAEIGALAERRIALLIDAT 361

Query: 361 LSGLPPFLVRDGGVNSGFMIAHVTAAALASENKTLAHPASVDSLPTSANQEDHVSMATFA 420
           LSGLPPFLVRDGGVNSGFMIAHVTAAALASENKTLAHPASVDSLPTSANQEDHVSMATFA
Sbjct: 362 LSGLPPFLVRDGGVNSGFMIAHVTAAALASENKTLAHPASVDSLPTSANQEDHVSMATFA 421

Query: 421 ARKLGDIAENTANILSIELLAAAQGVDLRAPHKTSPSLQKVMDAVRKDVAHYELDHYFAP 480
           ARKLGDIAENTANILSIELLAAAQGVDLRAPHKTSPSLQKVMD VRKDVAHYELDHYFAP
Sbjct: 422 ARKLGDIAENTANILSIELLAAAQGVDLRAPHKTSPSLQKVMDVVRKDVAHYELDHYFAP 481

Query: 481 DIAAVTRLVQDGTIAKLSPLSFASEQ 506
           DIAAVTRLVQ+GTIAKLSP SF SEQ
Sbjct: 482 DIAAVTRLVQNGTIAKLSPFSFVSEQ 507


Lambda     K      H
   0.318    0.133    0.374 

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: 941
Number of extensions: 30
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: 506
Length of database: 507
Length adjustment: 34
Effective length of query: 472
Effective length of database: 473
Effective search space:   223256
Effective search space used:   223256
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate H281DRAFT_04873 H281DRAFT_04873 (histidine ammonia-lyase)
to HMM TIGR01225 (hutH: histidine ammonia-lyase (EC 4.3.1.3))

# 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/TIGR01225.hmm
# target sequence database:        /tmp/gapView.13071.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01225  [M=506]
Accession:   TIGR01225
Description: hutH: histidine ammonia-lyase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
     1e-215  702.9   5.8   1.3e-215  702.6   5.8    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_04873  H281DRAFT_04873 histidine ammoni


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_04873  H281DRAFT_04873 histidine ammonia-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  702.6   5.8  1.3e-215  1.3e-215       1     497 [.       2     498 ..       2     504 .. 0.99

  Alignments for each domain:
  == domain 1  score: 702.6 bits;  conditional E-value: 1.3e-215
                                    TIGR01225   1 vvldgesltledleavarekarvelsaaaeeavaksravieeivaedktvYGvntGFGklasvkid 66 
                                                  ++l++++ltl +l+++are+ +++l+ a+++a+++ ++++++i+a+ ++ YG+ntGFG+las++i 
  lcl|FitnessBrowser__Burk376:H281DRAFT_04873   2 MTLKPGHLTLPQLRQIAREHVPLRLDPASHAAIDACAKAVADIAAKGEPAYGINTGFGRLASTHIP 67 
                                                  68999************************************************************* PP

                                    TIGR01225  67 kedlaeLqrnlvrsHaaGvGepleeevvRallvlrlnslakGysgvraevlellvallnaevlPvv 132
                                                  +++l+ Lqrnlv+sHa+GvGep+++ vvR+l++l+l sl +G+sg+r+ev+e+l+ l na+vlPv+
  lcl|FitnessBrowser__Burk376:H281DRAFT_04873  68 HDQLELLQRNLVLSHAVGVGEPMSRPVVRLLIALKLSSLGRGHSGIRREVMEALITLYNADVLPVI 133
                                                  ****************************************************************** PP

                                    TIGR01225 133 pekGsvGasGDLAPLahlalvliGeGeaefegevmdaaeaLaaaglePvtlkakEGlALinGtqlm 198
                                                  p kGsvGasGDLAPLah+++vl+G Ge++ +ge+++a+e L   gl+P+tl+akEGlAL+nGtq++
  lcl|FitnessBrowser__Burk376:H281DRAFT_04873 134 PVKGSVGASGDLAPLAHMSAVLLGVGEVFAKGERLPATEGLSLVGLKPLTLQAKEGLALLNGTQAS 199
                                                  ****************************************************************** PP

                                    TIGR01225 199 talavlalvdaekllesadiaaalsleallgtskafdpdihevrphrgqiavaarlrellagseia 264
                                                  tala+  ++ +e+l+++a +a+als++a+ g+ k+fd++ihe+r+h+gqi+ a++ r+ll+gs+i 
  lcl|FitnessBrowser__Burk376:H281DRAFT_04873 200 TALALYNMFAIEDLYRTALVAGALSVDAAAGSVKPFDARIHELRGHQGQIDAASAYRSLLQGSGIN 265
                                                  ****************************************************************** PP

                                    TIGR01225 265 eshkdedrvqDaYslRciPqvhGavldtldqvkevlaiElnsatDnPlvfadegevvsgGnFHgep 330
                                                   sh d+d+vqD+YslRc+Pqv+Ga+ld+++++++vl  E+n+++DnPl+f+d+gev sgGnFH+ep
  lcl|FitnessBrowser__Burk376:H281DRAFT_04873 266 VSHADCDKVQDPYSLRCQPQVMGACLDQMRHAADVLLLEANAVSDNPLIFPDTGEVLSGGNFHAEP 331
                                                  ****************************************************************** PP

                                    TIGR01225 331 vAlaldflaiaiaelgaiseRRierlldpalseLppFLaedsGlnsGlmiaqytaAaLvsenkaLa 396
                                                  vA+a+d+la+a+ae+ga++eRRi++l+d +ls+LppFL+ d+G+nsG+mia++taAaL+senk+La
  lcl|FitnessBrowser__Burk376:H281DRAFT_04873 332 VAFAADNLALAAAEIGALAERRIALLIDATLSGLPPFLVRDGGVNSGFMIAHVTAAALASENKTLA 397
                                                  ****************************************************************** PP

                                    TIGR01225 397 hPasvDsiptsanqEDHvsmgaaaarkllevvenvrrviaiEllaaaqglefrkaektaaelekvy 462
                                                  hPasvDs+ptsanqEDHvsm++ aarkl +++en++++++iEllaaaqg+++r+++kt+++l+kv+
  lcl|FitnessBrowser__Burk376:H281DRAFT_04873 398 HPASVDSLPTSANQEDHVSMATFAARKLGDIAENTANILSIELLAAAQGVDLRAPHKTSPSLQKVM 463
                                                  ****************************************************************** PP

                                    TIGR01225 463 eavRevveeleeDRvlapDleavkellekesleaa 497
                                                  + vR+ v+++e D ++apD++av++l++++++++ 
  lcl|FitnessBrowser__Burk376:H281DRAFT_04873 464 DVVRKDVAHYELDHYFAPDIAAVTRLVQNGTIAKL 498
                                                  *****************************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (506 nodes)
Target sequences:                          1  (507 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 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 6.86
//
[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