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

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.21520.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 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 8.46
//
[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