Alignments for a candidate for hutH in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutH in Stenotrophomonas chelatiphaga DSM 21508

Align Histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate WP_057506766.1 ABB28_RS00620 histidine ammonia-lyase

Query= reanno::Korea:Ga0059261_3963
         (497 letters)



>NCBI__GCF_001431535.1:WP_057506766.1
          Length = 517

 Score =  711 bits (1835), Expect = 0.0
 Identities = 373/505 (73%), Positives = 410/505 (81%), Gaps = 9/505 (1%)

Query: 1   MITPGYTPLSTWNAIYRGEAAPLDPSCRDKIQASADAVEAILARHEPVYGINTGFGKLAS 60
           ++ P + PL+ W  +YRG    LD +    ++ASA  VEAI+A+  PVYGINTGFGKLAS
Sbjct: 10  VLRPAHVPLAQWRQVYRGARIALDAAALPAVRASAATVEAIVAKGAPVYGINTGFGKLAS 69

Query: 61  VRIGDEDLETLQRNIVLSHAAGVGAPMPAPVVRLMIALKLASLAQGHSGVRPATIAMLQD 120
           VRI  EDL TLQRNIVLSHAAGVG PMP PVVRLM+ALKL SLAQG SGVR  T+ +L+ 
Sbjct: 70  VRIEPEDLATLQRNIVLSHAAGVGEPMPLPVVRLMMALKLVSLAQGASGVRVETLQLLEA 129

Query: 121 MLDRGITPIIPSQGSVGASGDLAPLAHLAAAMIGTGEVLVDGVVRPARDVLA-----PLT 175
           +L + + P+IP+QGSVGASGDLAPL+HLA+ MIG GE  V G    A D LA     PL 
Sbjct: 130 LLQQDVVPVIPAQGSVGASGDLAPLSHLASMMIGVGEAFVGGQRLSAADALARAGLQPLQ 189

Query: 176 LGPKEGLALLNGTQFSTAYALAALFETERLFRAALVTGALSTEAAKGSDTPFDPRIHQVR 235
           LG KEGLALLNGTQFSTAYALA LFE E +F+AALVTGALS EAAKGSDTPFDPRIH +R
Sbjct: 190 LGAKEGLALLNGTQFSTAYALAGLFEIEIVFQAALVTGALSVEAAKGSDTPFDPRIHSIR 249

Query: 236 GHRGQIEVADALAGLMSGSAIRASHREGDERVQDPYCLRCQPQVMGACLDLIRQAAATLA 295
           G RGQI  A AL  LM GSAIR SHR+ D RVQDPYCLRCQPQVMGA LD+IRQAA TL 
Sbjct: 250 GQRGQILTAAALRTLMQGSAIRESHRDNDVRVQDPYCLRCQPQVMGAALDIIRQAATTLE 309

Query: 296 IEANGVTDNPLIFPDTGEALSGGNFHAEPVAFAADMLAMALCEIGSLSERRIAMLVDPAL 355
           IEANGV+DNPL+F DTGEALSGGNFHAEPVAFAADMLAMA+CEIGS+SERR AMLVDPAL
Sbjct: 310 IEANGVSDNPLVFTDTGEALSGGNFHAEPVAFAADMLAMAICEIGSISERRTAMLVDPAL 369

Query: 356 SGLPAFLTPRPGLNSGFMIPQVTAAALVSENKQRAHPASVDSIPTSANQEDHVSMAGHGA 415
           SGLPAFLTPRPGLNSGFMIPQVTAAALVSENKQRA+PASVDSIPTSANQEDHVSMA HGA
Sbjct: 370 SGLPAFLTPRPGLNSGFMIPQVTAAALVSENKQRAYPASVDSIPTSANQEDHVSMAAHGA 429

Query: 416 RRLMEMAANLANVLGIEYLAAAQGCDFHAPLTSSEPLEAARSLLRNQVPHLEDDRHFAPD 475
           RRL++MA N ANV+GIE LAAAQGCDFHAPL SS PLEA R LLR QVP LE+DR+F PD
Sbjct: 430 RRLLQMAENAANVVGIELLAAAQGCDFHAPLQSSGPLEAVRVLLRAQVPTLEEDRYFHPD 489

Query: 476 MAAATALVAGGM----LGPYLPGIE 496
           M AAT LV  G     L   LP +E
Sbjct: 490 MLAATDLVRSGALASGLADVLPNVE 514


Lambda     K      H
   0.319    0.134    0.388 

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: 842
Number of extensions: 37
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: 497
Length of database: 517
Length adjustment: 34
Effective length of query: 463
Effective length of database: 483
Effective search space:   223629
Effective search space used:   223629
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 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate WP_057506766.1 ABB28_RS00620 (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.16868.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.7e-214  696.5   7.9   1.1e-213  696.2   7.9    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057506766.1  ABB28_RS00620 histidine ammonia-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057506766.1  ABB28_RS00620 histidine ammonia-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  696.2   7.9  1.1e-213  1.1e-213       2     498 ..      10     506 ..       9     512 .. 0.99

  Alignments for each domain:
  == domain 1  score: 696.2 bits;  conditional E-value: 1.1e-213
                                 TIGR01225   2 vldgesltledleavarekarvelsaaaeeavaksravieeivaedktvYGvntGFGklasvkidkedl 70 
                                               vl++ ++ l++ ++v+r +ar++l+aaa  av++s+a++e+iva+ ++vYG+ntGFGklasv+i+ edl
  lcl|NCBI__GCF_001431535.1:WP_057506766.1  10 VLRPAHVPLAQWRQVYR-GARIALDAAALPAVRASAATVEAIVAKGAPVYGINTGFGKLASVRIEPEDL 77 
                                               78888999999999987.689************************************************ PP

                                 TIGR01225  71 aeLqrnlvrsHaaGvGepleeevvRallvlrlnslakGysgvraevlellvallnaevlPvvpekGsvG 139
                                               a+Lqrn+v+sHaaGvGep++  vvR++++l+l sla+G+sgvr+e+l+ll all+++v+Pv+p +GsvG
  lcl|NCBI__GCF_001431535.1:WP_057506766.1  78 ATLQRNIVLSHAAGVGEPMPLPVVRLMMALKLVSLAQGASGVRVETLQLLEALLQQDVVPVIPAQGSVG 146
                                               ********************************************************************* PP

                                 TIGR01225 140 asGDLAPLahlalvliGeGeaefegevmdaaeaLaaaglePvtlkakEGlALinGtqlmtalavlalvd 208
                                               asGDLAPL+hla  +iG Gea++ g++++aa+aLa+agl+P++l akEGlAL+nGtq++ta+a+++l++
  lcl|NCBI__GCF_001431535.1:WP_057506766.1 147 ASGDLAPLSHLASMMIGVGEAFVGGQRLSAADALARAGLQPLQLGAKEGLALLNGTQFSTAYALAGLFE 215
                                               ********************************************************************* PP

                                 TIGR01225 209 aekllesadiaaalsleallgtskafdpdihevrphrgqiavaarlrellagseiaeshk.dedrvqDa 276
                                               +e + ++a +++als+ea++g++++fdp+ih++r++rgqi +aa+lr+l++gs i+esh+ ++ rvqD+
  lcl|NCBI__GCF_001431535.1:WP_057506766.1 216 IEIVFQAALVTGALSVEAAKGSDTPFDPRIHSIRGQRGQILTAAALRTLMQGSAIRESHRdNDVRVQDP 284
                                               ************************************************************8899***** PP

                                 TIGR01225 277 YslRciPqvhGavldtldqvkevlaiElnsatDnPlvfadegevvsgGnFHgepvAlaldflaiaiael 345
                                               Y+lRc+Pqv+Ga+ld ++q++++l+iE+n ++DnPlvf+d+ge  sgGnFH+epvA+a+d+la+ai+e+
  lcl|NCBI__GCF_001431535.1:WP_057506766.1 285 YCLRCQPQVMGAALDIIRQAATTLEIEANGVSDNPLVFTDTGEALSGGNFHAEPVAFAADMLAMAICEI 353
                                               ********************************************************************* PP

                                 TIGR01225 346 gaiseRRierlldpalseLppFLaedsGlnsGlmiaqytaAaLvsenkaLahPasvDsiptsanqEDHv 414
                                               g+iseRR++ l+dpals+Lp+FL++ +GlnsG+mi+q+taAaLvsenk+ a+PasvDsiptsanqEDHv
  lcl|NCBI__GCF_001431535.1:WP_057506766.1 354 GSISERRTAMLVDPALSGLPAFLTPRPGLNSGFMIPQVTAAALVSENKQRAYPASVDSIPTSANQEDHV 422
                                               ********************************************************************* PP

                                 TIGR01225 415 smgaaaarkllevvenvrrviaiEllaaaqglefrkaektaaelekvyeavRevveeleeDRvlapDle 483
                                               sm+a++ar+ll+++en+++v++iEllaaaqg +f+++ ++++ le+v+ ++R++v++leeDR++ pD+ 
  lcl|NCBI__GCF_001431535.1:WP_057506766.1 423 SMAAHGARRLLQMAENAANVVGIELLAAAQGCDFHAPLQSSGPLEAVRVLLRAQVPTLEEDRYFHPDML 491
                                               ********************************************************************* PP

                                 TIGR01225 484 avkellekesleaav 498
                                               a+++l++++ l++ +
  lcl|NCBI__GCF_001431535.1:WP_057506766.1 492 AATDLVRSGALASGL 506
                                               *********998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (506 nodes)
Target sequences:                          1  (517 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 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 12.72
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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