Alignments for a candidate for hutH in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutH in Sphingomonas koreensis DSMZ 15582

Align Histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate Ga0059261_3963 Ga0059261_3963 histidine ammonia-lyase (EC 4.3.1.3)

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



>FitnessBrowser__Korea:Ga0059261_3963
          Length = 497

 Score =  973 bits (2516), Expect = 0.0
 Identities = 497/497 (100%), Positives = 497/497 (100%)

Query: 1   MITPGYTPLSTWNAIYRGEAAPLDPSCRDKIQASADAVEAILARHEPVYGINTGFGKLAS 60
           MITPGYTPLSTWNAIYRGEAAPLDPSCRDKIQASADAVEAILARHEPVYGINTGFGKLAS
Sbjct: 1   MITPGYTPLSTWNAIYRGEAAPLDPSCRDKIQASADAVEAILARHEPVYGINTGFGKLAS 60

Query: 61  VRIGDEDLETLQRNIVLSHAAGVGAPMPAPVVRLMIALKLASLAQGHSGVRPATIAMLQD 120
           VRIGDEDLETLQRNIVLSHAAGVGAPMPAPVVRLMIALKLASLAQGHSGVRPATIAMLQD
Sbjct: 61  VRIGDEDLETLQRNIVLSHAAGVGAPMPAPVVRLMIALKLASLAQGHSGVRPATIAMLQD 120

Query: 121 MLDRGITPIIPSQGSVGASGDLAPLAHLAAAMIGTGEVLVDGVVRPARDVLAPLTLGPKE 180
           MLDRGITPIIPSQGSVGASGDLAPLAHLAAAMIGTGEVLVDGVVRPARDVLAPLTLGPKE
Sbjct: 121 MLDRGITPIIPSQGSVGASGDLAPLAHLAAAMIGTGEVLVDGVVRPARDVLAPLTLGPKE 180

Query: 181 GLALLNGTQFSTAYALAALFETERLFRAALVTGALSTEAAKGSDTPFDPRIHQVRGHRGQ 240
           GLALLNGTQFSTAYALAALFETERLFRAALVTGALSTEAAKGSDTPFDPRIHQVRGHRGQ
Sbjct: 181 GLALLNGTQFSTAYALAALFETERLFRAALVTGALSTEAAKGSDTPFDPRIHQVRGHRGQ 240

Query: 241 IEVADALAGLMSGSAIRASHREGDERVQDPYCLRCQPQVMGACLDLIRQAAATLAIEANG 300
           IEVADALAGLMSGSAIRASHREGDERVQDPYCLRCQPQVMGACLDLIRQAAATLAIEANG
Sbjct: 241 IEVADALAGLMSGSAIRASHREGDERVQDPYCLRCQPQVMGACLDLIRQAAATLAIEANG 300

Query: 301 VTDNPLIFPDTGEALSGGNFHAEPVAFAADMLAMALCEIGSLSERRIAMLVDPALSGLPA 360
           VTDNPLIFPDTGEALSGGNFHAEPVAFAADMLAMALCEIGSLSERRIAMLVDPALSGLPA
Sbjct: 301 VTDNPLIFPDTGEALSGGNFHAEPVAFAADMLAMALCEIGSLSERRIAMLVDPALSGLPA 360

Query: 361 FLTPRPGLNSGFMIPQVTAAALVSENKQRAHPASVDSIPTSANQEDHVSMAGHGARRLME 420
           FLTPRPGLNSGFMIPQVTAAALVSENKQRAHPASVDSIPTSANQEDHVSMAGHGARRLME
Sbjct: 361 FLTPRPGLNSGFMIPQVTAAALVSENKQRAHPASVDSIPTSANQEDHVSMAGHGARRLME 420

Query: 421 MAANLANVLGIEYLAAAQGCDFHAPLTSSEPLEAARSLLRNQVPHLEDDRHFAPDMAAAT 480
           MAANLANVLGIEYLAAAQGCDFHAPLTSSEPLEAARSLLRNQVPHLEDDRHFAPDMAAAT
Sbjct: 421 MAANLANVLGIEYLAAAQGCDFHAPLTSSEPLEAARSLLRNQVPHLEDDRHFAPDMAAAT 480

Query: 481 ALVAGGMLGPYLPGIER 497
           ALVAGGMLGPYLPGIER
Sbjct: 481 ALVAGGMLGPYLPGIER 497


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: 1023
Number of extensions: 27
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: 497
Length of database: 497
Length adjustment: 34
Effective length of query: 463
Effective length of database: 463
Effective search space:   214369
Effective search space used:   214369
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 Ga0059261_3963 Ga0059261_3963 (histidine ammonia-lyase (EC 4.3.1.3))
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.25294.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.4e-207  675.3   0.8     3e-207  675.0   0.8    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_3963  Ga0059261_3963 histidine ammonia


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_3963  Ga0059261_3963 histidine ammonia-lyase (EC 4.3.1.3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  675.0   0.8    3e-207    3e-207      20     495 ..      18     489 ..       2     496 .. 0.98

  Alignments for each domain:
  == domain 1  score: 675.0 bits;  conditional E-value: 3e-207
                                 TIGR01225  20 karvelsaaaeeavaksravieeivaedktvYGvntGFGklasvkidkedlaeLqrnlvrsHaaGvGep 88 
                                               ++ + l+ + ++++++s+ ++e+i+a +++vYG+ntGFGklasv+i  edl++Lqrn+v+sHaaGvG+p
  lcl|FitnessBrowser__Korea:Ga0059261_3963  18 GEAAPLDPSCRDKIQASADAVEAILARHEPVYGINTGFGKLASVRIGDEDLETLQRNIVLSHAAGVGAP 86 
                                               56678999************************************************************* PP

                                 TIGR01225  89 leeevvRallvlrlnslakGysgvraevlellvallnaevlPvvpekGsvGasGDLAPLahlalvliGe 157
                                               +++ vvR++++l+l sla+G+sgvr  ++ +l ++l+++++P++p++GsvGasGDLAPLahla+++iG 
  lcl|FitnessBrowser__Korea:Ga0059261_3963  87 MPAPVVRLMIALKLASLAQGHSGVRPATIAMLQDMLDRGITPIIPSQGSVGASGDLAPLAHLAAAMIGT 155
                                               ********************************************************************* PP

                                 TIGR01225 158 GeaefegevmdaaeaLaaaglePvtlkakEGlALinGtqlmtalavlalvdaekllesadiaaalslea 226
                                               Ge+ ++g v++a ++L     +P+tl  kEGlAL+nGtq++ta+a++al++ e+l ++a +++als+ea
  lcl|FitnessBrowser__Korea:Ga0059261_3963 156 GEVLVDGVVRPARDVL-----APLTLGPKEGLALLNGTQFSTAYALAALFETERLFRAALVTGALSTEA 219
                                               *************997.....59********************************************** PP

                                 TIGR01225 227 llgtskafdpdihevrphrgqiavaarlrellagseiaeshk.dedrvqDaYslRciPqvhGavldtld 294
                                               ++g++++fdp+ih+vr+hrgqi+va++l  l++gs i+ sh+ +++rvqD+Y+lRc+Pqv+Ga+ld ++
  lcl|FitnessBrowser__Korea:Ga0059261_3963 220 AKGSDTPFDPRIHQVRGHRGQIEVADALAGLMSGSAIRASHReGDERVQDPYCLRCQPQVMGACLDLIR 288
                                               ******************************************99************************* PP

                                 TIGR01225 295 qvkevlaiElnsatDnPlvfadegevvsgGnFHgepvAlaldflaiaiaelgaiseRRierlldpalse 363
                                               q++++laiE+n +tDnPl+f+d+ge  sgGnFH+epvA+a+d+la+a++e+g++seRRi+ l+dpals+
  lcl|FitnessBrowser__Korea:Ga0059261_3963 289 QAAATLAIEANGVTDNPLIFPDTGEALSGGNFHAEPVAFAADMLAMALCEIGSLSERRIAMLVDPALSG 357
                                               ********************************************************************* PP

                                 TIGR01225 364 LppFLaedsGlnsGlmiaqytaAaLvsenkaLahPasvDsiptsanqEDHvsmgaaaarkllevvenvr 432
                                               Lp+FL++ +GlnsG+mi+q+taAaLvsenk+ ahPasvDsiptsanqEDHvsm+ ++ar+l+e+++n++
  lcl|FitnessBrowser__Korea:Ga0059261_3963 358 LPAFLTPRPGLNSGFMIPQVTAAALVSENKQRAHPASVDSIPTSANQEDHVSMAGHGARRLMEMAANLA 426
                                               ********************************************************************* PP

                                 TIGR01225 433 rviaiEllaaaqglefrkaektaaelekvyeavRevveeleeDRvlapDleavkellekesle 495
                                               +v++iE+laaaqg +f+++ +++  le+++ ++R++v++le+DR +apD++a++ l++ + l 
  lcl|FitnessBrowser__Korea:Ga0059261_3963 427 NVLGIEYLAAAQGCDFHAPLTSSEPLEAARSLLRNQVPHLEDDRHFAPDMAAATALVAGGMLG 489
                                               *********************************************************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (506 nodes)
Target sequences:                          1  (497 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: 11.44
//
[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