Alignments for a candidate for hutH in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutH in Acidovorax sp. GW101-3H11

Align Histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate Ac3H11_2558 Histidine ammonia-lyase (EC 4.3.1.3)

Query= reanno::acidovorax_3H11:Ac3H11_2558
         (512 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2558
          Length = 512

 Score =  986 bits (2549), Expect = 0.0
 Identities = 512/512 (100%), Positives = 512/512 (100%)

Query: 1   MTHNASSLTLHPGRVTLAELRRIHAGPVQLVLDASARAGLQKSLATVQRIVDEDQVVYGI 60
           MTHNASSLTLHPGRVTLAELRRIHAGPVQLVLDASARAGLQKSLATVQRIVDEDQVVYGI
Sbjct: 1   MTHNASSLTLHPGRVTLAELRRIHAGPVQLVLDASARAGLQKSLATVQRIVDEDQVVYGI 60

Query: 61  NTGFGKLASTKIAHERLAELQRNLVLSHSVGTGDPLPDDVVRLILATKAVSLARGHSGVR 120
           NTGFGKLASTKIAHERLAELQRNLVLSHSVGTGDPLPDDVVRLILATKAVSLARGHSGVR
Sbjct: 61  NTGFGKLASTKIAHERLAELQRNLVLSHSVGTGDPLPDDVVRLILATKAVSLARGHSGVR 120

Query: 121 PELVDALLALANANVLPVIPAKGSVGASGDLAPLAHMACVLIGEGQAKVDGKVVPGAEAM 180
           PELVDALLALANANVLPVIPAKGSVGASGDLAPLAHMACVLIGEGQAKVDGKVVPGAEAM
Sbjct: 121 PELVDALLALANANVLPVIPAKGSVGASGDLAPLAHMACVLIGEGQAKVDGKVVPGAEAM 180

Query: 181 RSIGLQPFVLGPKEGLALLNGTQVSTALALAGLFGAESVFSAALVAGCLSLEAIKGSVKP 240
           RSIGLQPFVLGPKEGLALLNGTQVSTALALAGLFGAESVFSAALVAGCLSLEAIKGSVKP
Sbjct: 181 RSIGLQPFVLGPKEGLALLNGTQVSTALALAGLFGAESVFSAALVAGCLSLEAIKGSVKP 240

Query: 241 FDARIHEARGQAGQIAVAAAVRALLDGSAIDPSHPHCGRVQDPYSIRCVPQVMGACLDNL 300
           FDARIHEARGQAGQIAVAAAVRALLDGSAIDPSHPHCGRVQDPYSIRCVPQVMGACLDNL
Sbjct: 241 FDARIHEARGQAGQIAVAAAVRALLDGSAIDPSHPHCGRVQDPYSIRCVPQVMGACLDNL 300

Query: 301 HHAARVLTIEANAASDNPLVFDNGDVISGGNFHAEPVAFVADIIALAVAEIGAISERRLS 360
           HHAARVLTIEANAASDNPLVFDNGDVISGGNFHAEPVAFVADIIALAVAEIGAISERRLS
Sbjct: 301 HHAARVLTIEANAASDNPLVFDNGDVISGGNFHAEPVAFVADIIALAVAEIGAISERRLS 360

Query: 361 LLLDPGLSGLPAFLIRDSGVNSGFMIAQVTAAALAAENQCLANPSSVTSLPTSANQEDHV 420
           LLLDPGLSGLPAFLIRDSGVNSGFMIAQVTAAALAAENQCLANPSSVTSLPTSANQEDHV
Sbjct: 361 LLLDPGLSGLPAFLIRDSGVNSGFMIAQVTAAALAAENQCLANPSSVTSLPTSANQEDHV 420

Query: 421 SMATYGARRLGDMVRNAAVMVGIEAMAAAQGMEFDRSLKSSPLIEAQFAAIRERVAYLEQ 480
           SMATYGARRLGDMVRNAAVMVGIEAMAAAQGMEFDRSLKSSPLIEAQFAAIRERVAYLEQ
Sbjct: 421 SMATYGARRLGDMVRNAAVMVGIEAMAAAQGMEFDRSLKSSPLIEAQFAAIRERVAYLEQ 480

Query: 481 DRYLAPDIEAMRAWAQQSTWPAALTQCLPSFA 512
           DRYLAPDIEAMRAWAQQSTWPAALTQCLPSFA
Sbjct: 481 DRYLAPDIEAMRAWAQQSTWPAALTQCLPSFA 512


Lambda     K      H
   0.319    0.133    0.378 

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: 904
Number of extensions: 17
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: 512
Length of database: 512
Length adjustment: 35
Effective length of query: 477
Effective length of database: 477
Effective search space:   227529
Effective search space used:   227529
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 (21.8 bits)
S2: 52 (24.6 bits)

Align candidate Ac3H11_2558 (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.9214.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-207  676.5   7.7   1.2e-207  676.2   7.7    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2558  Histidine ammonia-lyase (EC 4.3.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2558  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 !  676.2   7.7  1.2e-207  1.2e-207       2     499 ..       9     505 ..       8     510 .. 0.99

  Alignments for each domain:
  == domain 1  score: 676.2 bits;  conditional E-value: 1.2e-207
                                        TIGR01225   2 vldgesltledleavarekarvelsaaaeeavaksravieeivaedktvYGvntGFGklasv 63 
                                                      +l+++++tl++l+++++   ++ l+a+a++ ++ks a++++iv+ed++vYG+ntGFGklas+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2558   9 TLHPGRVTLAELRRIHAGPVQLVLDASARAGLQKSLATVQRIVDEDQVVYGINTGFGKLAST 70 
                                                      78999********************************************************* PP

                                        TIGR01225  64 kidkedlaeLqrnlvrsHaaGvGepleeevvRallvlrlnslakGysgvraevlellvalln 125
                                                      ki++e+laeLqrnlv+sH++G G+pl+++vvR++l++++ sla+G+sgvr e++++l+al n
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2558  71 KIAHERLAELQRNLVLSHSVGTGDPLPDDVVRLILATKAVSLARGHSGVRPELVDALLALAN 132
                                                      ************************************************************** PP

                                        TIGR01225 126 aevlPvvpekGsvGasGDLAPLahlalvliGeGeaefegevmdaaeaLaaaglePvtlkakE 187
                                                      a+vlPv+p kGsvGasGDLAPLah+a vliGeG+a+++g+v+++aea++  gl+P+ l  kE
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2558 133 ANVLPVIPAKGSVGASGDLAPLAHMACVLIGEGQAKVDGKVVPGAEAMRSIGLQPFVLGPKE 194
                                                      ************************************************************** PP

                                        TIGR01225 188 GlALinGtqlmtalavlalvdaekllesadiaaalsleallgtskafdpdihevrphrgqia 249
                                                      GlAL+nGtq++tala+++l+ ae++ ++a +a+ lslea++g+ k+fd++ihe+r++ gqia
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2558 195 GLALLNGTQVSTALALAGLFGAESVFSAALVAGCLSLEAIKGSVKPFDARIHEARGQAGQIA 256
                                                      ************************************************************** PP

                                        TIGR01225 250 vaarlrellagseiaeshkdedrvqDaYslRciPqvhGavldtldqvkevlaiElnsatDnP 311
                                                      vaa++r ll+gs i  sh ++ rvqD+Ys+Rc+Pqv+Ga+ld l+++++vl+iE+n+a+DnP
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2558 257 VAAAVRALLDGSAIDPSHPHCGRVQDPYSIRCVPQVMGACLDNLHHAARVLTIEANAASDNP 318
                                                      ************************************************************** PP

                                        TIGR01225 312 lvfadegevvsgGnFHgepvAlaldflaiaiaelgaiseRRierlldpalseLppFLaedsG 373
                                                      lvf + g+v+sgGnFH+epvA+++d +a+a+ae+gaiseRR+++lldp ls+Lp+FL  dsG
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2558 319 LVFDN-GDVISGGNFHAEPVAFVADIIALAVAEIGAISERRLSLLLDPGLSGLPAFLIRDSG 379
                                                      ***99.5******************************************************* PP

                                        TIGR01225 374 lnsGlmiaqytaAaLvsenkaLahPasvDsiptsanqEDHvsmgaaaarkllevvenvrrvi 435
                                                      +nsG+miaq+taAaL+ en+ La+P+sv s+ptsanqEDHvsm++ +ar+l ++v n++ ++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2558 380 VNSGFMIAQVTAAALAAENQCLANPSSVTSLPTSANQEDHVSMATYGARRLGDMVRNAAVMV 441
                                                      ************************************************************** PP

                                        TIGR01225 436 aiEllaaaqglefrkaektaaelekvyeavRevveeleeDRvlapDleavkellekesleaa 497
                                                      +iE++aaaqg+ef +  k+++ +e+ ++a+Re v+ le+DR+lapD+ea++ + ++ ++ aa
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2558 442 GIEAMAAAQGMEFDRSLKSSPLIEAQFAAIRERVAYLEQDRYLAPDIEAMRAWAQQSTWPAA 503
                                                      ********************************************************999888 PP

                                        TIGR01225 498 ve 499
                                                      ++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2558 504 LT 505
                                                      76 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (506 nodes)
Target sequences:                          1  (512 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: 12.33
//
[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