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.17855.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 9.94
//
[ok]

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

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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