GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutH in Cupriavidus basilensis 4G11

Align Histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate RR42_RS16920 RR42_RS16920 histidine ammonia-lyase

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



>FitnessBrowser__Cup4G11:RR42_RS16920
          Length = 526

 Score =  745 bits (1923), Expect = 0.0
 Identities = 391/508 (76%), Positives = 429/508 (84%), Gaps = 5/508 (0%)

Query: 8   LTLHPGRVTLAELRRIHAGPVQLVLDASARAGLQKSLATVQRIVDEDQVVYGINTGFGKL 67
           LTL PG VTLA+LRRIH G V L +DASA AG++ S ATVQ I+D D VVYGINTGFGKL
Sbjct: 14  LTLQPGSVTLADLRRIHRGEVSLAMDASAWAGVRASQATVQDIIDADAVVYGINTGFGKL 73

Query: 68  ASTKIAHERLAELQRNLVLSHSVGTGDPLPDDVVRLILATKAVSLARGHSGVRPELVDAL 127
           A T+I H++LAELQRNLVLSHSVGTG  L  D VRLILA KAVSLARGHSG+RPE+++AL
Sbjct: 74  AQTRIPHDKLAELQRNLVLSHSVGTGADLHSDTVRLILAIKAVSLARGHSGIRPEIIEAL 133

Query: 128 LALANANVLPVIPAKGSVGASGDLAPLAHMACVLIGEGQAKVDGKVVPGAEAMRSIGLQP 187
           LAL NA V P IPAKGSVGASGDLAPLAHM+C LIG G+  +DG   P AE +   GL P
Sbjct: 134 LALTNAGVTPCIPAKGSVGASGDLAPLAHMSCTLIGVGEVMIDGVRRPAAEGLAHAGLAP 193

Query: 188 FVLGPKEGLALLNGTQVSTALALAGLFGAESVFSAALVAGCLSLEAIKGSVKPFDARIHE 247
           F LGPKEGLALLNGTQVSTALALAGLF AE +F+A LVAG LSLEAIKGSVKPFDARIH 
Sbjct: 194 FTLGPKEGLALLNGTQVSTALALAGLFAAEDIFAAGLVAGALSLEAIKGSVKPFDARIHA 253

Query: 248 ARGQAGQIAVAAAVRALLDGSAIDPSHPHCGRVQDPYSIRCVPQVMGACLDNLHHAARVL 307
           ARGQAGQIAVA AVRALLDGS I  SH  CGRVQDPYSIRC PQVMGACLDNL HAARVL
Sbjct: 254 ARGQAGQIAVAGAVRALLDGSKIVDSHVSCGRVQDPYSIRCQPQVMGACLDNLQHAARVL 313

Query: 308 TIEANAASDNPLVF-DNGDVISGGNFHAEPVAFVADIIALAVAEIGAISERRLSLLLDPG 366
            IEANAASDNPLVF + GDVISGGNFHAEPVAF ADIIALA+AEIGAISERRL+LLLD G
Sbjct: 314 QIEANAASDNPLVFPEQGDVISGGNFHAEPVAFAADIIALAIAEIGAISERRLALLLDSG 373

Query: 367 LSGLPAFLIRDSGVNSGFMIAQVTAAALAAENQCLANPSSVTSLPTSANQEDHVSMATYG 426
           LSGLP FL+RD G++SGFMIAQVTAAALA+EN+ LA+P+SV SLPTSANQEDHVSMATYG
Sbjct: 374 LSGLPPFLVRDGGLHSGFMIAQVTAAALASENKSLAHPASVDSLPTSANQEDHVSMATYG 433

Query: 427 ARRLGDMVRNAAVMVGIEAMAAAQGMEFDRSLKSSPLIEAQFAAIRERVAYLEQDRYLAP 486
           ARRLGDM  N AV+VGIEAMAAAQG+EF R L+SSPLIE++ A IRERVA++E DRY AP
Sbjct: 434 ARRLGDMAENTAVVVGIEAMAAAQGIEFHRPLESSPLIESEIARIRERVAFVEGDRYFAP 493

Query: 487 DIEAMRAWAQQ----STWPAALTQCLPS 510
           DIEAM+ W QQ    + WP A+ Q LPS
Sbjct: 494 DIEAMKQWVQQGDAGAGWPEAVRQVLPS 521


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: 774
Number of extensions: 25
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: 512
Length of database: 526
Length adjustment: 35
Effective length of query: 477
Effective length of database: 491
Effective search space:   234207
Effective search space used:   234207
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 RR42_RS16920 RR42_RS16920 (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.2733.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     2e-213  695.3   7.7   2.3e-213  695.1   7.7    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS16920  RR42_RS16920 histidine ammonia-l


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS16920  RR42_RS16920 histidine ammonia-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  695.1   7.7  2.3e-213  2.3e-213       2     496 ..      15     509 ..      14     519 .. 0.99

  Alignments for each domain:
  == domain 1  score: 695.1 bits;  conditional E-value: 2.3e-213
                                 TIGR01225   2 vldgesltledleavarekarvelsaaaeeavaksravieeivaedktvYGvntGFGklasvkidkedl 70 
                                               +l+++s+tl+dl++++r +  ++++a+a + v++s+a++++i++ d++vYG+ntGFGkla+++i +++l
  lcl|FitnessBrowser__Cup4G11:RR42_RS16920  15 TLQPGSVTLADLRRIHRGEVSLAMDASAWAGVRASQATVQDIIDADAVVYGINTGFGKLAQTRIPHDKL 83 
                                               7999***************************************************************** PP

                                 TIGR01225  71 aeLqrnlvrsHaaGvGepleeevvRallvlrlnslakGysgvraevlellvallnaevlPvvpekGsvG 139
                                               aeLqrnlv+sH++G G+ l++++vR++l++++ sla+G+sg+r e++e+l+al na+v+P +p kGsvG
  lcl|FitnessBrowser__Cup4G11:RR42_RS16920  84 AELQRNLVLSHSVGTGADLHSDTVRLILAIKAVSLARGHSGIRPEIIEALLALTNAGVTPCIPAKGSVG 152
                                               ********************************************************************* PP

                                 TIGR01225 140 asGDLAPLahlalvliGeGeaefegevmdaaeaLaaaglePvtlkakEGlALinGtqlmtalavlalvd 208
                                               asGDLAPLah++ +liG Ge+ ++g +++aae La+agl+P+tl  kEGlAL+nGtq++tala+++l+ 
  lcl|FitnessBrowser__Cup4G11:RR42_RS16920 153 ASGDLAPLAHMSCTLIGVGEVMIDGVRRPAAEGLAHAGLAPFTLGPKEGLALLNGTQVSTALALAGLFA 221
                                               ********************************************************************* PP

                                 TIGR01225 209 aekllesadiaaalsleallgtskafdpdihevrphrgqiavaarlrellagseiaeshkdedrvqDaY 277
                                               ae++ ++  +a+alslea++g+ k+fd++ih++r++ gqiava ++r ll+gs+i++sh  + rvqD+Y
  lcl|FitnessBrowser__Cup4G11:RR42_RS16920 222 AEDIFAAGLVAGALSLEAIKGSVKPFDARIHAARGQAGQIAVAGAVRALLDGSKIVDSHVSCGRVQDPY 290
                                               ********************************************************************* PP

                                 TIGR01225 278 slRciPqvhGavldtldqvkevlaiElnsatDnPlvfadegevvsgGnFHgepvAlaldflaiaiaelg 346
                                               s+Rc+Pqv+Ga+ld l+++++vl+iE+n+a+DnPlvf+++g+v+sgGnFH+epvA+a+d +a+aiae+g
  lcl|FitnessBrowser__Cup4G11:RR42_RS16920 291 SIRCQPQVMGACLDNLQHAARVLQIEANAASDNPLVFPEQGDVISGGNFHAEPVAFAADIIALAIAEIG 359
                                               ********************************************************************* PP

                                 TIGR01225 347 aiseRRierlldpalseLppFLaedsGlnsGlmiaqytaAaLvsenkaLahPasvDsiptsanqEDHvs 415
                                               aiseRR+++lld  ls+LppFL+ d+Gl+sG+miaq+taAaL+senk+LahPasvDs+ptsanqEDHvs
  lcl|FitnessBrowser__Cup4G11:RR42_RS16920 360 AISERRLALLLDSGLSGLPPFLVRDGGLHSGFMIAQVTAAALASENKSLAHPASVDSLPTSANQEDHVS 428
                                               ********************************************************************* PP

                                 TIGR01225 416 mgaaaarkllevvenvrrviaiEllaaaqglefrkaektaaelekvyeavRevveeleeDRvlapDlea 484
                                               m++ +ar+l +++en++ v++iE++aaaqg+ef+++ ++++ +e  ++ +Re v+ +e+DR++apD+ea
  lcl|FitnessBrowser__Cup4G11:RR42_RS16920 429 MATYGARRLGDMAENTAVVVGIEAMAAAQGIEFHRPLESSPLIESEIARIRERVAFVEGDRYFAPDIEA 497
                                               ********************************************************************* PP

                                 TIGR01225 485 vkellekeslea 496
                                               +k++++++   a
  lcl|FitnessBrowser__Cup4G11:RR42_RS16920 498 MKQWVQQGDAGA 509
                                               ******997655 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (506 nodes)
Target sequences:                          1  (526 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: 9.70
//
[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:

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