Alignments for a candidate for hutH in Cupriavidus basilensis 4G11

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.12366.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: 10.19
//
[ok]

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

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Protein sequences (fasta format)
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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