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_RS14640 RR42_RS14640 histidine ammonia-lyase

Query= reanno::pseudo6_N2E2:Pf6N2E2_3799
         (510 letters)



>FitnessBrowser__Cup4G11:RR42_RS14640
          Length = 510

 Score =  823 bits (2126), Expect = 0.0
 Identities = 422/510 (82%), Positives = 458/510 (89%)

Query: 1   MTALNLIPGQLSLAQLRDIYQQPVTLSLDASASAQIEASVACVEQILAENRTAYGINTGF 60
           M ALNL PGQL+LAQLR  Y QP+ +SLD  A+  I ASVACVE I+AE RTAYGINTGF
Sbjct: 1   MNALNLKPGQLTLAQLRQAYLQPLRVSLDGGAAEAIAASVACVENIVAEGRTAYGINTGF 60

Query: 61  GLLASTRIASEDLENLQRSLVLSHAAGVGEPISDALVRLVMVLKVNSLSRGFSGIRRQVI 120
           GLLA TRIA EDLENLQRSLVLSHAAGVGEP+ DA+VRL+M+LK+NSL+RGFSGIRR+VI
Sbjct: 61  GLLAQTRIAREDLENLQRSLVLSHAAGVGEPLDDAMVRLIMLLKINSLARGFSGIRRKVI 120

Query: 121 DALIALINAEVYPHIPLKGSVGASGDLAPLAHMSLVLLGEGKARYKGEWLPAVEALKVAG 180
           DALIAL+NAEVYPHIPLKGSVGASGDLAPLAHMSLVLLGE +ARY+GEWLPA +AL  AG
Sbjct: 121 DALIALVNAEVYPHIPLKGSVGASGDLAPLAHMSLVLLGESRARYQGEWLPARQALARAG 180

Query: 181 LAPLTLAAKEGLALLNGTQVSTAFALRGLFEGEDLFAGALALGGLTVEAVLGSRSPFDAR 240
           L PLTLAAKEGLALLNGTQVSTA+ALRGLFE EDLFA A   G L+VEA+LGSR+PFDAR
Sbjct: 181 LEPLTLAAKEGLALLNGTQVSTAYALRGLFEAEDLFAAATVCGSLSVEAMLGSRAPFDAR 240

Query: 241 IHAARGQKGQIDAAAAYRDLLGERSEVSDSHQNCDKVQDPYSLRCQPQVMGACLTQFRQA 300
           IHA RGQ+GQIDAAA YR LL + SE++ SH  CDKVQDPYSLRCQPQVMGACLTQ RQA
Sbjct: 241 IHAVRGQRGQIDAAATYRGLLTDTSELARSHAQCDKVQDPYSLRCQPQVMGACLTQLRQA 300

Query: 301 AEVLVIEANAVSDNPLVFAAEGDVISGGNFHAEPVAMAADNMALAIAEIGSLSERRISLM 360
           AEVL +EANAVSDNPLVFAAEGDVISGGNFHAEPVAMAADN+ALAIAEIGSLSERRISLM
Sbjct: 301 AEVLEVEANAVSDNPLVFAAEGDVISGGNFHAEPVAMAADNLALAIAEIGSLSERRISLM 360

Query: 361 MDKHMSQLPPFLVANGGVNSGFMIAQVTAAALASENKALSHPHSVDSLPTSANQEDHVSM 420
           MD+HMSQLPPFLVANGGVNSGFMIAQVTAAALAS+NKAL+HPHSVDSLPTSANQEDHVSM
Sbjct: 361 MDRHMSQLPPFLVANGGVNSGFMIAQVTAAALASDNKALAHPHSVDSLPTSANQEDHVSM 420

Query: 421 APAAGKRLWEMAENTRGILAVEWLAACQGLDLRGGLKTSTKLERARGLLRAQVPFYEKDR 480
           AP AGKRLW MAEN RGILAVEWL ACQGLD R GLK+S KLE+AR LLRA+VP+YEKDR
Sbjct: 421 APNAGKRLWAMAENVRGILAVEWLGACQGLDFREGLKSSPKLEQARSLLRAEVPYYEKDR 480

Query: 481 FFAPDINAASELLASRCLNELVTAQLLPSL 510
           FFAPDI  AS LLA+  LN L+ A+LLPSL
Sbjct: 481 FFAPDIETASRLLAAGTLNALLPARLLPSL 510


Lambda     K      H
   0.318    0.132    0.370 

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: 770
Number of extensions: 10
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: 510
Length of database: 510
Length adjustment: 34
Effective length of query: 476
Effective length of database: 476
Effective search space:   226576
Effective search space used:   226576
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate RR42_RS14640 RR42_RS14640 (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.9276.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.4e-226  737.5   4.0   3.8e-226  737.3   4.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS14640  RR42_RS14640 histidine ammonia-l


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS14640  RR42_RS14640 histidine ammonia-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  737.3   4.0  3.8e-226  3.8e-226       2     504 ..       5     508 ..       4     510 .] 0.99

  Alignments for each domain:
  == domain 1  score: 737.3 bits;  conditional E-value: 3.8e-226
                                 TIGR01225   2 vldgesltledleavarekarvelsaaaeeavaksravieeivaedktvYGvntGFGklasvkidkedl 70 
                                                l++++ltl++l++ + +  rv+l+  a+ea+a+s a++e+ivae +t YG+ntGFG la+++i++edl
  lcl|FitnessBrowser__Cup4G11:RR42_RS14640   5 NLKPGQLTLAQLRQAYLQPLRVSLDGGAAEAIAASVACVENIVAEGRTAYGINTGFGLLAQTRIAREDL 73 
                                               58999**************************************************************** PP

                                 TIGR01225  71 aeLqrnlvrsHaaGvGepleeevvRallvlrlnslakGysgvraevlellvallnaevlPvvpekGsvG 139
                                               ++Lqr+lv+sHaaGvGepl++++vR++++l++nsla+G+sg+r++v+++l+al+naev+P++p kGsvG
  lcl|FitnessBrowser__Cup4G11:RR42_RS14640  74 ENLQRSLVLSHAAGVGEPLDDAMVRLIMLLKINSLARGFSGIRRKVIDALIALVNAEVYPHIPLKGSVG 142
                                               ********************************************************************* PP

                                 TIGR01225 140 asGDLAPLahlalvliGeGeaefegevmdaaeaLaaaglePvtlkakEGlALinGtqlmtalavlalvd 208
                                               asGDLAPLah++lvl+Ge  a+++ge+++a +aLa+agleP+tl+akEGlAL+nGtq++ta+a+++l++
  lcl|FitnessBrowser__Cup4G11:RR42_RS14640 143 ASGDLAPLAHMSLVLLGESRARYQGEWLPARQALARAGLEPLTLAAKEGLALLNGTQVSTAYALRGLFE 211
                                               ********************************************************************* PP

                                 TIGR01225 209 aekllesadiaaalsleallgtskafdpdihevrphrgqiavaarlrella.gseiaeshkdedrvqDa 276
                                               ae+l ++a+++++ls+ea+lg++++fd++ih+vr++rgqi+ aa+ r ll+  se+a+sh ++d+vqD+
  lcl|FitnessBrowser__Cup4G11:RR42_RS14640 212 AEDLFAAATVCGSLSVEAMLGSRAPFDARIHAVRGQRGQIDAAATYRGLLTdTSELARSHAQCDKVQDP 280
                                               *************************************************9978**************** PP

                                 TIGR01225 277 YslRciPqvhGavldtldqvkevlaiElnsatDnPlvfadegevvsgGnFHgepvAlaldflaiaiael 345
                                               YslRc+Pqv+Ga+l++l+q++evl++E+n+++DnPlvfa+eg+v+sgGnFH+epvA+a+d+la+aiae+
  lcl|FitnessBrowser__Cup4G11:RR42_RS14640 281 YSLRCQPQVMGACLTQLRQAAEVLEVEANAVSDNPLVFAAEGDVISGGNFHAEPVAMAADNLALAIAEI 349
                                               ********************************************************************* PP

                                 TIGR01225 346 gaiseRRierlldpalseLppFLaedsGlnsGlmiaqytaAaLvsenkaLahPasvDsiptsanqEDHv 414
                                               g++seRRi++++d+++s+LppFL++++G+nsG+miaq+taAaL+s+nkaLahP+svDs+ptsanqEDHv
  lcl|FitnessBrowser__Cup4G11:RR42_RS14640 350 GSLSERRISLMMDRHMSQLPPFLVANGGVNSGFMIAQVTAAALASDNKALAHPHSVDSLPTSANQEDHV 418
                                               ********************************************************************* PP

                                 TIGR01225 415 smgaaaarkllevvenvrrviaiEllaaaqglefrkaektaaelekvyeavRevveeleeDRvlapDle 483
                                               sm+  a+++l+ ++envr ++a+E+l a+qgl+fr+  k++++le+++ ++R++v+ +e+DR++apD+e
  lcl|FitnessBrowser__Cup4G11:RR42_RS14640 419 SMAPNAGKRLWAMAENVRGILAVEWLGACQGLDFREGLKSSPKLEQARSLLRAEVPYYEKDRFFAPDIE 487
                                               ********************************************************************* PP

                                 TIGR01225 484 avkellekesleaaveakvka 504
                                               ++++ll++++l+a ++a++++
  lcl|FitnessBrowser__Cup4G11:RR42_RS14640 488 TASRLLAAGTLNALLPARLLP 508
                                               ************999987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (506 nodes)
Target sequences:                          1  (510 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: 00:00:00.03
# Mc/sec: 7.11
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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