Alignments for a candidate for hutH in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutH in Shewanella oneidensis MR-1

Align histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate 199295 SO0098 histidine ammonia-lyase (NCBI ptt file)

Query= BRENDA::P21310
         (510 letters)



>FitnessBrowser__MR1:199295
          Length = 513

 Score =  670 bits (1729), Expect = 0.0
 Identities = 349/510 (68%), Positives = 411/510 (80%)

Query: 1   MTELTLKPGTLTLAQLRAIHAAPVRLQLDASAAPAIDASVACVEQIIAEDRTAYGINTGF 60
           +  L L PG+L+LAQLR I    + L+L   A   I+ S   V++++ E RT YGINTGF
Sbjct: 4   VNHLVLTPGSLSLAQLREISRHKLTLELAPEAINDINISAQIVQKVLDEGRTVYGINTGF 63

Query: 61  GLLASTRIASHDLENLQRSLVLSHAAGIGAPLDDDLVRLIMVLKINSLSRGFSGIRRKVI 120
           GLLA+T+IA  DL+ LQRS+VLSHAAG G  + D  VRL+MVLKINSLSRGFSGIR +VI
Sbjct: 64  GLLANTKIAPEDLQLLQRSIVLSHAAGTGQYMQDATVRLMMVLKINSLSRGFSGIRLEVI 123

Query: 121 DALIALVNAEVYPHIPLKGSVGASGDLAPLAHMSLVLLGEGKARYKGQWLSATEALAVAG 180
           + LI+LVNAEVYP +P KGSVGASGDLAPLAHM L LLGEG+  Y+GQ +SA E L +AG
Sbjct: 124 NFLISLVNAEVYPCVPEKGSVGASGDLAPLAHMCLPLLGEGEMSYQGQIISAAEGLEIAG 183

Query: 181 LEPLTLAAKEGLALLNGTQASTAYALRGLFYAEDLYAAAIACGGLSVEAVLGSRSPFDAR 240
           L+P+ LAAKEGLALLNGTQASTA AL GLF+AEDL+AA+   G +SVEA +GSRSPFD R
Sbjct: 184 LKPIDLAAKEGLALLNGTQASTALALEGLFHAEDLFAASSVIGAMSVEAAMGSRSPFDPR 243

Query: 241 IHEARGQRGQIDTAACFRDLLGDSSEVSLSHKNCDKVQDPYSLRCQPQVMGACLTQLRQA 300
           IH ARGQ+GQID+A  FR LLG+ SE+SLSH NC+KVQDPYSLRCQPQV+GACLTQ+RQA
Sbjct: 244 IHAARGQKGQIDSAMVFRYLLGEESEISLSHANCEKVQDPYSLRCQPQVLGACLTQIRQA 303

Query: 301 AEVLGIEANAVSDNPLVFAAEGDVISGGNFHAEPVAMAADNLALAIAEIGSLSERRISLM 360
           AEVL  EAN V+DNPLVF   GD+ISGGNFHAEPVAMAADNLA+AIAE+G+++ERRI+L+
Sbjct: 304 AEVLATEANGVTDNPLVFQDTGDIISGGNFHAEPVAMAADNLAIAIAELGAIAERRIALL 363

Query: 361 MDKHMSQLPPFLVENGGVNSGFMIAQVTAAALASENKALSHPHSVDSLPTSANQEDHVSM 420
           +D  +S+LPPFLV+NGGVNSGFMIAQVTAAALASENK  +HP SVDSLPTSANQEDHVSM
Sbjct: 364 IDSSLSKLPPFLVKNGGVNSGFMIAQVTAAALASENKTYAHPASVDSLPTSANQEDHVSM 423

Query: 421 APAAGKRLWEMAENTRGVLAIEWLGACQGLDLRKGLKTSAKLEKARQALRSEVAHYDRDR 480
           A  A +RL +M+ENTRGVLAIE L A QGLD R  L  S  + +A+  LR  VA+YD+DR
Sbjct: 424 ATFAARRLRDMSENTRGVLAIELLAAAQGLDFRAPLTPSKAVAQAKAELREVVAYYDKDR 483

Query: 481 FFAPDIEKAVELLAKGSLTGLLPAGVLPSL 510
           +FAPDIE A +LL   S    LP GVLPSL
Sbjct: 484 YFAPDIEAATDLLYTASFNAYLPLGVLPSL 513


Lambda     K      H
   0.318    0.132    0.374 

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: 722
Number of extensions: 21
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: 513
Length adjustment: 35
Effective length of query: 475
Effective length of database: 478
Effective search space:   227050
Effective search space used:   227050
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 199295 SO0098 (histidine ammonia-lyase (NCBI ptt file))
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.22678.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   3.7e-219  714.2   4.2   4.2e-219  714.1   4.2    1.0  1  lcl|FitnessBrowser__MR1:199295  SO0098 histidine ammonia-lyase (


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:199295  SO0098 histidine ammonia-lyase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  714.1   4.2  4.2e-219  4.2e-219       2     502 ..       8     509 ..       7     513 .] 0.99

  Alignments for each domain:
  == domain 1  score: 714.1 bits;  conditional E-value: 4.2e-219
                       TIGR01225   2 vldgesltledleavarekarvelsaaaeeavaksravieeivaedktvYGvntGFGklasvkidkedlaeLqrnlvrs 80 
                                     vl ++sl+l++l+++ r+k  +el+ +a + ++ s+++++++++e +tvYG+ntGFG la++ki+ edl+ Lqr++v+s
  lcl|FitnessBrowser__MR1:199295   8 VLTPGSLSLAQLREISRHKLTLELAPEAINDINISAQIVQKVLDEGRTVYGINTGFGLLANTKIAPEDLQLLQRSIVLS 86 
                                     78999************************************************************************** PP

                       TIGR01225  81 HaaGvGepleeevvRallvlrlnslakGysgvraevlellvallnaevlPvvpekGsvGasGDLAPLahlalvliGeGe 159
                                     HaaG G+++++++vR+++vl++nsl++G+sg+r ev++ l+ l+naev+P vpekGsvGasGDLAPLah+ l l+GeGe
  lcl|FitnessBrowser__MR1:199295  87 HAAGTGQYMQDATVRLMMVLKINSLSRGFSGIRLEVINFLISLVNAEVYPCVPEKGSVGASGDLAPLAHMCLPLLGEGE 165
                                     ******************************************************************************* PP

                       TIGR01225 160 aefegevmdaaeaLaaaglePvtlkakEGlALinGtqlmtalavlalvdaekllesadiaaalsleallgtskafdpdi 238
                                     + ++g++++aae L+ agl+P+ l+akEGlAL+nGtq++tala+++l++ae+l +++++++a+s+ea++g++++fdp+i
  lcl|FitnessBrowser__MR1:199295 166 MSYQGQIISAAEGLEIAGLKPIDLAAKEGLALLNGTQASTALALEGLFHAEDLFAASSVIGAMSVEAAMGSRSPFDPRI 244
                                     ******************************************************************************* PP

                       TIGR01225 239 hevrphrgqiavaarlrella.gseiaeshkdedrvqDaYslRciPqvhGavldtldqvkevlaiElnsatDnPlvfad 316
                                     h++r+++gqi++a  +r ll  +sei+ sh ++++vqD+YslRc+Pqv Ga+l++++q++evla+E+n +tDnPlvf+d
  lcl|FitnessBrowser__MR1:199295 245 HAARGQKGQIDSAMVFRYLLGeESEISLSHANCEKVQDPYSLRCQPQVLGACLTQIRQAAEVLATEANGVTDNPLVFQD 323
                                     ********************989******************************************************** PP

                       TIGR01225 317 egevvsgGnFHgepvAlaldflaiaiaelgaiseRRierlldpalseLppFLaedsGlnsGlmiaqytaAaLvsenkaL 395
                                     +g+++sgGnFH+epvA+a+d+laiaiaelgai+eRRi++l+d +ls+LppFL++++G+nsG+miaq+taAaL+senk+ 
  lcl|FitnessBrowser__MR1:199295 324 TGDIISGGNFHAEPVAMAADNLAIAIAELGAIAERRIALLIDSSLSKLPPFLVKNGGVNSGFMIAQVTAAALASENKTY 402
                                     ******************************************************************************* PP

                       TIGR01225 396 ahPasvDsiptsanqEDHvsmgaaaarkllevvenvrrviaiEllaaaqglefrkaektaaelekvyeavRevveelee 474
                                     ahPasvDs+ptsanqEDHvsm++ aar+l+++ en+r v+aiEllaaaqgl+fr++ + + +++++ +++Revv+ +++
  lcl|FitnessBrowser__MR1:199295 403 AHPASVDSLPTSANQEDHVSMATFAARRLRDMSENTRGVLAIELLAAAQGLDFRAPLTPSKAVAQAKAELREVVAYYDK 481
                                     ******************************************************************************* PP

                       TIGR01225 475 DRvlapDleavkellekesleaaveakv 502
                                     DR++apD+ea+++ll + s++a ++  v
  lcl|FitnessBrowser__MR1:199295 482 DRYFAPDIEAATDLLYTASFNAYLPLGV 509
                                     ***************9999988777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (506 nodes)
Target sequences:                          1  (513 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 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.66
//
[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