GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutH in Shewanella loihica PV-4

Align histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate 5211344 Shew_3756 histidine ammonia-lyase (RefSeq)

Query= BRENDA::P21310
         (510 letters)



>FitnessBrowser__PV4:5211344
          Length = 510

 Score =  686 bits (1770), Expect = 0.0
 Identities = 356/510 (69%), Positives = 414/510 (81%)

Query: 1   MTELTLKPGTLTLAQLRAIHAAPVRLQLDASAAPAIDASVACVEQIIAEDRTAYGINTGF 60
           M+ L LKPGTL+LAQLRAI    V L+L  SA   I+ S   V++++ E RT YGINTGF
Sbjct: 1   MSHLVLKPGTLSLAQLRAISRGKVSLELCDSAVADINTSAGLVQKVLDEGRTVYGINTGF 60

Query: 61  GLLASTRIASHDLENLQRSLVLSHAAGIGAPLDDDLVRLIMVLKINSLSRGFSGIRRKVI 120
           GLLA+T+I   DL+ LQRS+VLSHAAG G  + D  VRL+MVLKINSLSRGFSGIR +VI
Sbjct: 61  GLLANTKIGEQDLQLLQRSIVLSHAAGTGQYMQDATVRLMMVLKINSLSRGFSGIRLEVI 120

Query: 121 DALIALVNAEVYPHIPLKGSVGASGDLAPLAHMSLVLLGEGKARYKGQWLSATEALAVAG 180
           + LIALVNAEVYP +P KGSVGASGDLAPL+HM L LLGEG+  YKGQ +SA E L +AG
Sbjct: 121 NFLIALVNAEVYPCVPEKGSVGASGDLAPLSHMCLPLLGEGEMSYKGQIISAAEGLEIAG 180

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

Query: 241 IHEARGQRGQIDTAACFRDLLGDSSEVSLSHKNCDKVQDPYSLRCQPQVMGACLTQLRQA 300
           IH ARGQ+GQID+AA FR LLGD SE+SL H NC+KVQDPYSLRCQPQV+GACLTQ+R A
Sbjct: 241 IHAARGQKGQIDSAAVFRHLLGDESEISLDHINCEKVQDPYSLRCQPQVLGACLTQIRHA 300

Query: 301 AEVLGIEANAVSDNPLVFAAEGDVISGGNFHAEPVAMAADNLALAIAEIGSLSERRISLM 360
           AEVL  EAN V+DNPLVF   GD+ISGGNFHAEPVAMAADNLA+A+AE+GS++ERRI+L+
Sbjct: 301 AEVLATEANGVTDNPLVFQDTGDIISGGNFHAEPVAMAADNLAIALAELGSIAERRIALL 360

Query: 361 MDKHMSQLPPFLVENGGVNSGFMIAQVTAAALASENKALSHPHSVDSLPTSANQEDHVSM 420
           +D ++S+LPPFLVENGGVNSGFMIAQVTAAALASENK  +HP SVDSLPTSANQEDHVSM
Sbjct: 361 IDSNLSKLPPFLVENGGVNSGFMIAQVTAAALASENKTYAHPASVDSLPTSANQEDHVSM 420

Query: 421 APAAGKRLWEMAENTRGVLAIEWLGACQGLDLRKGLKTSAKLEKARQALRSEVAHYDRDR 480
           A  A +RL +M+ENTRGVLA+E L A QGLD R  L+ +  + KA+  LR  VA+YD+DR
Sbjct: 421 ATFAARRLRDMSENTRGVLAVELLAAAQGLDFRAPLQPATAVAKAKAELREVVAYYDKDR 480

Query: 481 FFAPDIEKAVELLAKGSLTGLLPAGVLPSL 510
           FF PDIE A +LL   S    LPAGVLPSL
Sbjct: 481 FFGPDIEAATDLLLSASYNQYLPAGVLPSL 510


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: 738
Number of extensions: 23
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 5211344 Shew_3756 (histidine ammonia-lyase (RefSeq))
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.21676.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   3.6e-219  714.3   4.9   4.1e-219  714.1   4.9    1.0  1  lcl|FitnessBrowser__PV4:5211344  Shew_3756 histidine ammonia-lyas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5211344  Shew_3756 histidine ammonia-lyase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  714.1   4.9  4.1e-219  4.1e-219       2     504 ..       5     508 ..       4     510 .] 0.99

  Alignments for each domain:
  == domain 1  score: 714.1 bits;  conditional E-value: 4.1e-219
                        TIGR01225   2 vldgesltledleavarekarvelsaaaeeavaksravieeivaedktvYGvntGFGklasvkidkedlaeLqrnlvr 79 
                                      vl++++l+l++l+a+ r k  +el ++a + ++ s+  ++++++e +tvYG+ntGFG la++ki ++dl+ Lqr++v+
  lcl|FitnessBrowser__PV4:5211344   5 VLKPGTLSLAQLRAISRGKVSLELCDSAVADINTSAGLVQKVLDEGRTVYGINTGFGLLANTKIGEQDLQLLQRSIVL 82 
                                      7999************************************************************************** PP

                        TIGR01225  80 sHaaGvGepleeevvRallvlrlnslakGysgvraevlellvallnaevlPvvpekGsvGasGDLAPLahlalvliGe 157
                                      sHaaG G+++++++vR+++vl++nsl++G+sg+r ev++ l+al+naev+P vpekGsvGasGDLAPL+h+ l l+Ge
  lcl|FitnessBrowser__PV4:5211344  83 SHAAGTGQYMQDATVRLMMVLKINSLSRGFSGIRLEVINFLIALVNAEVYPCVPEKGSVGASGDLAPLSHMCLPLLGE 160
                                      ****************************************************************************** PP

                        TIGR01225 158 GeaefegevmdaaeaLaaaglePvtlkakEGlALinGtqlmtalavlalvdaekllesadiaaalsleallgtskafd 235
                                      Ge+ ++g++++aae L+ agl+P++l+akEGlAL+nGtq++tala+++l++ae+l +++++++a+s+ea++g++++fd
  lcl|FitnessBrowser__PV4:5211344 161 GEMSYKGQIISAAEGLEIAGLKPIELAAKEGLALLNGTQASTALALEGLFNAEDLFAASSVIGAMSVEAAMGSRSPFD 238
                                      ****************************************************************************** PP

                        TIGR01225 236 pdihevrphrgqiavaarlrella.gseiaeshkdedrvqDaYslRciPqvhGavldtldqvkevlaiElnsatDnPl 312
                                      p+ih++r+++gqi++aa +r+ll  +sei+  h ++++vqD+YslRc+Pqv Ga+l+++++++evla+E+n +tDnPl
  lcl|FitnessBrowser__PV4:5211344 239 PRIHAARGQKGQIDSAAVFRHLLGdESEISLDHINCEKVQDPYSLRCQPQVLGACLTQIRHAAEVLATEANGVTDNPL 316
                                      ***********************879**************************************************** PP

                        TIGR01225 313 vfadegevvsgGnFHgepvAlaldflaiaiaelgaiseRRierlldpalseLppFLaedsGlnsGlmiaqytaAaLvs 390
                                      vf+d+g+++sgGnFH+epvA+a+d+laia+aelg+i+eRRi++l+d +ls+LppFL+e++G+nsG+miaq+taAaL+s
  lcl|FitnessBrowser__PV4:5211344 317 VFQDTGDIISGGNFHAEPVAMAADNLAIALAELGSIAERRIALLIDSNLSKLPPFLVENGGVNSGFMIAQVTAAALAS 394
                                      ****************************************************************************** PP

                        TIGR01225 391 enkaLahPasvDsiptsanqEDHvsmgaaaarkllevvenvrrviaiEllaaaqglefrkaektaaelekvyeavRev 468
                                      enk+ ahPasvDs+ptsanqEDHvsm++ aar+l+++ en+r v+a+Ellaaaqgl+fr++ + a++++k+ +++Rev
  lcl|FitnessBrowser__PV4:5211344 395 ENKTYAHPASVDSLPTSANQEDHVSMATFAARRLRDMSENTRGVLAVELLAAAQGLDFRAPLQPATAVAKAKAELREV 472
                                      ****************************************************************************** PP

                        TIGR01225 469 veeleeDRvlapDleavkellekesleaaveakvka 504
                                      v+ +++DR++ pD+ea+++ll + s+++ ++a v++
  lcl|FitnessBrowser__PV4:5211344 473 VAYYDKDRFFGPDIEAATDLLLSASYNQYLPAGVLP 508
                                      *********************999999988887765 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 11.32
//
[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