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

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.27466.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 9.42
//
[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