GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutH in Pseudomonas putida KT2440

Align histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate PP_5032 PP_5032 Histidine ammonia-lyase

Query= BRENDA::P21310
         (510 letters)



>FitnessBrowser__Putida:PP_5032
          Length = 510

 Score =  970 bits (2507), Expect = 0.0
 Identities = 501/510 (98%), Positives = 505/510 (99%)

Query: 1   MTELTLKPGTLTLAQLRAIHAAPVRLQLDASAAPAIDASVACVEQIIAEDRTAYGINTGF 60
           MTELTLKPGTLTLAQLRAIHAAPVRLQLDASAAPAIDASVACVEQIIAEDRTAYGINTGF
Sbjct: 1   MTELTLKPGTLTLAQLRAIHAAPVRLQLDASAAPAIDASVACVEQIIAEDRTAYGINTGF 60

Query: 61  GLLASTRIASHDLENLQRSLVLSHAAGIGAPLDDDLVRLIMVLKINSLSRGFSGIRRKVI 120
           GLLASTRIASHDLENLQRSLVLSHAAGIGAPLDDDLVRLIMVLKINSLSRGFSGIRRKVI
Sbjct: 61  GLLASTRIASHDLENLQRSLVLSHAAGIGAPLDDDLVRLIMVLKINSLSRGFSGIRRKVI 120

Query: 121 DALIALVNAEVYPHIPLKGSVGASGDLAPLAHMSLVLLGEGKARYKGQWLSATEALAVAG 180
           DALIALVNAEVYPHIPLKGSVGASGDLAPLAHMSLVLLGEGKARYKGQWL ATEALA+AG
Sbjct: 121 DALIALVNAEVYPHIPLKGSVGASGDLAPLAHMSLVLLGEGKARYKGQWLPATEALAIAG 180

Query: 181 LEPLTLAAKEGLALLNGTQASTAYALRGLFYAEDLYAAAIACGGLSVEAVLGSRSPFDAR 240
           LEPLTLAAKEGLALLNGTQASTAYALRGLF AEDLYAAAIACGGLSVEA LGSRSPFDAR
Sbjct: 181 LEPLTLAAKEGLALLNGTQASTAYALRGLFQAEDLYAAAIACGGLSVEAALGSRSPFDAR 240

Query: 241 IHEARGQRGQIDTAACFRDLLGDSSEVSLSHKNCDKVQDPYSLRCQPQVMGACLTQLRQA 300
           +HE RGQRGQIDTAACFRDLLGDSSEVSLSHKNCDKVQDPYSLRCQPQVMGACLTQLRQA
Sbjct: 241 VHEVRGQRGQIDTAACFRDLLGDSSEVSLSHKNCDKVQDPYSLRCQPQVMGACLTQLRQA 300

Query: 301 AEVLGIEANAVSDNPLVFAAEGDVISGGNFHAEPVAMAADNLALAIAEIGSLSERRISLM 360
           AEVLGIEANAVSDNPLVFAAEGDVISGGNFHAEPVAMAADNLALAIAEIGSLSERRISLM
Sbjct: 301 AEVLGIEANAVSDNPLVFAAEGDVISGGNFHAEPVAMAADNLALAIAEIGSLSERRISLM 360

Query: 361 MDKHMSQLPPFLVENGGVNSGFMIAQVTAAALASENKALSHPHSVDSLPTSANQEDHVSM 420
           MDKHMSQLPPFLVENGGVNSGFMIAQVTAAALASENKALSHPHSVDSLPTSANQEDHVSM
Sbjct: 361 MDKHMSQLPPFLVENGGVNSGFMIAQVTAAALASENKALSHPHSVDSLPTSANQEDHVSM 420

Query: 421 APAAGKRLWEMAENTRGVLAIEWLGACQGLDLRKGLKTSAKLEKARQALRSEVAHYDRDR 480
           APAAGKRLWEMAENTRGVLAIEWLGACQGLDLRKGLKTSAKLE+ARQALRSEV HYDRDR
Sbjct: 421 APAAGKRLWEMAENTRGVLAIEWLGACQGLDLRKGLKTSAKLEQARQALRSEVPHYDRDR 480

Query: 481 FFAPDIEKAVELLAKGSLTGLLPAGVLPSL 510
           FFAPDIEKAV+LLAKGSLTGLLPAGVLPSL
Sbjct: 481 FFAPDIEKAVDLLAKGSLTGLLPAGVLPSL 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: 909
Number of extensions: 11
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 PP_5032 PP_5032 (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.12209.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   3.3e-235  767.2   3.4   3.7e-235  767.1   3.4    1.0  1  lcl|FitnessBrowser__Putida:PP_5032  PP_5032 Histidine ammonia-lyase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_5032  PP_5032 Histidine ammonia-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  767.1   3.4  3.7e-235  3.7e-235       2     505 ..       5     509 ..       4     510 .] 0.99

  Alignments for each domain:
  == domain 1  score: 767.1 bits;  conditional E-value: 3.7e-235
                           TIGR01225   2 vldgesltledleavarekarvelsaaaeeavaksravieeivaedktvYGvntGFGklasvkidkedlaeLqrn 76 
                                         +l++++ltl++l+a++++  r++l+a+a+ a+++s a++e+i+aed+t YG+ntGFG las++i+++dl++Lqr+
  lcl|FitnessBrowser__Putida:PP_5032   5 TLKPGTLTLAQLRAIHAAPVRLQLDASAAPAIDASVACVEQIIAEDRTAYGINTGFGLLASTRIASHDLENLQRS 79 
                                         7999*********************************************************************** PP

                           TIGR01225  77 lvrsHaaGvGepleeevvRallvlrlnslakGysgvraevlellvallnaevlPvvpekGsvGasGDLAPLahla 151
                                         lv+sHaaG+G+pl++++vR+++vl++nsl++G+sg+r++v+++l+al+naev+P++p kGsvGasGDLAPLah++
  lcl|FitnessBrowser__Putida:PP_5032  80 LVLSHAAGIGAPLDDDLVRLIMVLKINSLSRGFSGIRRKVIDALIALVNAEVYPHIPLKGSVGASGDLAPLAHMS 154
                                         *************************************************************************** PP

                           TIGR01225 152 lvliGeGeaefegevmdaaeaLaaaglePvtlkakEGlALinGtqlmtalavlalvdaekllesadiaaalslea 226
                                         lvl+GeG+a+++g++++a+eaLa agleP+tl+akEGlAL+nGtq++ta+a+++l++ae+l+++a+++++ls+ea
  lcl|FitnessBrowser__Putida:PP_5032 155 LVLLGEGKARYKGQWLPATEALAIAGLEPLTLAAKEGLALLNGTQASTAYALRGLFQAEDLYAAAIACGGLSVEA 229
                                         *************************************************************************** PP

                           TIGR01225 227 llgtskafdpdihevrphrgqiavaarlrella.gseiaeshkdedrvqDaYslRciPqvhGavldtldqvkevl 300
                                         +lg++++fd+++hevr++rgqi++aa++r+ll  +se++ shk++d+vqD+YslRc+Pqv+Ga+l++l+q++evl
  lcl|FitnessBrowser__Putida:PP_5032 230 ALGSRSPFDARVHEVRGQRGQIDTAACFRDLLGdSSEVSLSHKNCDKVQDPYSLRCQPQVMGACLTQLRQAAEVL 304
                                         ********************************9689*************************************** PP

                           TIGR01225 301 aiElnsatDnPlvfadegevvsgGnFHgepvAlaldflaiaiaelgaiseRRierlldpalseLppFLaedsGln 375
                                         +iE+n+++DnPlvfa+eg+v+sgGnFH+epvA+a+d+la+aiae+g++seRRi++++d+++s+LppFL+e++G+n
  lcl|FitnessBrowser__Putida:PP_5032 305 GIEANAVSDNPLVFAAEGDVISGGNFHAEPVAMAADNLALAIAEIGSLSERRISLMMDKHMSQLPPFLVENGGVN 379
                                         *************************************************************************** PP

                           TIGR01225 376 sGlmiaqytaAaLvsenkaLahPasvDsiptsanqEDHvsmgaaaarkllevvenvrrviaiEllaaaqglefrk 450
                                         sG+miaq+taAaL+senkaL+hP+svDs+ptsanqEDHvsm+ aa+++l+e++en+r v+aiE+l a+qgl++rk
  lcl|FitnessBrowser__Putida:PP_5032 380 SGFMIAQVTAAALASENKALSHPHSVDSLPTSANQEDHVSMAPAAGKRLWEMAENTRGVLAIEWLGACQGLDLRK 454
                                         *************************************************************************** PP

                           TIGR01225 451 aektaaelekvyeavRevveeleeDRvlapDleavkellekesleaaveakvkak 505
                                           kt+a+le++++a+R++v+++++DR++apD+e++ +ll+k+sl+  ++a v+++
  lcl|FitnessBrowser__Putida:PP_5032 455 GLKTSAKLEQARQALRSEVPHYDRDRFFAPDIEKAVDLLAKGSLTGLLPAGVLPS 509
                                         *********************************************9999888765 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: 9.99
//
[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