Alignments for a candidate for hutH in Pseudomonas putida KT2440

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.27642.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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.25
//
[ok]

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

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Protein sequences (fasta format)
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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