Alignments for a candidate for hutH in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutH in Pseudomonas fluorescens FW300-N2C3

Align Histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate AO356_09605 AO356_09605 histidine ammonia-lyase

Query= reanno::pseudo5_N2C3_1:AO356_09605
         (507 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_09605
          Length = 507

 Score =  987 bits (2552), Expect = 0.0
 Identities = 507/507 (100%), Positives = 507/507 (100%)

Query: 1   MSQAEKIVITGAPLRWQDVVAVARFGAELELSTQTWARIDNAQAIVQRIVESGERAYGVN 60
           MSQAEKIVITGAPLRWQDVVAVARFGAELELSTQTWARIDNAQAIVQRIVESGERAYGVN
Sbjct: 1   MSQAEKIVITGAPLRWQDVVAVARFGAELELSTQTWARIDNAQAIVQRIVESGERAYGVN 60

Query: 61  TGLGALCNVSLKDEQLSQLSRNTLLSHACGVGAPLTDEQTRAILCAAILNYSQGKSGIHR 120
           TGLGALCNVSLKDEQLSQLSRNTLLSHACGVGAPLTDEQTRAILCAAILNYSQGKSGIHR
Sbjct: 61  TGLGALCNVSLKDEQLSQLSRNTLLSHACGVGAPLTDEQTRAILCAAILNYSQGKSGIHR 120

Query: 121 RVVEALLALLNRGITPQVPSQGSVGYLTHMAHIGIALLGVGQVSYRGQIVPAQQALVAEG 180
           RVVEALLALLNRGITPQVPSQGSVGYLTHMAHIGIALLGVGQVSYRGQIVPAQQALVAEG
Sbjct: 121 RVVEALLALLNRGITPQVPSQGSVGYLTHMAHIGIALLGVGQVSYRGQIVPAQQALVAEG 180

Query: 181 LQPVQLGAKDGLCLVNGTPCMTGLSCLALADATRLVQWADVIGAMSFEAQRGQIAAFDAE 240
           LQPVQLGAKDGLCLVNGTPCMTGLSCLALADATRLVQWADVIGAMSFEAQRGQIAAFDAE
Sbjct: 181 LQPVQLGAKDGLCLVNGTPCMTGLSCLALADATRLVQWADVIGAMSFEAQRGQIAAFDAE 240

Query: 241 IIALKPHPGMQQVGVNLRALLDGSEVIAASRGIRTQDALSIRSIPQVHGAARDQLAHARQ 300
           IIALKPHPGMQQVGVNLRALLDGSEVIAASRGIRTQDALSIRSIPQVHGAARDQLAHARQ
Sbjct: 241 IIALKPHPGMQQVGVNLRALLDGSEVIAASRGIRTQDALSIRSIPQVHGAARDQLAHARQ 300

Query: 301 QIETELNAVTDNPLLLGTPENFRVMSQANPHGQSVALAADLLAIAMAEIGSIAERRLDRL 360
           QIETELNAVTDNPLLLGTPENFRVMSQANPHGQSVALAADLLAIAMAEIGSIAERRLDRL
Sbjct: 301 QIETELNAVTDNPLLLGTPENFRVMSQANPHGQSVALAADLLAIAMAEIGSIAERRLDRL 360

Query: 361 INPHVSGLPAFLVANPGVNSGMMIVQYVAASLCAENKQLAQPAVLDNFVTSGLQEDHLSM 420
           INPHVSGLPAFLVANPGVNSGMMIVQYVAASLCAENKQLAQPAVLDNFVTSGLQEDHLSM
Sbjct: 361 INPHVSGLPAFLVANPGVNSGMMIVQYVAASLCAENKQLAQPAVLDNFVTSGLQEDHLSM 420

Query: 421 GTNAALKLHRALENCTQILAIEYLLAAQAFEFLKAQRFGAGTDIAWKLLRERVPPYDQDR 480
           GTNAALKLHRALENCTQILAIEYLLAAQAFEFLKAQRFGAGTDIAWKLLRERVPPYDQDR
Sbjct: 421 GTNAALKLHRALENCTQILAIEYLLAAQAFEFLKAQRFGAGTDIAWKLLRERVPPYDQDR 480

Query: 481 WLAPDIASAAGLLKDPNVLHNVLPNLN 507
           WLAPDIASAAGLLKDPNVLHNVLPNLN
Sbjct: 481 WLAPDIASAAGLLKDPNVLHNVLPNLN 507


Lambda     K      H
   0.320    0.133    0.385 

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: 998
Number of extensions: 24
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: 507
Length of database: 507
Length adjustment: 34
Effective length of query: 473
Effective length of database: 473
Effective search space:   223729
Effective search space used:   223729
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

Align candidate AO356_09605 AO356_09605 (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.24425.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   3.9e-169  549.2   4.6   4.8e-169  548.9   4.6    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09605  AO356_09605 histidine ammonia-ly


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09605  AO356_09605 histidine ammonia-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  548.9   4.6  4.8e-169  4.8e-169       1     494 [.       7     498 ..       7     505 .. 0.98

  Alignments for each domain:
  == domain 1  score: 548.9 bits;  conditional E-value: 4.8e-169
                                       TIGR01225   1 vvldgesltledleavarekarvelsaaaeeavaksravieeivaedktvYGvntGFGklasv 63 
                                                     +v+ g  l+ +d++avar +a++els ++ +++++++a++++iv++ +  YGvntG G+l +v
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09605   7 IVITGAPLRWQDVVAVARFGAELELSTQTWARIDNAQAIVQRIVESGERAYGVNTGLGALCNV 69 
                                                     6789999******************************************************** PP

                                       TIGR01225  64 kidkedlaeLqrnlvrsHaaGvGepleeevvRallvlrlnslakGysgvraevlellvallna 126
                                                      ++ e+l +L rn ++sHa+GvG+pl++e +Ra+l   +   ++G sg+ ++v+e+l+alln+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09605  70 SLKDEQLSQLSRNTLLSHACGVGAPLTDEQTRAILCAAILNYSQGKSGIHRRVVEALLALLNR 132
                                                     *************************************************************** PP

                                       TIGR01225 127 evlPvvpekGsvGasGDLAPLahlalvliGeGeaefegevmdaaeaLaaaglePvtlkakEGl 189
                                                     +++P vp++GsvG    L  +ah++++l+G G++ ++g++++a++aL a gl+Pv+l ak+Gl
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09605 133 GITPQVPSQGSVG---YLTHMAHIGIALLGVGQVSYRGQIVPAQQALVAEGLQPVQLGAKDGL 192
                                                     ************7...6999******************************************* PP

                                       TIGR01225 190 ALinGtqlmtalavlalvdaekllesadiaaalsleallgtskafdpdihevrphrgqiavaa 252
                                                      L+nGt +mt+l +lal+da +l++ ad+++a+s+ea  g  +afd++i +++ph+g  +v+ 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09605 193 CLVNGTPCMTGLSCLALADATRLVQWADVIGAMSFEAQRGQIAAFDAEIIALKPHPGMQQVGV 255
                                                     *************************************************************** PP

                                       TIGR01225 253 rlrellagseiaeshkdedrvqDaYslRciPqvhGavldtldqvkevlaiElnsatDnPlvf. 314
                                                     +lr ll+gse+        r qDa s+R+iPqvhGa++d+l+++++ +++Eln++tDnPl++ 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09605 256 NLRALLDGSEVIAAS-RGIRTQDALSIRSIPQVHGAARDQLAHARQQIETELNAVTDNPLLLg 317
                                                     ************999.5689*****************************************83 PP

                                       TIGR01225 315 .adegevvsgGnFHgepvAlaldflaiaiaelgaiseRRierlldpalseLppFLaedsGlns 376
                                                      +++ +v+s  n Hg+ vAla+d laia+ae+g+i+eRR++rl++p+ s+Lp+FL++++G+ns
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09605 318 tPENFRVMSQANPHGQSVALAADLLAIAMAEIGSIAERRLDRLINPHVSGLPAFLVANPGVNS 380
                                                     357789********************************************************* PP

                                       TIGR01225 377 GlmiaqytaAaLvsenkaLahPasvDsiptsanqEDHvsmgaaaarkllevvenvrrviaiEl 439
                                                     G+mi qy aA+L+ enk+La+Pa +D+  ts+ qEDH smg+ aa kl ++ en ++++aiE+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09605 381 GMMIVQYVAASLCAENKQLAQPAVLDNFVTSGLQEDHLSMGTNAALKLHRALENCTQILAIEY 443
                                                     *************************************************************** PP

                                       TIGR01225 440 laaaqglefrkaektaaelekvyeavRevveeleeDRvlapDleavkellekesl 494
                                                     l+aaq+ ef+ka++  a ++ + +++Re v+++++DR lapD++ +  ll++ ++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09605 444 LLAAQAFEFLKAQRFGAGTDIAWKLLRERVPPYDQDRWLAPDIASAAGLLKDPNV 498
                                                     **********************************************999987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (506 nodes)
Target sequences:                          1  (507 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: 00:00:00.02
# Mc/sec: 9.62
//
[ok]

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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