Alignments for a candidate for hutH in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutH in Pseudomonas fluorescens FW300-N1B4

Align Histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate Pf1N1B4_1582 Histidine ammonia-lyase (EC 4.3.1.3)

Query= reanno::pseudo1_N1B4:Pf1N1B4_1582
         (507 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1582
          Length = 507

 Score =  988 bits (2554), Expect = 0.0
 Identities = 507/507 (100%), Positives = 507/507 (100%)

Query: 1   MSQAEKIVIADAPLRWQDVVAVARHGAQLELSPQIWTRIENAQAIVQRIVASGERAYGVN 60
           MSQAEKIVIADAPLRWQDVVAVARHGAQLELSPQIWTRIENAQAIVQRIVASGERAYGVN
Sbjct: 1   MSQAEKIVIADAPLRWQDVVAVARHGAQLELSPQIWTRIENAQAIVQRIVASGERAYGVN 60

Query: 61  TGLGALCNVSLKGEQLSQLSRNTLLSHACGVGAPLADEQTRAIICAAIRNYSHGKSGIHR 120
           TGLGALCNVSLKGEQLSQLSRNTLLSHACGVGAPLADEQTRAIICAAIRNYSHGKSGIHR
Sbjct: 61  TGLGALCNVSLKGEQLSQLSRNTLLSHACGVGAPLADEQTRAIICAAIRNYSHGKSGIHR 120

Query: 121 RVVEALLALLNRGITPQVPSQGSVGYLTHMAHIGITLLGVGNVSYRGQIVTAQQALSEEG 180
           RVVEALLALLNRGITPQVPSQGSVGYLTHMAHIGITLLGVGNVSYRGQIVTAQQALSEEG
Sbjct: 121 RVVEALLALLNRGITPQVPSQGSVGYLTHMAHIGITLLGVGNVSYRGQIVTAQQALSEEG 180

Query: 181 LQPVQLGAKDGLCLVNGTPCMTGLSCLAIADATRLVQWADVIGAMSFEAQRGQIAAFDAE 240
           LQPVQLGAKDGLCLVNGTPCMTGLSCLAIADATRLVQWADVIGAMSFEAQRGQIAAFDAE
Sbjct: 181 LQPVQLGAKDGLCLVNGTPCMTGLSCLAIADATRLVQWADVIGAMSFEAQRGQIAAFDAE 240

Query: 241 IIALKPHLGMQQVGINLRALLDGSEVIASSKGIRTQDALSIRSIPQVHGAARDQLEHAKK 300
           IIALKPHLGMQQVGINLRALLDGSEVIASSKGIRTQDALSIRSIPQVHGAARDQLEHAKK
Sbjct: 241 IIALKPHLGMQQVGINLRALLDGSEVIASSKGIRTQDALSIRSIPQVHGAARDQLEHAKK 300

Query: 301 QIETELNSVTDNPMLLGTPDNFRVMSQANPHGQSVALAADLLAIAMAEIGSIAERRLDRL 360
           QIETELNSVTDNPMLLGTPDNFRVMSQANPHGQSVALAADLLAIAMAEIGSIAERRLDRL
Sbjct: 301 QIETELNSVTDNPMLLGTPDNFRVMSQANPHGQSVALAADLLAIAMAEIGSIAERRLDRL 360

Query: 361 INPHVSGLPAFLVANPGVNSGMMIVQYVAASLCAENRQLAQPAVLDNYVTSGLQEDHLSM 420
           INPHVSGLPAFLVANPGVNSGMMIVQYVAASLCAENRQLAQPAVLDNYVTSGLQEDHLSM
Sbjct: 361 INPHVSGLPAFLVANPGVNSGMMIVQYVAASLCAENRQLAQPAVLDNYVTSGLQEDHLSM 420

Query: 421 GTNAALKLHRALENCTQILAIEYLLAAQAFEFLKEQRFGAGTDTAWRLLRERVPAYDQDR 480
           GTNAALKLHRALENCTQILAIEYLLAAQAFEFLKEQRFGAGTDTAWRLLRERVPAYDQDR
Sbjct: 421 GTNAALKLHRALENCTQILAIEYLLAAQAFEFLKEQRFGAGTDTAWRLLRERVPAYDQDR 480

Query: 481 WLAPDIAAAAGVLKDPILLHKALPNLN 507
           WLAPDIAAAAGVLKDPILLHKALPNLN
Sbjct: 481 WLAPDIAAAAGVLKDPILLHKALPNLN 507


Lambda     K      H
   0.319    0.133    0.384 

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: 1032
Number of extensions: 26
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 Pf1N1B4_1582 (Histidine ammonia-lyase (EC 4.3.1.3))
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.13148.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   4.5e-168  545.7   5.6   5.5e-168  545.4   5.6    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1582  Histidine ammonia-lyase (EC 4.3.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1582  Histidine ammonia-lyase (EC 4.3.1.3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  545.4   5.6  5.5e-168  5.5e-168       2     493 ..       8     497 ..       7     505 .. 0.97

  Alignments for each domain:
  == domain 1  score: 545.4 bits;  conditional E-value: 5.5e-168
                                      TIGR01225   2 vldgesltledleavarekarvelsaaaeeavaksravieeivaedktvYGvntGFGklasvki 65 
                                                    v+    l+ +d++avar++a++els +   ++++++a++++iva+ +  YGvntG G+l +v +
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1582   8 VIADAPLRWQDVVAVARHGAQLELSPQIWTRIENAQAIVQRIVASGERAYGVNTGLGALCNVSL 71 
                                                    667778999******************************************************* PP

                                      TIGR01225  66 dkedlaeLqrnlvrsHaaGvGepleeevvRallvlrlnslakGysgvraevlellvallnaevl 129
                                                    + e+l +L rn ++sHa+GvG+pl +e +Ra++   ++  ++G sg+ ++v+e+l+alln++++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1582  72 KGEQLSQLSRNTLLSHACGVGAPLADEQTRAIICAAIRNYSHGKSGIHRRVVEALLALLNRGIT 135
                                                    **************************************************************** PP

                                      TIGR01225 130 PvvpekGsvGasGDLAPLahlalvliGeGeaefegevmdaaeaLaaaglePvtlkakEGlALin 193
                                                    P vp++GsvG    L  +ah++++l+G G++ ++g+++ a++aL + gl+Pv+l ak+Gl L+n
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1582 136 PQVPSQGSVG---YLTHMAHIGITLLGVGNVSYRGQIVTAQQALSEEGLQPVQLGAKDGLCLVN 196
                                                    *********7...6999*********************************************** PP

                                      TIGR01225 194 Gtqlmtalavlalvdaekllesadiaaalsleallgtskafdpdihevrphrgqiavaarlrel 257
                                                    Gt +mt+l +la++da +l++ ad+++a+s+ea  g  +afd++i +++ph g  +v+ +lr l
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1582 197 GTPCMTGLSCLAIADATRLVQWADVIGAMSFEAQRGQIAAFDAEIIALKPHLGMQQVGINLRAL 260
                                                    **************************************************************** PP

                                      TIGR01225 258 lagseiaeshkdedrvqDaYslRciPqvhGavldtldqvkevlaiElnsatDnPlvf..adege 319
                                                    l+gse+  s  +  r qDa s+R+iPqvhGa++d+l+++k+ +++Elns+tDnP+++  +d+ +
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1582 261 LDGSEVIASS-KGIRTQDALSIRSIPQVHGAARDQLEHAKKQIETELNSVTDNPMLLgtPDNFR 323
                                                    *********9.6789****************************************983357789 PP

                                      TIGR01225 320 vvsgGnFHgepvAlaldflaiaiaelgaiseRRierlldpalseLppFLaedsGlnsGlmiaqy 383
                                                    v+s  n Hg+ vAla+d laia+ae+g+i+eRR++rl++p+ s+Lp+FL++++G+nsG+mi qy
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1582 324 VMSQANPHGQSVALAADLLAIAMAEIGSIAERRLDRLINPHVSGLPAFLVANPGVNSGMMIVQY 387
                                                    **************************************************************** PP

                                      TIGR01225 384 taAaLvsenkaLahPasvDsiptsanqEDHvsmgaaaarkllevvenvrrviaiEllaaaqgle 447
                                                     aA+L+ en++La+Pa +D+  ts+ qEDH smg+ aa kl ++ en ++++aiE+l+aaq+ e
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1582 388 VAASLCAENRQLAQPAVLDNYVTSGLQEDHLSMGTNAALKLHRALENCTQILAIEYLLAAQAFE 451
                                                    **************************************************************** PP

                                      TIGR01225 448 frkaektaaelekvyeavRevveeleeDRvlapDleavkellekes 493
                                                    f+k+++  a ++ +  ++Re v+ +++DR lapD++a+  +l++  
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1582 452 FLKEQRFGAGTDTAWRLLRERVPAYDQDRWLAPDIAAAAGVLKDPI 497
                                                    *************************************998887654 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 11.56
//
[ok]

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

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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