Aligments for a candidate for hutH in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Aligments for a candidate for hutH in Pseudomonas fluorescens GW456-L13

Align Histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate PfGW456L13_321 Histidine ammonia-lyase (EC 4.3.1.3)

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_321
          Length = 507

 Score =  910 bits (2352), Expect = 0.0
 Identities = 462/507 (91%), Positives = 484/507 (95%)

Query: 1   MSQAEKIVIADAPLRWQDVVAVARHGAQLELSPQIWTRIENAQAIVQRIVASGERAYGVN 60
           MSQAEKIVI ++ + WQDVVAVARHGAQLELS  IW RIENAQAIVQRIV SGERAYG+N
Sbjct: 1   MSQAEKIVITESQVSWQDVVAVARHGAQLELSAPIWARIENAQAIVQRIVTSGERAYGIN 60

Query: 61  TGLGALCNVSLKGEQLSQLSRNTLLSHACGVGAPLADEQTRAIICAAIRNYSHGKSGIHR 120
           TGLGALCNVSL+ EQLSQLSRNTLLSHACGVG PL DEQTR+I+CAAI NYSHGKSG+HR
Sbjct: 61  TGLGALCNVSLQDEQLSQLSRNTLLSHACGVGVPLTDEQTRSIMCAAIVNYSHGKSGLHR 120

Query: 121 RVVEALLALLNRGITPQVPSQGSVGYLTHMAHIGITLLGVGNVSYRGQIVTAQQALSEEG 180
           +VVEALLALLNRGITPQVPSQGSVGYLTHMAHIGI LLGVGNVSYRGQIV+AQQAL+EEG
Sbjct: 121 QVVEALLALLNRGITPQVPSQGSVGYLTHMAHIGIALLGVGNVSYRGQIVSAQQALAEEG 180

Query: 181 LQPVQLGAKDGLCLVNGTPCMTGLSCLAIADATRLVQWADVIGAMSFEAQRGQIAAFDAE 240
           LQPV+LGAKDGLCLVNGTPCM+GLSCLAIADATRL++WADVIGAMSFEAQRGQI AFDAE
Sbjct: 181 LQPVKLGAKDGLCLVNGTPCMSGLSCLAIADATRLLEWADVIGAMSFEAQRGQIDAFDAE 240

Query: 241 IIALKPHLGMQQVGINLRALLDGSEVIASSKGIRTQDALSIRSIPQVHGAARDQLEHAKK 300
           IIALKPH GMQQVGINLRALLDGSEVIA SKGIRTQDALSIRSIPQVHGAARDQL HA K
Sbjct: 241 IIALKPHPGMQQVGINLRALLDGSEVIAQSKGIRTQDALSIRSIPQVHGAARDQLVHAIK 300

Query: 301 QIETELNSVTDNPMLLGTPDNFRVMSQANPHGQSVALAADLLAIAMAEIGSIAERRLDRL 360
           QIETELN  TDNP++LGT DN+RV+SQANPHGQSVA+AADLLAIAMAEIGSIAERRLDRL
Sbjct: 301 QIETELNGATDNPLVLGTADNYRVVSQANPHGQSVAMAADLLAIAMAEIGSIAERRLDRL 360

Query: 361 INPHVSGLPAFLVANPGVNSGMMIVQYVAASLCAENRQLAQPAVLDNYVTSGLQEDHLSM 420
           INPHVSGLPAFLVANPGVNSGMMIVQYVAASLCAENRQLAQPAVLDNYVTSGLQEDHLS+
Sbjct: 361 INPHVSGLPAFLVANPGVNSGMMIVQYVAASLCAENRQLAQPAVLDNYVTSGLQEDHLSL 420

Query: 421 GTNAALKLHRALENCTQILAIEYLLAAQAFEFLKEQRFGAGTDTAWRLLRERVPAYDQDR 480
           GTNAALKLHRALENCTQILAIEYLLAAQAFEFLKEQRFGAGTDTAWRLLRERVPAYDQDR
Sbjct: 421 GTNAALKLHRALENCTQILAIEYLLAAQAFEFLKEQRFGAGTDTAWRLLRERVPAYDQDR 480

Query: 481 WLAPDIAAAAGVLKDPILLHKALPNLN 507
           WLAPDIAAAA VLKDP+LL K LPNLN
Sbjct: 481 WLAPDIAAAASVLKDPVLLQKTLPNLN 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: 953
Number of extensions: 27
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 PfGW456L13_321 (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.21883.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                              -----------
   2.1e-166  540.2   6.9   2.6e-166  539.9   6.9    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_321  Histidine ammonia-lyase (EC 4.3.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_321  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 !  539.9   6.9  2.6e-166  2.6e-166       1     495 [.       7     499 ..       7     505 .. 0.98

  Alignments for each domain:
  == domain 1  score: 539.9 bits;  conditional E-value: 2.6e-166
                                              TIGR01225   1 vvldgesltledleavarekarvelsaaaeeavaksravieeivaedktvYGvntG 56 
                                                            +v+ +++++ +d++avar++a++elsa   +++++++a++++iv++ +  YG+ntG
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_321   7 IVITESQVSWQDVVAVARHGAQLELSAPIWARIENAQAIVQRIVTSGERAYGINTG 62 
                                                            6889999************************************************* PP

                                              TIGR01225  57 FGklasvkidkedlaeLqrnlvrsHaaGvGepleeevvRallvlrlnslakGysgv 112
                                                             G+l +v ++ e+l +L rn ++sHa+GvG pl++e +R ++   +   ++G sg+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_321  63 LGALCNVSLQDEQLSQLSRNTLLSHACGVGVPLTDEQTRSIMCAAIVNYSHGKSGL 118
                                                            ******************************************************** PP

                                              TIGR01225 113 raevlellvallnaevlPvvpekGsvGasGDLAPLahlalvliGeGeaefegevmd 168
                                                             ++v+e+l+alln++++P vp++GsvG    L  +ah++++l+G G++ ++g++++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_321 119 HRQVVEALLALLNRGITPQVPSQGSVG---YLTHMAHIGIALLGVGNVSYRGQIVS 171
                                                            **************************7...6999********************** PP

                                              TIGR01225 169 aaeaLaaaglePvtlkakEGlALinGtqlmtalavlalvdaekllesadiaaalsl 224
                                                            a++aLa+ gl+Pv+l ak+Gl L+nGt +m++l +la++da +lle ad+++a+s+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_321 172 AQQALAEEGLQPVKLGAKDGLCLVNGTPCMSGLSCLAIADATRLLEWADVIGAMSF 227
                                                            ******************************************************** PP

                                              TIGR01225 225 eallgtskafdpdihevrphrgqiavaarlrellagseiaeshkdedrvqDaYslR 280
                                                            ea  g  +afd++i +++ph+g  +v+ +lr ll+gse+  +  +  r qDa s+R
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_321 228 EAQRGQIDAFDAEIIALKPHPGMQQVGINLRALLDGSEVIAQS-KGIRTQDALSIR 282
                                                            ***************************************9998.678********* PP

                                              TIGR01225 281 ciPqvhGavldtldqvkevlaiElnsatDnPlvf..adegevvsgGnFHgepvAla 334
                                                            +iPqvhGa++d+l ++ + +++Eln atDnPlv+  ad+ +vvs  n Hg+ vA+a
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_321 283 SIPQVHGAARDQLVHAIKQIETELNGATDNPLVLgtADNYRVVSQANPHGQSVAMA 338
                                                            *********************************83356789*************** PP

                                              TIGR01225 335 ldflaiaiaelgaiseRRierlldpalseLppFLaedsGlnsGlmiaqytaAaLvs 390
                                                            +d laia+ae+g+i+eRR++rl++p+ s+Lp+FL++++G+nsG+mi qy aA+L+ 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_321 339 ADLLAIAMAEIGSIAERRLDRLINPHVSGLPAFLVANPGVNSGMMIVQYVAASLCA 394
                                                            ******************************************************** PP

                                              TIGR01225 391 enkaLahPasvDsiptsanqEDHvsmgaaaarkllevvenvrrviaiEllaaaqgl 446
                                                            en++La+Pa +D+  ts+ qEDH s+g+ aa kl ++ en ++++aiE+l+aaq+ 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_321 395 ENRQLAQPAVLDNYVTSGLQEDHLSLGTNAALKLHRALENCTQILAIEYLLAAQAF 450
                                                            ******************************************************** PP

                                              TIGR01225 447 efrkaektaaelekvyeavRevveeleeDRvlapDleavkellekesle 495
                                                            ef+k+++  a ++ +  ++Re v+ +++DR lapD++a+ ++l++ +l 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_321 451 EFLKEQRFGAGTDTAWRLLRERVPAYDQDRWLAPDIAAAASVLKDPVLL 499
                                                            ****************************************999987665 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02
# Mc/sec: 11.28
//
[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, or view the source code.

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