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_1581 Histidine ammonia-lyase (EC 4.3.1.3)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_320
         (510 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1581
          Length = 510

 Score =  955 bits (2469), Expect = 0.0
 Identities = 494/510 (96%), Positives = 505/510 (99%)

Query: 1   MTALNLIPGQLTLAQLRDVYQQPVKLTLDNSASAQIEASVACVEQILAENRTAYGINTGF 60
           MTALNLIPGQL+LAQLRDVYQQPVK+TLDNSASAQIEASVACVEQILAENRTAYGINTGF
Sbjct: 1   MTALNLIPGQLSLAQLRDVYQQPVKITLDNSASAQIEASVACVEQILAENRTAYGINTGF 60

Query: 61  GLLASTRIASEDLENLQRSLVLSHAAGVGQPISDELVRLIMVLKVNSLSRGFSGIRRVVI 120
           GLLASTRIASEDLENLQRSLVLSHAAGVG+PISD LVRL+MVLKVNSLSRGFSGIRRVVI
Sbjct: 61  GLLASTRIASEDLENLQRSLVLSHAAGVGEPISDALVRLVMVLKVNSLSRGFSGIRRVVI 120

Query: 121 DALIALINAEVYPHIPLKGSVGASGDLAPLAHMSLVLLGEGKARYKGEWMEATEALKVAG 180
           DALIALINAEVYPHIPLKGSVGASGDLAPLAHMSLVLLGEGKARYKGEWMEATEALKVAG
Sbjct: 121 DALIALINAEVYPHIPLKGSVGASGDLAPLAHMSLVLLGEGKARYKGEWMEATEALKVAG 180

Query: 181 LTPLTLAAKEGLALLNGTQVSTAFALRGLFEGEDLFAGALALGGLTVEAVLGSRSPFDAR 240
           LTPLTLAAKEGLALLNGTQVSTA+ALRGLFEGEDLFAGALA+GG+TVEAVLGSRSPFDAR
Sbjct: 181 LTPLTLAAKEGLALLNGTQVSTAYALRGLFEGEDLFAGALAIGGMTVEAVLGSRSPFDAR 240

Query: 241 IHAARGQKGQIDAAAAYRDLLGERSEVSDSHENCEKVQDPYSLRCQPQVMGACLTQFRQA 300
           IHAARGQKGQIDAAAAYRDLLGERSEVSDSH+NCEKVQDPYSLRCQPQVMGACLTQFRQA
Sbjct: 241 IHAARGQKGQIDAAAAYRDLLGERSEVSDSHQNCEKVQDPYSLRCQPQVMGACLTQFRQA 300

Query: 301 AEVLAIESNAVSDNPLVFAAEGDVISGGNFHAEPVAMAADNMALAIAEIGSLSERRISLM 360
           AEVLAIE+NAVSDNPLVFAAEGDVISGGNFHAEPVAMAADNMALAIAEIGSLSERRISLM
Sbjct: 301 AEVLAIEANAVSDNPLVFAAEGDVISGGNFHAEPVAMAADNMALAIAEIGSLSERRISLM 360

Query: 361 MDKHMSQLPPFLVANGGVNSGFMIAQVTAAALASENKALSHPHSVDSLPTSANQEDHVSM 420
           MDKHMSQLPPFLVANGGVNSGFMIAQVTAAALASENKALSHPHSVDSLPTSANQEDHVSM
Sbjct: 361 MDKHMSQLPPFLVANGGVNSGFMIAQVTAAALASENKALSHPHSVDSLPTSANQEDHVSM 420

Query: 421 APAAGKRLWEMAENTRGILAVEWLAAVQGLDLRNGLKTSPKLEKARAILRNEVPFYEKDR 480
           APAAGKRLWEMAENTRG+LAVEWLAA QGLDLR GLKTS KLEKARAILR EVPFYEKDR
Sbjct: 421 APAAGKRLWEMAENTRGVLAVEWLAAAQGLDLREGLKTSTKLEKARAILRAEVPFYEKDR 480

Query: 481 FFAPDINAASELLASRCLNELVSAKLLPSL 510
           FFAPDINAASELLA+RCLNELVSAKLLPSL
Sbjct: 481 FFAPDINAASELLATRCLNELVSAKLLPSL 510


Lambda     K      H
   0.317    0.131    0.366 

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: 828
Number of extensions: 13
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 Pf1N1B4_1581 (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.1628.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   2.4e-223  728.1   6.8   2.7e-223  727.9   6.8    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1581  Histidine ammonia-lyase (EC 4.3.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1581  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 !  727.9   6.8  2.7e-223  2.7e-223       4     504 ..       7     508 ..       4     510 .] 0.99

  Alignments for each domain:
  == domain 1  score: 727.9 bits;  conditional E-value: 2.7e-223
                                      TIGR01225   4 dgesltledleavarekarvelsaaaeeavaksravieeivaedktvYGvntGFGklasvkidk 67 
                                                     +++l+l++l+ v+++  +++l+++a++++++s a++e+i+ae++t YG+ntGFG las++i++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1581   7 IPGQLSLAQLRDVYQQPVKITLDNSASAQIEASVACVEQILAENRTAYGINTGFGLLASTRIAS 70 
                                                    56799*********************************************************** PP

                                      TIGR01225  68 edlaeLqrnlvrsHaaGvGepleeevvRallvlrlnslakGysgvraevlellvallnaevlPv 131
                                                    edl++Lqr+lv+sHaaGvGep+++++vR+++vl++nsl++G+sg+r+ v+++l+al+naev+P+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1581  71 EDLENLQRSLVLSHAAGVGEPISDALVRLVMVLKVNSLSRGFSGIRRVVIDALIALINAEVYPH 134
                                                    **************************************************************** PP

                                      TIGR01225 132 vpekGsvGasGDLAPLahlalvliGeGeaefegevmdaaeaLaaaglePvtlkakEGlALinGt 195
                                                    +p kGsvGasGDLAPLah++lvl+GeG+a+++ge+m+a+eaL+ agl P+tl+akEGlAL+nGt
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1581 135 IPLKGSVGASGDLAPLAHMSLVLLGEGKARYKGEWMEATEALKVAGLTPLTLAAKEGLALLNGT 198
                                                    **************************************************************** PP

                                      TIGR01225 196 qlmtalavlalvdaekllesadiaaalsleallgtskafdpdihevrphrgqiavaarlrella 259
                                                    q++ta+a+++l++ e+l + a +++++++ea+lg++++fd++ih++r+++gqi+ aa+ r+ll 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1581 199 QVSTAYALRGLFEGEDLFAGALAIGGMTVEAVLGSRSPFDARIHAARGQKGQIDAAAAYRDLLG 262
                                                    ***************************************************************9 PP

                                      TIGR01225 260 .gseiaeshkdedrvqDaYslRciPqvhGavldtldqvkevlaiElnsatDnPlvfadegevvs 322
                                                      se+++sh+++++vqD+YslRc+Pqv+Ga+l++++q++evlaiE+n+++DnPlvfa+eg+v+s
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1581 263 eRSEVSDSHQNCEKVQDPYSLRCQPQVMGACLTQFRQAAEVLAIEANAVSDNPLVFAAEGDVIS 326
                                                    78************************************************************** PP

                                      TIGR01225 323 gGnFHgepvAlaldflaiaiaelgaiseRRierlldpalseLppFLaedsGlnsGlmiaqytaA 386
                                                    gGnFH+epvA+a+d++a+aiae+g++seRRi++++d+++s+LppFL++++G+nsG+miaq+taA
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1581 327 GGNFHAEPVAMAADNMALAIAEIGSLSERRISLMMDKHMSQLPPFLVANGGVNSGFMIAQVTAA 390
                                                    **************************************************************** PP

                                      TIGR01225 387 aLvsenkaLahPasvDsiptsanqEDHvsmgaaaarkllevvenvrrviaiEllaaaqglefrk 450
                                                    aL+senkaL+hP+svDs+ptsanqEDHvsm+ aa+++l+e++en+r v+a+E+laaaqgl++r+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1581 391 ALASENKALSHPHSVDSLPTSANQEDHVSMAPAAGKRLWEMAENTRGVLAVEWLAAAQGLDLRE 454
                                                    **************************************************************** PP

                                      TIGR01225 451 aektaaelekvyeavRevveeleeDRvlapDleavkellekesleaaveakvka 504
                                                      kt+++lek+++ +R++v+ +e+DR++apD++a++ell+++ l++ v+ak+++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1581 455 GLKTSTKLEKARAILRAEVPFYEKDRFFAPDINAASELLATRCLNELVSAKLLP 508
                                                    ********************************************9999988766 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: 7.14
//
[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