Alignments for a candidate for hutH in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutH in Pseudomonas fluorescens FW300-N2E2

Align Histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate Pf6N2E2_3799 Histidine ammonia-lyase (EC 4.3.1.3)

Query= reanno::pseudo6_N2E2:Pf6N2E2_3799
         (510 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3799
          Length = 510

 Score =  978 bits (2528), Expect = 0.0
 Identities = 510/510 (100%), Positives = 510/510 (100%)

Query: 1   MTALNLIPGQLSLAQLRDIYQQPVTLSLDASASAQIEASVACVEQILAENRTAYGINTGF 60
           MTALNLIPGQLSLAQLRDIYQQPVTLSLDASASAQIEASVACVEQILAENRTAYGINTGF
Sbjct: 1   MTALNLIPGQLSLAQLRDIYQQPVTLSLDASASAQIEASVACVEQILAENRTAYGINTGF 60

Query: 61  GLLASTRIASEDLENLQRSLVLSHAAGVGEPISDALVRLVMVLKVNSLSRGFSGIRRQVI 120
           GLLASTRIASEDLENLQRSLVLSHAAGVGEPISDALVRLVMVLKVNSLSRGFSGIRRQVI
Sbjct: 61  GLLASTRIASEDLENLQRSLVLSHAAGVGEPISDALVRLVMVLKVNSLSRGFSGIRRQVI 120

Query: 121 DALIALINAEVYPHIPLKGSVGASGDLAPLAHMSLVLLGEGKARYKGEWLPAVEALKVAG 180
           DALIALINAEVYPHIPLKGSVGASGDLAPLAHMSLVLLGEGKARYKGEWLPAVEALKVAG
Sbjct: 121 DALIALINAEVYPHIPLKGSVGASGDLAPLAHMSLVLLGEGKARYKGEWLPAVEALKVAG 180

Query: 181 LAPLTLAAKEGLALLNGTQVSTAFALRGLFEGEDLFAGALALGGLTVEAVLGSRSPFDAR 240
           LAPLTLAAKEGLALLNGTQVSTAFALRGLFEGEDLFAGALALGGLTVEAVLGSRSPFDAR
Sbjct: 181 LAPLTLAAKEGLALLNGTQVSTAFALRGLFEGEDLFAGALALGGLTVEAVLGSRSPFDAR 240

Query: 241 IHAARGQKGQIDAAAAYRDLLGERSEVSDSHQNCDKVQDPYSLRCQPQVMGACLTQFRQA 300
           IHAARGQKGQIDAAAAYRDLLGERSEVSDSHQNCDKVQDPYSLRCQPQVMGACLTQFRQA
Sbjct: 241 IHAARGQKGQIDAAAAYRDLLGERSEVSDSHQNCDKVQDPYSLRCQPQVMGACLTQFRQA 300

Query: 301 AEVLVIEANAVSDNPLVFAAEGDVISGGNFHAEPVAMAADNMALAIAEIGSLSERRISLM 360
           AEVLVIEANAVSDNPLVFAAEGDVISGGNFHAEPVAMAADNMALAIAEIGSLSERRISLM
Sbjct: 301 AEVLVIEANAVSDNPLVFAAEGDVISGGNFHAEPVAMAADNMALAIAEIGSLSERRISLM 360

Query: 361 MDKHMSQLPPFLVANGGVNSGFMIAQVTAAALASENKALSHPHSVDSLPTSANQEDHVSM 420
           MDKHMSQLPPFLVANGGVNSGFMIAQVTAAALASENKALSHPHSVDSLPTSANQEDHVSM
Sbjct: 361 MDKHMSQLPPFLVANGGVNSGFMIAQVTAAALASENKALSHPHSVDSLPTSANQEDHVSM 420

Query: 421 APAAGKRLWEMAENTRGILAVEWLAACQGLDLRGGLKTSTKLERARGLLRAQVPFYEKDR 480
           APAAGKRLWEMAENTRGILAVEWLAACQGLDLRGGLKTSTKLERARGLLRAQVPFYEKDR
Sbjct: 421 APAAGKRLWEMAENTRGILAVEWLAACQGLDLRGGLKTSTKLERARGLLRAQVPFYEKDR 480

Query: 481 FFAPDINAASELLASRCLNELVTAQLLPSL 510
           FFAPDINAASELLASRCLNELVTAQLLPSL
Sbjct: 481 FFAPDINAASELLASRCLNELVTAQLLPSL 510


Lambda     K      H
   0.318    0.132    0.370 

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: 899
Number of extensions: 8
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 Pf6N2E2_3799 (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.998128.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   4.2e-222  724.0   5.0   4.7e-222  723.8   5.0    1.0  1  FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3799  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3799  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  723.8   5.0  4.7e-222  4.7e-222       4     504 ..       7     508 ..       4     510 .] 0.99

  Alignments for each domain:
  == domain 1  score: 723.8 bits;  conditional E-value: 4.7e-222
                                  TIGR01225   4 dgesltledleavarekarvelsaaaeeavaksravieeivaedktvYGvntGFGklasvkidkedla 71 
                                                 +++l+l++l+ ++++   ++l+a+a++++++s a++e+i+ae++t YG+ntGFG las++i++edl+
  FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3799   7 IPGQLSLAQLRDIYQQPVTLSLDASASAQIEASVACVEQILAENRTAYGINTGFGLLASTRIASEDLE 74 
                                                567999************************************************************** PP

                                  TIGR01225  72 eLqrnlvrsHaaGvGepleeevvRallvlrlnslakGysgvraevlellvallnaevlPvvpekGsvG 139
                                                +Lqr+lv+sHaaGvGep+++++vR+++vl++nsl++G+sg+r++v+++l+al+naev+P++p kGsvG
  FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3799  75 NLQRSLVLSHAAGVGEPISDALVRLVMVLKVNSLSRGFSGIRRQVIDALIALINAEVYPHIPLKGSVG 142
                                                ******************************************************************** PP

                                  TIGR01225 140 asGDLAPLahlalvliGeGeaefegevmdaaeaLaaaglePvtlkakEGlALinGtqlmtalavlalv 207
                                                asGDLAPLah++lvl+GeG+a+++ge+++a eaL+ agl+P+tl+akEGlAL+nGtq++ta+a+++l+
  FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3799 143 ASGDLAPLAHMSLVLLGEGKARYKGEWLPAVEALKVAGLAPLTLAAKEGLALLNGTQVSTAFALRGLF 210
                                                ******************************************************************** PP

                                  TIGR01225 208 daekllesadiaaalsleallgtskafdpdihevrphrgqiavaarlrella.gseiaeshkdedrvq 274
                                                + e+l + a + ++l++ea+lg++++fd++ih++r+++gqi+ aa+ r+ll   se+++sh+++d+vq
  FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3799 211 EGEDLFAGALALGGLTVEAVLGSRSPFDARIHAARGQKGQIDAAAAYRDLLGeRSEVSDSHQNCDKVQ 278
                                                ***************************************************978************** PP

                                  TIGR01225 275 DaYslRciPqvhGavldtldqvkevlaiElnsatDnPlvfadegevvsgGnFHgepvAlaldflaiai 342
                                                D+YslRc+Pqv+Ga+l++++q++evl iE+n+++DnPlvfa+eg+v+sgGnFH+epvA+a+d++a+ai
  FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3799 279 DPYSLRCQPQVMGACLTQFRQAAEVLVIEANAVSDNPLVFAAEGDVISGGNFHAEPVAMAADNMALAI 346
                                                ******************************************************************** PP

                                  TIGR01225 343 aelgaiseRRierlldpalseLppFLaedsGlnsGlmiaqytaAaLvsenkaLahPasvDsiptsanq 410
                                                ae+g++seRRi++++d+++s+LppFL++++G+nsG+miaq+taAaL+senkaL+hP+svDs+ptsanq
  FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3799 347 AEIGSLSERRISLMMDKHMSQLPPFLVANGGVNSGFMIAQVTAAALASENKALSHPHSVDSLPTSANQ 414
                                                ******************************************************************** PP

                                  TIGR01225 411 EDHvsmgaaaarkllevvenvrrviaiEllaaaqglefrkaektaaelekvyeavRevveeleeDRvl 478
                                                EDHvsm+ aa+++l+e++en+r ++a+E+laa+qgl++r   kt+++le+++ ++R++v+ +e+DR++
  FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3799 415 EDHVSMAPAAGKRLWEMAENTRGILAVEWLAACQGLDLRGGLKTSTKLERARGLLRAQVPFYEKDRFF 482
                                                ******************************************************************** PP

                                  TIGR01225 479 apDleavkellekesleaaveakvka 504
                                                apD++a++ell+++ l++ v+a++++
  FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3799 483 APDINAASELLASRCLNELVTAQLLP 508
                                                ****************9999887765 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 23.46
//
[ok]

This GapMind analysis is from Apr 09 2024. 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)
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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 2024 update 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