Alignments for a candidate for hutH in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutH in Pseudomonas fluorescens FW300-N2E3

Align Histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate AO353_12270 AO353_12270 histidine ammonia-lyase

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



>FitnessBrowser__pseudo3_N2E3:AO353_12270
          Length = 510

 Score =  936 bits (2418), Expect = 0.0
 Identities = 484/510 (94%), Positives = 497/510 (97%)

Query: 1   MTALNLIPGQLSLAQLRDIYQQPVTLSLDASASAQIEASVACVEQILAENRTAYGINTGF 60
           +TALNLIPGQLSLAQLR +YQQPV + LD SASAQIEASVACVEQIL ENRTAYGINTGF
Sbjct: 1   VTALNLIPGQLSLAQLRAVYQQPVNVRLDDSASAQIEASVACVEQILVENRTAYGINTGF 60

Query: 61  GLLASTRIASEDLENLQRSLVLSHAAGVGEPISDALVRLVMVLKVNSLSRGFSGIRRQVI 120
           GLLASTRIASEDLENLQRSLVLSHAAGVGEPISDALVRL+MVLKVNSLSRGFSGIRR VI
Sbjct: 61  GLLASTRIASEDLENLQRSLVLSHAAGVGEPISDALVRLIMVLKVNSLSRGFSGIRRVVI 120

Query: 121 DALIALINAEVYPHIPLKGSVGASGDLAPLAHMSLVLLGEGKARYKGEWLPAVEALKVAG 180
           DALIALINAEVYPHIPLKGSVGASGDLAPLAHMSLVLLGEGKARYKGEWLPA EALKVAG
Sbjct: 121 DALIALINAEVYPHIPLKGSVGASGDLAPLAHMSLVLLGEGKARYKGEWLPATEALKVAG 180

Query: 181 LAPLTLAAKEGLALLNGTQVSTAFALRGLFEGEDLFAGALALGGLTVEAVLGSRSPFDAR 240
           L PLTLAAKEGLALLNGTQVSTA+ALRGLFEGEDLFAGALALGGLTVEAVLGSRSPFDAR
Sbjct: 181 LKPLTLAAKEGLALLNGTQVSTAYALRGLFEGEDLFAGALALGGLTVEAVLGSRSPFDAR 240

Query: 241 IHAARGQKGQIDAAAAYRDLLGERSEVSDSHQNCDKVQDPYSLRCQPQVMGACLTQFRQA 300
           IHAARGQKGQIDAAAAYRDLLGERSEVSDSH+NC+KVQDPYSLRCQPQVMGACLTQFRQA
Sbjct: 241 IHAARGQKGQIDAAAAYRDLLGERSEVSDSHENCEKVQDPYSLRCQPQVMGACLTQFRQA 300

Query: 301 AEVLVIEANAVSDNPLVFAAEGDVISGGNFHAEPVAMAADNMALAIAEIGSLSERRISLM 360
           AEVL IEANAVSDNPLVFAAEGDVISGGNFHAEPVAMAADNMALAIAEIGSLSERRISLM
Sbjct: 301 AEVLAIEANAVSDNPLVFAAEGDVISGGNFHAEPVAMAADNMALAIAEIGSLSERRISLM 360

Query: 361 MDKHMSQLPPFLVANGGVNSGFMIAQVTAAALASENKALSHPHSVDSLPTSANQEDHVSM 420
           MDKHMSQLPPFLVANGGVNSGFMIAQVTAAALASENKAL+HPHSVDSLPTSANQEDHVSM
Sbjct: 361 MDKHMSQLPPFLVANGGVNSGFMIAQVTAAALASENKALAHPHSVDSLPTSANQEDHVSM 420

Query: 421 APAAGKRLWEMAENTRGILAVEWLAACQGLDLRGGLKTSTKLERARGLLRAQVPFYEKDR 480
           APAAGKRLWEMAENTRG+LAVEWLAACQGLDLR GLKTS+KLE+AR  LRA+VPFYEKDR
Sbjct: 421 APAAGKRLWEMAENTRGVLAVEWLAACQGLDLRDGLKTSSKLEKARSTLRAKVPFYEKDR 480

Query: 481 FFAPDINAASELLASRCLNELVTAQLLPSL 510
           FFAPDINAASELLASRCLNELV A+LLPSL
Sbjct: 481 FFAPDINAASELLASRCLNELVMAKLLPSL 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: 838
Number of extensions: 10
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 AO353_12270 AO353_12270 (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.23039.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-224  731.5   5.1   2.4e-224  731.4   5.1    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_12270  AO353_12270 histidine ammonia-ly


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_12270  AO353_12270 histidine ammonia-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  731.4   5.1  2.4e-224  2.4e-224       4     504 ..       7     508 ..       4     510 .] 0.99

  Alignments for each domain:
  == domain 1  score: 731.4 bits;  conditional E-value: 2.4e-224
                                     TIGR01225   4 dgesltledleavarekarvelsaaaeeavaksravieeivaedktvYGvntGFGklasvkidke 68 
                                                    +++l+l++l+av+++  +v+l+++a++++++s a++e+i+ e++t YG+ntGFG las++i++e
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_12270   7 IPGQLSLAQLRAVYQQPVNVRLDDSASAQIEASVACVEQILVENRTAYGINTGFGLLASTRIASE 71 
                                                   56799************************************************************ PP

                                     TIGR01225  69 dlaeLqrnlvrsHaaGvGepleeevvRallvlrlnslakGysgvraevlellvallnaevlPvvp 133
                                                   dl++Lqr+lv+sHaaGvGep+++++vR+++vl++nsl++G+sg+r+ v+++l+al+naev+P++p
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_12270  72 DLENLQRSLVLSHAAGVGEPISDALVRLIMVLKVNSLSRGFSGIRRVVIDALIALINAEVYPHIP 136
                                                   ***************************************************************** PP

                                     TIGR01225 134 ekGsvGasGDLAPLahlalvliGeGeaefegevmdaaeaLaaaglePvtlkakEGlALinGtqlm 198
                                                    kGsvGasGDLAPLah++lvl+GeG+a+++ge+++a+eaL+ agl+P+tl+akEGlAL+nGtq++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_12270 137 LKGSVGASGDLAPLAHMSLVLLGEGKARYKGEWLPATEALKVAGLKPLTLAAKEGLALLNGTQVS 201
                                                   ***************************************************************** PP

                                     TIGR01225 199 talavlalvdaekllesadiaaalsleallgtskafdpdihevrphrgqiavaarlrella.gse 262
                                                   ta+a+++l++ e+l + a + ++l++ea+lg++++fd++ih++r+++gqi+ aa+ r+ll   se
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_12270 202 TAYALRGLFEGEDLFAGALALGGLTVEAVLGSRSPFDARIHAARGQKGQIDAAAAYRDLLGeRSE 266
                                                   ************************************************************978** PP

                                     TIGR01225 263 iaeshkdedrvqDaYslRciPqvhGavldtldqvkevlaiElnsatDnPlvfadegevvsgGnFH 327
                                                   +++sh+++++vqD+YslRc+Pqv+Ga+l++++q++evlaiE+n+++DnPlvfa+eg+v+sgGnFH
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_12270 267 VSDSHENCEKVQDPYSLRCQPQVMGACLTQFRQAAEVLAIEANAVSDNPLVFAAEGDVISGGNFH 331
                                                   ***************************************************************** PP

                                     TIGR01225 328 gepvAlaldflaiaiaelgaiseRRierlldpalseLppFLaedsGlnsGlmiaqytaAaLvsen 392
                                                   +epvA+a+d++a+aiae+g++seRRi++++d+++s+LppFL++++G+nsG+miaq+taAaL+sen
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_12270 332 AEPVAMAADNMALAIAEIGSLSERRISLMMDKHMSQLPPFLVANGGVNSGFMIAQVTAAALASEN 396
                                                   ***************************************************************** PP

                                     TIGR01225 393 kaLahPasvDsiptsanqEDHvsmgaaaarkllevvenvrrviaiEllaaaqglefrkaektaae 457
                                                   kaLahP+svDs+ptsanqEDHvsm+ aa+++l+e++en+r v+a+E+laa+qgl++r+  kt+++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_12270 397 KALAHPHSVDSLPTSANQEDHVSMAPAAGKRLWEMAENTRGVLAVEWLAACQGLDLRDGLKTSSK 461
                                                   ***************************************************************** PP

                                     TIGR01225 458 lekvyeavRevveeleeDRvlapDleavkellekesleaaveakvka 504
                                                   lek++ ++R++v+ +e+DR++apD++a++ell+++ l++ v ak+++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_12270 462 LEKARSTLRAKVPFYEKDRFFAPDINAASELLASRCLNELVMAKLLP 508
                                                   ************************************99998887765 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: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 8.01
//
[ok]

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

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Protein sequences (fasta format)
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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