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

GapMind for Amino acid biosynthesis

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

Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate AO353_25585 AO353_25585 argininosuccinate lyase

Query= BRENDA::P9WPY7
         (470 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_25585
          Length = 475

 Score =  461 bits (1185), Expect = e-134
 Identities = 241/459 (52%), Positives = 318/459 (69%), Gaps = 1/459 (0%)

Query: 8   LWGGRFAGGPSDALAALSKSTHFDWVLAPYDLTASRAHTMVLFRAGLLTEEQRDGLLAGL 67
           LWG RF  GPS+ALAALS+     + L PYDL  S+AH   L RAGLL   +   +L  L
Sbjct: 8   LWGARFKSGPSEALAALSRCPERYFRLTPYDLAGSKAHAGELHRAGLLDALETQTMLDAL 67

Query: 68  DSLAQDVADGSFGPLVTDEDVHAALERGLIDRVGPDLGGRLRAGRSRNDQVAALFRMWLR 127
           + + +D   G   P + DEDVH  +ER L +R+G  LGG+LRAGRSRNDQ A   R++LR
Sbjct: 68  ERIGEDFRAGFVSPTLDDEDVHTFIERLLTERLGA-LGGKLRAGRSRNDQTANDLRLFLR 126

Query: 128 DAVRRVATGVLDVVGALAEQAAAHPSAIMPGKTHLQSAQPILLAHHLLAHAHPLLRDLDR 187
           D  R + T VL +  AL EQA  H  +I PG THLQ AQPI+ AHHLLAHA  +LRD+ R
Sbjct: 127 DHARTLTTEVLALQQALVEQAELHIDSICPGFTHLQQAQPIVFAHHLLAHAQSMLRDVQR 186

Query: 188 IVDFDKRAAVSPYGSGALAGSSLGLDPDAIAADLGFSAAADNSVDATAARDFAAEAAFVF 247
           +VD+D R ++SP G+ A+AGS++   P   A ++G+S   +NS+DA A+RD  AE  FV 
Sbjct: 187 LVDWDVRTSLSPLGAAAMAGSAIARQPQQSAKEMGYSGVCENSIDAVASRDHVAEFLFVA 246

Query: 248 AMIAVDLSRLAEDIIVWSSTEFGYVTLHDSWSTGSSIMPQKKNPDIAELARGKSGRLIGN 307
           +M+ V++SRLAE+  +WSS +F +V L D+++TGSSIMPQKKNPDIAELARGK+GRLIGN
Sbjct: 247 SMLGVNISRLAEEFCLWSSRQFRWVALDDAYATGSSIMPQKKNPDIAELARGKAGRLIGN 306

Query: 308 LAGLLATLKAQPLAYNRDLQEDKEPVFDSVAQLELLLPAMAGLVASLTFNVQRMAELAPA 367
           L GLL+TLK+ PL+YNRDL EDK  V DSV  L L+LPAMAG+VA++  NV+ +   AP 
Sbjct: 307 LTGLLSTLKSLPLSYNRDLSEDKNGVLDSVDTLLLVLPAMAGMVATMKVNVEELRRQAPL 366

Query: 368 GYTLATDLAEWLVRQGVPFRSAHEAAGAAVRAAEQRGVGLQELTDDELAAISPELTPQVR 427
           G+TLAT++A+WL  +GVPF+ AHE  GA V+A E+  + L E +   LA I   LTP+VR
Sbjct: 367 GFTLATEVADWLAVRGVPFKEAHEITGALVQACEKHDIELWEASPALLAEIDMRLTPEVR 426

Query: 428 EVLTIEGSVSARDCRGGTAPGRVAEQLNAIGEAAERLRR 466
           + LT+E +++AR   GGTAP +V EQ+  +  A    +R
Sbjct: 427 DSLTLEAAIAARSGWGGTAPQQVREQIGRLKTALAAQQR 465


Lambda     K      H
   0.318    0.133    0.382 

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: 570
Number of extensions: 26
Number of successful extensions: 2
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: 470
Length of database: 475
Length adjustment: 33
Effective length of query: 437
Effective length of database: 442
Effective search space:   193154
Effective search space used:   193154
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: 51 (24.3 bits)

Align candidate AO353_25585 AO353_25585 (argininosuccinate lyase)
to HMM TIGR00838 (argH: argininosuccinate lyase (EC 4.3.2.1))

# 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.aa/TIGR00838.hmm
# target sequence database:        /tmp/gapView.20627.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00838  [M=455]
Accession:   TIGR00838
Description: argH: argininosuccinate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   1.7e-160  520.9   0.0     2e-160  520.7   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25585  AO353_25585 argininosuccinate ly


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_25585  AO353_25585 argininosuccinate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  520.7   0.0    2e-160    2e-160       1     454 [.       8     460 ..       8     461 .. 0.99

  Alignments for each domain:
  == domain 1  score: 520.7 bits;  conditional E-value: 2e-160
                                     TIGR00838   1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelke 65 
                                                   lwg R+k+++++a+a++++  +   +l+ +D+ gs+ah+  L++ag+l + e++ + +aLe++ e
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25585   8 LWGARFKSGPSEALAALSRCPERYFRLTPYDLAGSKAHAGELHRAGLLDALETQTMLDALERIGE 72 
                                                   7**************************************************************** PP

                                     TIGR00838  66 evkegklelevdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaeal 130
                                                   + ++g ++++ d+eD+H+ +Er l++++g  +g+kl++grsRnDq a dlrl+lrd+ ++l++++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25585  73 DFRAGFVSPTLDDEDVHTFIERLLTERLG-ALGGKLRAGRSRNDQTANDLRLFLRDHARTLTTEV 136
                                                   *****************************.*********************************** PP

                                     TIGR00838 131 kdllkalvekAekevetlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGs 195
                                                   ++l++alve+Ae +++ + pg+tHLq+AqPi +aHhlla+a+++ rD++Rl+d   R+  sPlG+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25585 137 LALQQALVEQAELHIDSICPGFTHLQQAQPIVFAHHLLAHAQSMLRDVQRLVDWDVRTSLSPLGA 201
                                                   ***************************************************************** PP

                                     TIGR00838 196 gAlagtsfeidrellaelLgFdavvensldavsdRDfiiEllsaaallmvhlsrlaEelilfsse 260
                                                   +A+ag++ + +++++a+ +g++ v+ens+dav++RD+++E+l++a++l v++srlaEe+ l+ss+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25585 202 AAMAGSAIARQPQQSAKEMGYSGVCENSIDAVASRDHVAEFLFVASMLGVNISRLAEEFCLWSSR 266
                                                   ***************************************************************** PP

                                     TIGR00838 261 EfgfvelsdevssgssimPqKKnpDvaEliRgktgrviGnltglltilKalPlaYnkDlqEdkea 325
                                                    f +v l+d++++gssimPqKKnpD+aEl+Rgk+gr+iGnltgll +lK+lPl+Yn+Dl Edk++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25585 267 QFRWVALDDAYATGSSIMPQKKNPDIAELARGKAGRLIGNLTGLLSTLKSLPLSYNRDLSEDKNG 331
                                                   ***************************************************************** PP

                                     TIGR00838 326 lfdalktveellevvtgllkelkvnkerleeaakknfalatdlAdylvrkGvPFReaheivGevv 390
                                                   + d+++t+  +l +++g+++++kvn e+l+++a  +f+lat++Ad+l+ +GvPF+eahei+G++v
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25585 332 VLDSVDTLLLVLPAMAGMVATMKVNVEELRRQAPLGFTLATEVADWLAVRGVPFKEAHEITGALV 396
                                                   ***************************************************************** PP

                                     TIGR00838 391 akaiekGkkleeltleelqklsekleedvlevldleeavekrdakGGtakeevekaieeakael 454
                                                   ++++++ ++l e + + l++++ +l+++v++ l+le a+++r+  GGta+++v+++i  +k+ l
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25585 397 QACEKHDIELWEASPALLAEIDMRLTPEVRDSLTLEAAIAARSGWGGTAPQQVREQIGRLKTAL 460
                                                   **********************************************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (475 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: 10.32
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis