Alignments for a candidate for argH in Pseudomonas fluorescens FW300-N2C3

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Pseudomonas fluorescens FW300-N2C3

Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate AO356_29670 AO356_29670 argininosuccinate lyase

Query= BRENDA::P9WPY7
         (470 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_29670
          Length = 475

 Score =  475 bits (1222), Expect = e-138
 Identities = 247/460 (53%), Positives = 324/460 (70%), Gaps = 1/460 (0%)

Query: 1   MSTNEGSLWGGRFAGGPSDALAALSKSTHFDWVLAPYDLTASRAHTMVLFRAGLLTEEQR 60
           MS     LWG RF  GPS+ALAALS+     + L PYDL  S+AH   L RAGLLTE++ 
Sbjct: 1   MSQTTDRLWGARFKCGPSEALAALSRCPERYFRLTPYDLAGSKAHARELQRAGLLTEQET 60

Query: 61  DGLLAGLDSLAQDVADGSFGPLVTDEDVHAALERGLIDRVGPDLGGRLRAGRSRNDQVAA 120
             +L  L+ +  D   GS  P + DEDVH  +ER L +R+G  LGG+LRAGRSRNDQ A 
Sbjct: 61  QTMLDALERIGADYRAGSIAPTLDDEDVHTFIERLLTERLGA-LGGKLRAGRSRNDQTAN 119

Query: 121 LFRMWLRDAVRRVATGVLDVVGALAEQAAAHPSAIMPGKTHLQSAQPILLAHHLLAHAHP 180
             R++LRD VR VA  VL +  AL EQA  H  +I PG THLQ AQPI+ AHHLLAHA  
Sbjct: 120 DLRLFLRDHVRTVAVEVLGLQQALVEQAEQHIESICPGFTHLQQAQPIVFAHHLLAHAQS 179

Query: 181 LLRDLDRIVDFDKRAAVSPYGSGALAGSSLGLDPDAIAADLGFSAAADNSVDATAARDFA 240
           +LRD+ R+VD+D R ++SP G+ A+AGS++   P   A ++G+S   +NS+DA A+RD  
Sbjct: 180 MLRDVQRLVDWDARTSLSPLGAAAMAGSAIARLPQQSAKEMGYSGVCENSIDAVASRDHV 239

Query: 241 AEAAFVFAMIAVDLSRLAEDIIVWSSTEFGYVTLHDSWSTGSSIMPQKKNPDIAELARGK 300
           AE  F+ +M+ +++SRLAE+  +WSS +F +V L D+++TGSSIMPQKKNPDIAELARGK
Sbjct: 240 AEFLFIASMLGINISRLAEEFCLWSSRQFRWVALDDAYATGSSIMPQKKNPDIAELARGK 299

Query: 301 SGRLIGNLAGLLATLKAQPLAYNRDLQEDKEPVFDSVAQLELLLPAMAGLVASLTFNVQR 360
           +GRLIGNL GLL+TLK+ PL+YNRDL EDK  V DSV  L L+LPAMAG+VA++  NV+ 
Sbjct: 300 AGRLIGNLTGLLSTLKSLPLSYNRDLSEDKNGVLDSVDTLLLVLPAMAGMVATMKVNVEE 359

Query: 361 MAELAPAGYTLATDLAEWLVRQGVPFRSAHEAAGAAVRAAEQRGVGLQELTDDELAAISP 420
           +   AP G+TLAT++A+WL  +GVPF+ AHE  GA V+A E+  + L E +   LA I P
Sbjct: 360 LRRQAPLGFTLATEVADWLAVRGVPFKEAHEITGALVQACEKHDIELWEASPALLAEIDP 419

Query: 421 ELTPQVREVLTIEGSVSARDCRGGTAPGRVAEQLNAIGEA 460
            LTP+VRE LT+E +++AR+  GGTAP +V EQ+  +  A
Sbjct: 420 RLTPEVRESLTLEAAIAARNGWGGTAPQQVREQIGRLKTA 459


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: 556
Number of extensions: 23
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 AO356_29670 AO356_29670 (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.30714.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   1.9e-163  530.6   0.0   2.2e-163  530.4   0.0    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_29670  AO356_29670 argininosuccinate ly


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_29670  AO356_29670 argininosuccinate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  530.4   0.0  2.2e-163  2.2e-163       1     454 [.       8     460 ..       8     461 .. 0.99

  Alignments for each domain:
  == domain 1  score: 530.4 bits;  conditional E-value: 2.2e-163
                                       TIGR00838   1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeel 63 
                                                     lwg R+k ++++a+a++++  +   +l+ +D+ gs+ah++ L++ag+lte+e++ + +aLe++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_29670   8 LWGARFKCGPSEALAALSRCPERYFRLTPYDLAGSKAHARELQRAGLLTEQETQTMLDALERI 70 
                                                     7************************************************************** PP

                                       TIGR00838  64 keevkegklelevdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkel 126
                                                       ++++g++ ++ d+eD+H+ +Er l++++g  +g+kl++grsRnDq a dlrl+lrd+v+++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_29670  71 GADYRAGSIAPTLDDEDVHTFIERLLTERLG-ALGGKLRAGRSRNDQTANDLRLFLRDHVRTV 132
                                                     *******************************.******************************* PP

                                       TIGR00838 127 aealkdllkalvekAekevetlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvn 189
                                                     a +++ l++alve+Ae+++e + pg+tHLq+AqPi +aHhlla+a+++ rD++Rl+d   R+ 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_29670 133 AVEVLGLQQALVEQAEQHIESICPGFTHLQQAQPIVFAHHLLAHAQSMLRDVQRLVDWDARTS 195
                                                     *************************************************************** PP

                                       TIGR00838 190 ksPlGsgAlagtsfeidrellaelLgFdavvensldavsdRDfiiEllsaaallmvhlsrlaE 252
                                                      sPlG++A+ag++ +  ++++a+ +g++ v+ens+dav++RD+++E+l+ a++l +++srlaE
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_29670 196 LSPLGAAAMAGSAIARLPQQSAKEMGYSGVCENSIDAVASRDHVAEFLFIASMLGINISRLAE 258
                                                     *************************************************************** PP

                                       TIGR00838 253 elilfsseEfgfvelsdevssgssimPqKKnpDvaEliRgktgrviGnltglltilKalPlaY 315
                                                     e+ l+ss+ f +v l+d++++gssimPqKKnpD+aEl+Rgk+gr+iGnltgll +lK+lPl+Y
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_29670 259 EFCLWSSRQFRWVALDDAYATGSSIMPQKKNPDIAELARGKAGRLIGNLTGLLSTLKSLPLSY 321
                                                     *************************************************************** PP

                                       TIGR00838 316 nkDlqEdkealfdalktveellevvtgllkelkvnkerleeaakknfalatdlAdylvrkGvP 378
                                                     n+Dl Edk+++ d+++t+  +l +++g+++++kvn e+l+++a  +f+lat++Ad+l+ +GvP
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_29670 322 NRDLSEDKNGVLDSVDTLLLVLPAMAGMVATMKVNVEELRRQAPLGFTLATEVADWLAVRGVP 384
                                                     *************************************************************** PP

                                       TIGR00838 379 FReaheivGevvakaiekGkkleeltleelqklsekleedvlevldleeavekrdakGGtake 441
                                                     F+eahei+G++v++++++ ++l e + + l++++++l+++v+e l+le a+++r+  GGta++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_29670 385 FKEAHEITGALVQACEKHDIELWEASPALLAEIDPRLTPEVRESLTLEAAIAARNGWGGTAPQ 447
                                                     *************************************************************** PP

                                       TIGR00838 442 evekaieeakael 454
                                                     +v+++i  +k+ l
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_29670 448 QVREQIGRLKTAL 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: 7.66
//
[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