Alignments for a candidate for argH in Pseudomonas simiae WCS417

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Pseudomonas simiae WCS417

Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate GFF4252 PS417_21780 argininosuccinate lyase

Query= BRENDA::P9WPY7
         (470 letters)



>FitnessBrowser__WCS417:GFF4252
          Length = 475

 Score =  462 bits (1188), Expect = e-134
 Identities = 239/457 (52%), Positives = 316/457 (69%), Gaps = 1/457 (0%)

Query: 1   MSTNEGSLWGGRFAGGPSDALAALSKSTHFDWVLAPYDLTASRAHTMVLFRAGLLTEEQR 60
           MS     LWG RF  GPS ALAALS+     + L PYDL  SRAH   L RAGLL E + 
Sbjct: 1   MSQPTDRLWGARFKTGPSAALAALSRCPERYFRLTPYDLAGSRAHARELQRAGLLDESET 60

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

Query: 121 LFRMWLRDAVRRVATGVLDVVGALAEQAAAHPSAIMPGKTHLQSAQPILLAHHLLAHAHP 180
             R++LRD  R + T VL +  AL +QA  H  ++ PG THLQ AQPI+ AHHLLAHA  
Sbjct: 120 DLRLFLRDHARTITTEVLGLQQALVDQAEQHIESVCPGFTHLQQAQPIVFAHHLLAHAQS 179

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

Query: 241 AEAAFVFAMIAVDLSRLAEDIIVWSSTEFGYVTLHDSWSTGSSIMPQKKNPDIAELARGK 300
           AE  FV  M+ V++SRL+E+  +WSS +F +V L D+++TGSSIMPQKKNPDIAELARGK
Sbjct: 240 AEFLFVAGMLGVNISRLSEEFCLWSSRQFRWVVLDDAYATGSSIMPQKKNPDIAELARGK 299

Query: 301 SGRLIGNLAGLLATLKAQPLAYNRDLQEDKEPVFDSVAQLELLLPAMAGLVASLTFNVQR 360
           +GRLIGNL GL++TLK+ PL+YNRDL EDK  V DSV  L L+LPAMAG+VA++   V+ 
Sbjct: 300 AGRLIGNLTGLMSTLKSLPLSYNRDLSEDKHSVLDSVDTLLLVLPAMAGMVATMKVQVEE 359

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

Query: 421 ELTPQVREVLTIEGSVSARDCRGGTAPGRVAEQLNAI 457
            L P+VR+ L++E +++AR   GGTAP RV EQ+  +
Sbjct: 420 RLLPEVRDCLSLEAAIAARSGWGGTAPERVREQIGRL 456


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: 554
Number of extensions: 21
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 GFF4252 PS417_21780 (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.19543.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
     1e-158  515.0   0.0   1.2e-158  514.8   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF4252  PS417_21780 argininosuccinate ly


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF4252  PS417_21780 argininosuccinate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  514.8   0.0  1.2e-158  1.2e-158       1     453 [.       8     459 ..       8     461 .. 0.99

  Alignments for each domain:
  == domain 1  score: 514.8 bits;  conditional E-value: 1.2e-158
                           TIGR00838   1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkegklele 75 
                                         lwg R+k +++ a+a++++  +   +l+ +D+ gs ah++ L++ag+l e e+ +  eaL+++  + ++g+l+++
  lcl|FitnessBrowser__WCS417:GFF4252   8 LWGARFKTGPSAALAALSRCPERYFRLTPYDLAGSRAHARELQRAGLLDESETLRTLEALDSIGMDFAAGTLHPT 82 
                                         7************************************************************************** PP

                           TIGR00838  76 vdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAekevetlmp 150
                                          d+eD+H+ +Er l++++g  +g+kl++grsRnDq a dlrl+lrd+ ++++++++ l++alv++Ae+++e + p
  lcl|FitnessBrowser__WCS417:GFF4252  83 LDDEDVHTFIERVLTERLG-ALGGKLRAGRSRNDQTANDLRLFLRDHARTITTEVLGLQQALVDQAEQHIESVCP 156
                                         *******************.******************************************************* PP

                           TIGR00838 151 gytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFdavvensld 225
                                         g+tHLq+AqPi +aHhlla+a+++ rD++Rl+d   R++ sPlG++A+ag++ + ++e +a+ +g+   +ens+d
  lcl|FitnessBrowser__WCS417:GFF4252 157 GFTHLQQAQPIVFAHHLLAHAQSMLRDVQRLVDWDARTALSPLGAAAMAGSAIARQPEHSAKEMGYTGPCENSID 231
                                         *************************************************************************** PP

                           TIGR00838 226 avsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKKnpDvaEliRgktgrviGn 300
                                         av++RD+++E+l++a +l v++srl+Ee+ l+ss+ f +v l+d++++gssimPqKKnpD+aEl+Rgk+gr+iGn
  lcl|FitnessBrowser__WCS417:GFF4252 232 AVASRDHVAEFLFVAGMLGVNISRLSEEFCLWSSRQFRWVVLDDAYATGSSIMPQKKNPDIAELARGKAGRLIGN 306
                                         *************************************************************************** PP

                           TIGR00838 301 ltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllkelkvnkerleeaakknfalatdlAdylvrk 375
                                         ltgl+ +lK+lPl+Yn+Dl Edk ++ d+++t+  +l +++g+++++kv+ e+l+++a  +f+lat++Ad+l+++
  lcl|FitnessBrowser__WCS417:GFF4252 307 LTGLMSTLKSLPLSYNRDLSEDKHSVLDSVDTLLLVLPAMAGMVATMKVQVEELRRQAPMGFTLATEVADWLATR 381
                                         *************************************************************************** PP

                           TIGR00838 376 GvPFReaheivGevvakaiekGkkleeltleelqklsekleedvlevldleeavekrdakGGtakeevekaieea 450
                                         GvPF+eahei+G++v++++++ ++l e + + l++++ +l ++v++ l+le a+++r+  GGta+e+v+++i  +
  lcl|FitnessBrowser__WCS417:GFF4252 382 GVPFKEAHEITGALVQACEKHEIELWEASSAMLAEVDARLLPEVRDCLSLEAAIAARSGWGGTAPERVREQIGRL 456
                                         ************************************************************************998 PP

                           TIGR00838 451 kae 453
                                         k  
  lcl|FitnessBrowser__WCS417:GFF4252 457 KIA 459
                                         865 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.72
//
[ok]

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

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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
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