Alignments for a candidate for argH in Halomonas desiderata SP1

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Halomonas desiderata SP1

Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate WP_086511733.1 BZY95_RS20465 argininosuccinate lyase

Query= BRENDA::Q8DVX5
         (460 letters)



>NCBI__GCF_002151265.1:WP_086511733.1
          Length = 473

 Score =  459 bits (1181), Expect = e-134
 Identities = 232/459 (50%), Positives = 318/459 (69%)

Query: 2   TTKNHKLWGGRFEAGLAQWVEEFGASISFDQKLAEFDLKGSIAHVTMLGEKGIISQEDAA 61
           T   ++ WGGRF      +VE F AS+ FDQ+LA  D++GSIAH TML   G+++ ++  
Sbjct: 7   TPGTNQSWGGRFSEPTDAFVERFTASVGFDQRLALQDIQGSIAHATMLARVGVLTDDERD 66

Query: 62  TIKAGLEDLLEEYKAGQLKFDVSNEDIHMNMESLLTAKIGPVAGKLHTARSRNDQVATDM 121
            I AGL ++  E + G+ ++ V  ED+HMN+E+ LT KIG    KLHT RSRNDQVATD+
Sbjct: 67  AIVAGLTEIRGEIERGEFQWSVKLEDVHMNVEARLTDKIGITGKKLHTGRSRNDQVATDI 126

Query: 122 HLYLKAKLDEVIEKLANLRTVLVDLADKHVHTIMPGYTHLQHAQPISFGHHLMAYYNMFT 181
            L+L+ ++D V  +L  LR  L+ LA++   TIMPG+THLQ AQP++FGHHL+A+  M  
Sbjct: 127 RLFLRDEIDVVEAELGRLREGLIALAEREADTIMPGFTHLQTAQPVTFGHHLLAWQEMLA 186

Query: 182 RDSERFIFNVKHTDLSPLGAAALAGTTFPIDREMTAQLMGFAEPYSNSLDAVSDRDFILE 241
           RD ER +   K  ++ PLGAAALAGTT+PIDR +TA+L+GF  P  NSLDAVSDRDF +E
Sbjct: 187 RDHERLLDCRKRVNVMPLGAAALAGTTYPIDRHVTAELLGFERPAENSLDAVSDRDFAIE 246

Query: 242 FLSNASILMMHMSRMCEEVISWCSHEYQFVTLSDTFSTGSSIMPQKKNPDMAELIRGKSG 301
           F S ASIL+MH+SRM EE++ W S ++ F+ L D F TGSSIMPQKKNPD+ EL+RGK+G
Sbjct: 247 FASFASILLMHLSRMSEELVLWTSAQFDFIDLPDRFCTGSSIMPQKKNPDVPELVRGKTG 306

Query: 302 RVYANLFGLLTVMKALPLAYNKDLQEDKEGMFDTAETITVALDILAGMLSSMIVNDKHMA 361
           RVY +L GLLT+MK+ PLAYNKD QEDKE +FDT +T+   L   A M+ ++    + M 
Sbjct: 307 RVYGHLMGLLTLMKSQPLAYNKDNQEDKEPLFDTLDTVRDCLKAFADMVPAIEARKESMY 366

Query: 362 ESTQKDFSNATELADYLASKGMPFRQAHEIVGKLILECSKNGHYLQDVPLERYQTISDLI 421
           E+ ++ FS AT+LADYL  +G+ FR AHEIVG+ +    +    L ++ L+  +  SD+I
Sbjct: 367 EAARRGFSTATDLADYLVRRGVAFRDAHEIVGQSVAFGIREKKDLSEMSLDELRQFSDVI 426

Query: 422 EEDVYETLKSHTAVERRHSLGGTGFEQVKWQIAEAKKAL 460
           E DV+E L    +V  R+ +GGT  +QV+   + A++AL
Sbjct: 427 ESDVFEVLTLEGSVAARNHIGGTAPDQVRAAASRAREAL 465


Lambda     K      H
   0.318    0.132    0.378 

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: 597
Number of extensions: 22
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: 460
Length of database: 473
Length adjustment: 33
Effective length of query: 427
Effective length of database: 440
Effective search space:   187880
Effective search space used:   187880
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 WP_086511733.1 BZY95_RS20465 (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.10976.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.5e-194  632.4   0.0   2.9e-194  632.2   0.0    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086511733.1  BZY95_RS20465 argininosuccinate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086511733.1  BZY95_RS20465 argininosuccinate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  632.2   0.0  2.9e-194  2.9e-194       2     454 ..      14     465 ..      13     466 .. 0.99

  Alignments for each domain:
  == domain 1  score: 632.2 bits;  conditional E-value: 2.9e-194
                                 TIGR00838   2 wggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkeg 70 
                                               wggR+++ +d  v++f+as+ fD++la +Di+gsiah+++La++g+lt++e++ ++++L+e++ e+++g
  lcl|NCBI__GCF_002151265.1:WP_086511733.1  14 WGGRFSEPTDAFVERFTASVGFDQRLALQDIQGSIAHATMLARVGVLTDDERDAIVAGLTEIRGEIERG 82 
                                               9******************************************************************** PP

                                 TIGR00838  71 klelevdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalve 139
                                               +++++v+ eD+H++vE++l+dk+g   gkklhtgrsRnDqvatd+rl+lrd+++ +  +l  l++ l+ 
  lcl|NCBI__GCF_002151265.1:WP_086511733.1  83 EFQWSVKLEDVHMNVEARLTDKIG-ITGKKLHTGRSRNDQVATDIRLFLRDEIDVVEAELGRLREGLIA 150
                                               ************************.999***************************************** PP

                                 TIGR00838 140 kAekevetlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidre 208
                                               +Ae+e +t+mpg+tHLq AqP+t++Hhlla++eml+rD eRlld  kRvn+ PlG++Alagt+++idr+
  lcl|NCBI__GCF_002151265.1:WP_086511733.1 151 LAEREADTIMPGFTHLQTAQPVTFGHHLLAWQEMLARDHERLLDCRKRVNVMPLGAAALAGTTYPIDRH 219
                                               ********************************************************************* PP

                                 TIGR00838 209 llaelLgFdavvensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssi 277
                                               ++aelLgF++ +ensldavsdRDf+iE+ s a++l +hlsr++Eel+l++s+ f+f++l+d++++gssi
  lcl|NCBI__GCF_002151265.1:WP_086511733.1 220 VTAELLGFERPAENSLDAVSDRDFAIEFASFASILLMHLSRMSEELVLWTSAQFDFIDLPDRFCTGSSI 288
                                               ********************************************************************* PP

                                 TIGR00838 278 mPqKKnpDvaEliRgktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllke 346
                                               mPqKKnpDv El+Rgktgrv+G+l+gllt++K++PlaYnkD qEdke+lfd+l+tv+++l++++ ++  
  lcl|NCBI__GCF_002151265.1:WP_086511733.1 289 MPQKKNPDVPELVRGKTGRVYGHLMGLLTLMKSQPLAYNKDNQEDKEPLFDTLDTVRDCLKAFADMVPA 357
                                               ********************************************************************* PP

                                 TIGR00838 347 lkvnkerleeaakknfalatdlAdylvrkGvPFReaheivGevvakaiekGkkleeltleelqklsekl 415
                                               ++ +ke + eaa+++f++atdlAdylvr+Gv FR+aheivG+ va  i++ k+l+e++l+el+++s  +
  lcl|NCBI__GCF_002151265.1:WP_086511733.1 358 IEARKESMYEAARRGFSTATDLADYLVRRGVAFRDAHEIVGQSVAFGIREKKDLSEMSLDELRQFSDVI 426
                                               ********************************************************************* PP

                                 TIGR00838 416 eedvlevldleeavekrdakGGtakeevekaieeakael 454
                                               e dv+evl+le +v++r+ +GGta+++v+ a + a++ l
  lcl|NCBI__GCF_002151265.1:WP_086511733.1 427 ESDVFEVLTLEGSVAARNHIGGTAPDQVRAAASRAREAL 465
                                               ******************************999988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (473 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: 00:00:00.03
# Mc/sec: 7.17
//
[ok]

This GapMind analysis is from Apr 10 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