Alignments for a candidate for argG in Derxia gummosa DSM 723

GapMind for Amino acid biosynthesis

Alignments for a candidate for argG in Derxia gummosa DSM 723

Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate WP_051377926.1 H566_RS22575 argininosuccinate synthase

Query= SwissProt::P59846
         (400 letters)



>NCBI__GCF_000482785.1:WP_051377926.1
          Length = 507

 Score =  491 bits (1265), Expect = e-143
 Identities = 241/397 (60%), Positives = 304/397 (76%), Gaps = 7/397 (1%)

Query: 2   KIVLAYSGGLDTSIILKWLKETYRAEVIAFTADIGQGEEVEEAREKALRTGAS--KAIAL 59
           K+VLAYSGGLDTS+ILKWL++ Y+ EV+ FTADIGQGEEVE AR+KA+  G         
Sbjct: 7   KVVLAYSGGLDTSVILKWLQDVYQCEVVTFTADIGQGEEVEPARKKAIALGIKPENIFIQ 66

Query: 60  DLKEEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKG 119
           DL+EEFVRDFVFPM RA  VYEG YLLGTSIARPLIAK L+ IA++ GA+AI+HGATGKG
Sbjct: 67  DLREEFVRDFVFPMFRANTVYEGEYLLGTSIARPLIAKQLIEIAKKTGADAISHGATGKG 126

Query: 120 NDQVRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQEK----PYSMD 175
           NDQVRFEL AYAL P++KVIAPWREW    R++++AYA+AH IPV   + K    PYSMD
Sbjct: 127 NDQVRFELGAYALLPNVKVIAPWREWDLLSREKLLAYADAHKIPVDFKKRKGGGAPYSMD 186

Query: 176 ANLLHISYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSP 235
           ANLLHISYEGG+LEDP   P   M+R+T  PE+AP  P+ +E+ + +GD VA++G+RL P
Sbjct: 187 ANLLHISYEGGILEDPNFAPEDNMWRLTVSPEKAPGKPQIIELTYEKGDVVAIDGQRLKP 246

Query: 236 AALLQRLNEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVL 295
             +L  LN++GG+HG+GR+D+VENR+VGMKSRG YETPGGTIL    RA+ES+TLDREV+
Sbjct: 247 HEVLDTLNKLGGKHGIGRLDLVENRYVGMKSRGCYETPGGTILLKGHRAIESITLDREVV 306

Query: 296 HQRDMLSPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGRKAPK 355
             +D L P+YA ++Y G+W++PERE LQ   D     V G  +LKLYKG + VVGR++  
Sbjct: 307 ALKDDLMPRYARMIYNGYWFSPERELLQGLIDASQAKVNGTVKLKLYKGTIMVVGRESAN 366

Query: 356 SLYRQDLVSFDEAGG-YDQKDAEGFIKIQALRLRVRA 391
           SL+   + +FD+ GG Y+Q DA GFIK+ ALRLR+ A
Sbjct: 367 SLFDAKISTFDDDGGAYNQADAGGFIKLNALRLRIAA 403


Lambda     K      H
   0.319    0.137    0.402 

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: 630
Number of extensions: 23
Number of successful extensions: 4
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: 400
Length of database: 507
Length adjustment: 33
Effective length of query: 367
Effective length of database: 474
Effective search space:   173958
Effective search space used:   173958
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_051377926.1 H566_RS22575 (argininosuccinate synthase)
to HMM TIGR00032 (argG: argininosuccinate synthase (EC 6.3.4.5))

# 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/TIGR00032.hmm
# target sequence database:        /tmp/gapView.26664.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00032  [M=394]
Accession:   TIGR00032
Description: argG: argininosuccinate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.6e-141  456.1   0.0     8e-141  455.8   0.0    1.0  1  lcl|NCBI__GCF_000482785.1:WP_051377926.1  H566_RS22575 argininosuccinate s


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000482785.1:WP_051377926.1  H566_RS22575 argininosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  455.8   0.0    8e-141    8e-141       1     392 [.       7     405 ..       7     407 .. 0.96

  Alignments for each domain:
  == domain 1  score: 455.8 bits;  conditional E-value: 8e-141
                                 TIGR00032   1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqpeedldaieekalklGa..ekayviDareefvk 66 
                                               kvvlaysGGlDtsv+lk+l++   +ev+++t+d+Gq+ e+++ +++ka++lG   e+  + D reefv+
  lcl|NCBI__GCF_000482785.1:WP_051377926.1   7 KVVLAYSGGLDTSVILKWLQDVyQCEVVTFTADIGQG-EEVEPARKKAIALGIkpENIFIQDLREEFVR 74 
                                               8*********************899***********9.9*************733577788******** PP

                                 TIGR00032  67 dylfaaiqanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdl 135
                                               d++f+  +an+vyeg+Yll+t++aRpliak+l+e+akk ga+a++hG+tgKGnDqvRFel  ++l p++
  lcl|NCBI__GCF_000482785.1:WP_051377926.1  75 DFVFPMFRANTVYEGEYLLGTSIARPLIAKQLIEIAKKTGADAISHGATGKGNDQVRFELGAYALLPNV 143
                                               ********************************************************************* PP

                                 TIGR00032 136 kviaPvreleli.ReeeieyaaekGievpvekek....aysiDenllgrsiEageLEdpsteppediye 199
                                               kviaP+re++l  Re++++ya ++ i+v  +k k    +ys+D nll++s+E+g+LEdp+++p +++++
  lcl|NCBI__GCF_000482785.1:WP_051377926.1 144 KVIAPWREWDLLsREKLLAYADAHKIPVDFKKRKgggaPYSMDANLLHISYEGGILEDPNFAPEDNMWR 212
                                               **********987*****************998766669****************************** PP

                                 TIGR00032 200 lvkdpiektedepevveieFekGvPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsRei 268
                                               l+++p++++  +p+++e+++ekG  va++g++l+p e++ ++n+++gkhG+Gr+D vE+R++g+KsR++
  lcl|NCBI__GCF_000482785.1:WP_051377926.1 213 LTVSPEKAP-GKPQIIELTYEKGDVVAIDGQRLKPHEVLDTLNKLGGKHGIGRLDLVENRYVGMKSRGC 280
                                               ***998887.*********************************************************** PP

                                 TIGR00032 269 YEapalllLikAhkdLetlvltkdvlefkeiveekyseliYkGlwfdplaealdalikktqervtGtvr 337
                                               YE+p+ ++L+k h+++e+ +l+++v+ +k+    +y+++iY+G+wf+p++e l+ li+ +q +v+Gtv+
  lcl|NCBI__GCF_000482785.1:WP_051377926.1 281 YETPGGTILLKGHRAIESITLDREVVALKDDLMPRYARMIYNGYWFSPERELLQGLIDASQAKVNGTVK 349
                                               ********************************************************************* PP

                                 TIGR00032 338 vklfkGnaivigrkseyslYdeelvsfek.dkefdqkdaiGfikirglqikvyrek 392
                                               +kl+kG+ +v+gr+s +sl+d+++++f+    +++q da Gfik+++l+ ++ ++k
  lcl|NCBI__GCF_000482785.1:WP_051377926.1 350 LKLYKGTIMVVGRESANSLFDAKISTFDDdGGAYNQADAGGFIKLNALRLRIAANK 405
                                               ****************************8446799*************99887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (507 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: 8.12
//
[ok]

This GapMind analysis is from Apr 10 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