Alignments for a candidate for argG in Sphingomonas koreensis DSMZ 15582

GapMind for Amino acid biosynthesis

Alignments for a candidate for argG in Sphingomonas koreensis DSMZ 15582

Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate Ga0059261_1393 Ga0059261_1393 argininosuccinate synthase (EC 6.3.4.5)

Query= SwissProt::P59846
         (400 letters)



>FitnessBrowser__Korea:Ga0059261_1393
          Length = 405

 Score =  513 bits (1322), Expect = e-150
 Identities = 253/401 (63%), Positives = 312/401 (77%), Gaps = 7/401 (1%)

Query: 2   KIVLAYSGGLDTSIILKWLKETYRAEVIAFTADIGQGEEVEEAREKALRTGASKAIAL-- 59
           ++VLAYSGGLDTS+ILKWL++ Y+ EV+ FTAD+GQGEE+E AR+KAL  G         
Sbjct: 7   RVVLAYSGGLDTSVILKWLQQEYQCEVVTFTADLGQGEELEPARQKALNAGVKPEHIFID 66

Query: 60  DLKEEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKG 119
           DL+EEFVRDFVFPMMRA A+YEG YLLGTSIARPLI+K L+ IA+E  A+A++HGATGKG
Sbjct: 67  DLREEFVRDFVFPMMRANALYEGLYLLGTSIARPLISKRLIEIAKEVNADAVSHGATGKG 126

Query: 120 NDQVRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQ--EKPYSMDAN 177
           NDQVRFEL+AYAL PDIKVIAPWREW    R ++I +AE H I V   +  E P+S DAN
Sbjct: 127 NDQVRFELSAYALNPDIKVIAPWREWDLTSRTKLIEFAEKHQIQVAKDKRGEAPFSTDAN 186

Query: 178 LLHISYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPAA 237
           LLH S EG VLEDPW E P  +F  T +PE+APD PEY+ ++F +GD  A+NGE +SPA 
Sbjct: 187 LLHTSSEGKVLEDPWEEVPDYVFSRTVNPEDAPDTPEYITIDFEKGDGTALNGEAMSPAT 246

Query: 238 LLQRLNEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVLHQ 297
           LL  LN++G +HG+GR+D+VENRFVGMKSRG+YETPGGTI + A R +ES+TLDR   H 
Sbjct: 247 LLAALNDLGRKHGIGRLDLVENRFVGMKSRGMYETPGGTIYHLAHRGIESITLDRGAAHL 306

Query: 298 RDMLSPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGRKAPKSL 357
           +D L+P+YAEL+Y GFW+APERE LQA  DH  ++V G  RLKLYKG VYVVGRK+P SL
Sbjct: 307 KDELAPRYAELIYNGFWFAPEREMLQAAIDHSQQNVNGTVRLKLYKGGVYVVGRKSPNSL 366

Query: 358 YRQDLVSF-DEAGGYDQKDAEGFIKIQALRLRVRALVEREG 397
           Y + +V+F D+ G YDQ+DA GFIK+ ALRLR+  L  R+G
Sbjct: 367 YSEKVVTFEDDQGAYDQRDAAGFIKLNALRLRL--LGRRDG 405


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: 514
Number of extensions: 21
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: 405
Length adjustment: 31
Effective length of query: 369
Effective length of database: 374
Effective search space:   138006
Effective search space used:   138006
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: 50 (23.9 bits)

Align candidate Ga0059261_1393 Ga0059261_1393 (argininosuccinate synthase (EC 6.3.4.5))
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.25336.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.3e-146  474.0   0.0   2.8e-146  473.8   0.0    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_1393  Ga0059261_1393 argininosuccinate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_1393  Ga0059261_1393 argininosuccinate synthase (EC 6.3.4.5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  473.8   0.0  2.8e-146  2.8e-146       1     389 [.       7     400 ..       7     404 .. 0.97

  Alignments for each domain:
  == domain 1  score: 473.8 bits;  conditional E-value: 2.8e-146
                                 TIGR00032   1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqpeedldaieekalklGae.kayvi.Dareefvk 66 
                                               +vvlaysGGlDtsv+lk+l+++  +ev+++t+d+Gq+ e+l+ +++kal+ G++ +++ i D reefv+
  lcl|FitnessBrowser__Korea:Ga0059261_1393   7 RVVLAYSGGLDTSVILKWLQQEyQCEVVTFTADLGQG-EELEPARQKALNAGVKpEHIFIdDLREEFVR 74 
                                               69********************899***********9.9*************97466777358****** PP

                                 TIGR00032  67 dylfaaiqanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdl 135
                                               d++f+ ++ana+yeg Yll+t++aRpli+k+l+e+ak+ +a+av+hG+tgKGnDqvRFels ++lnpd+
  lcl|FitnessBrowser__Korea:Ga0059261_1393  75 DFVFPMMRANALYEGLYLLGTSIARPLISKRLIEIAKEVNADAVSHGATGKGNDQVRFELSAYALNPDI 143
                                               ********************************************************************* PP

                                 TIGR00032 136 kviaPvreleli.ReeeieyaaekGievpvek..ekaysiDenllgrsiEageLEdpsteppediyelv 201
                                               kviaP+re++l+ R+++ie+a+++ i+v+ +k  e ++s+D nll+ s E++ LEdp+ e p+ +++ +
  lcl|FitnessBrowser__Korea:Ga0059261_1393 144 KVIAPWREWDLTsRTKLIEFAEKHQIQVAKDKrgEAPFSTDANLLHTSSEGKVLEDPWEEVPDYVFSRT 212
                                               ***********99***************99875579********************************* PP

                                 TIGR00032 202 kdpiektedepevveieFekGvPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYE 270
                                               ++p++++ d+pe+++i+FekG   alnge ++p +l+ ++n++++khG+Gr+D vE+R +g+KsR++YE
  lcl|FitnessBrowser__Korea:Ga0059261_1393 213 VNPEDAP-DTPEYITIDFEKGDGTALNGEAMSPATLLAALNDLGRKHGIGRLDLVENRFVGMKSRGMYE 280
                                               *999888.************************************************************* PP

                                 TIGR00032 271 apalllLikAhkdLetlvltkdvlefkeiveekyseliYkGlwfdplaealdalikktqervtGtvrvk 339
                                               +p+ ++ + Ah+ +e+ +l++  +++k+    +y+eliY+G+wf p++e+l+a+i+++q++v+Gtvr+k
  lcl|FitnessBrowser__Korea:Ga0059261_1393 281 TPGGTIYHLAHRGIESITLDRGAAHLKDELAPRYAELIYNGFWFAPEREMLQAAIDHSQQNVNGTVRLK 349
                                               ********************************************************************* PP

                                 TIGR00032 340 lfkGnaivigrkseyslYdeelvsfek.dkefdqkdaiGfikirglqikvy 389
                                               l+kG ++v+grks++slY+e+ v+fe  + ++dq+da+Gfik+++l+ +  
  lcl|FitnessBrowser__Korea:Ga0059261_1393 350 LYKGGVYVVGRKSPNSLYSEKVVTFEDdQGAYDQRDAAGFIKLNALRLRLL 400
                                               **************************955689**************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (405 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.49
//
[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