Alignments for a candidate for argG in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for argG in Dinoroseobacter shibae DFL-12

Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate 3610091 Dshi_3472 Argininosuccinate synthase (RefSeq)

Query= SwissProt::P59846
         (400 letters)



>FitnessBrowser__Dino:3610091
          Length = 406

 Score =  502 bits (1292), Expect = e-147
 Identities = 251/393 (63%), Positives = 301/393 (76%), Gaps = 3/393 (0%)

Query: 2   KIVLAYSGGLDTSIILKWLKETYRAEVIAFTADIGQGEEVEEAREKALRTGASKAIALDL 61
           K+VLAYSGGLDTSIILKWL+  Y  EV+ FTAD+GQGEE+E AR KA   GAS     DL
Sbjct: 6   KVVLAYSGGLDTSIILKWLQTEYDCEVVTFTADLGQGEELEPARAKAEMMGASAIYIEDL 65

Query: 62  KEEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKGND 121
           +EEFVRDFVFPM RA AVYEG YLLGTSIARPLI+K LV IAE EGA+A+AHGATGKGND
Sbjct: 66  REEFVRDFVFPMFRANAVYEGLYLLGTSIARPLISKRLVEIAEAEGADAVAHGATGKGND 125

Query: 122 QVRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQ--EKPYSMDANLL 179
           QVRFEL AYAL PDIKVIAPWREW    R ++I +AE H IP+   +  E P+S+DANLL
Sbjct: 126 QVRFELAAYALNPDIKVIAPWREWDLSSRTKLIDFAEKHQIPIAKDKRGEAPFSVDANLL 185

Query: 180 HISYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPAALL 239
           H S EG VLEDP  + P  +++ T +PE+AP+ PEY+EV F  GD V++NGE +SPA +L
Sbjct: 186 HTSSEGKVLEDPAEDAPDYVYQRTVNPEDAPNTPEYIEVGFERGDAVSINGEAMSPATVL 245

Query: 240 QRLNEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVLHQRD 299
            +LNE+GG HG+GR+D+VE RFVGMKSRG+YETPGGTIL  A R +E +TLDR   H +D
Sbjct: 246 TKLNELGGAHGIGRLDLVEGRFVGMKSRGIYETPGGTILLEAHRGIEQITLDRGAAHLKD 305

Query: 300 MLSPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGRKAPKSLYR 359
            L P+YAEL+Y GFW++PERE LQA  D     VTG  RLKLYKG+V  VGR +  SLY 
Sbjct: 306 ELMPRYAELIYNGFWFSPEREMLQAAIDASQAHVTGTVRLKLYKGSVRTVGRWSDHSLYS 365

Query: 360 QDLVSF-DEAGGYDQKDAEGFIKIQALRLRVRA 391
           +  V+F D+AG YDQKDA GFI++ ALRL++ A
Sbjct: 366 EAHVTFEDDAGAYDQKDAAGFIQLNALRLKLLA 398


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: 502
Number of extensions: 20
Number of successful extensions: 3
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: 406
Length adjustment: 31
Effective length of query: 369
Effective length of database: 375
Effective search space:   138375
Effective search space used:   138375
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 3610091 Dshi_3472 (Argininosuccinate synthase (RefSeq))
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.20844.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   6.2e-147  475.9   0.0   7.3e-147  475.7   0.0    1.0  1  lcl|FitnessBrowser__Dino:3610091  Dshi_3472 Argininosuccinate synt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3610091  Dshi_3472 Argininosuccinate synthase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  475.7   0.0  7.3e-147  7.3e-147       1     390 [.       6     398 ..       6     402 .. 0.98

  Alignments for each domain:
  == domain 1  score: 475.7 bits;  conditional E-value: 7.3e-147
                         TIGR00032   1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqpeedldaieekalklGaekayviDareefvkdylfaaiqan 76 
                                       kvvlaysGGlDts++lk+l+ +  +ev+++t+d+Gq+ e+l+ ++ ka  +Ga   y+ D reefv+d++f+  +an
  lcl|FitnessBrowser__Dino:3610091   6 KVVLAYSGGLDTSIILKWLQTEyDCEVVTFTADLGQG-EELEPARAKAEMMGASAIYIEDLREEFVRDFVFPMFRAN 81 
                                       8*********************999***********9.9************************************** PP

                         TIGR00032  77 avyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkviaPvreleli.Reeei 152
                                       avyeg Yll+t++aRpli+k+lve+a+ ega+avahG+tgKGnDqvRFel  ++lnpd+kviaP+re++l+ R+++i
  lcl|FitnessBrowser__Dino:3610091  82 AVYEGLYLLGTSIARPLISKRLVEIAEAEGADAVAHGATGKGNDQVRFELAAYALNPDIKVIAPWREWDLSsRTKLI 158
                                       **********************************************************************99***** PP

                         TIGR00032 153 eyaaekGievpvek..ekaysiDenllgrsiEageLEdpsteppediyelvkdpiektedepevveieFekGvPval 227
                                       ++a+++ i+++ +k  e ++s+D nll+ s E++ LEdp    p+ +y+ +++p++++ ++pe++e++Fe+G  v++
  lcl|FitnessBrowser__Dino:3610091 159 DFAEKHQIPIAKDKrgEAPFSVDANLLHTSSEGKVLEDPAEDAPDYVYQRTVNPEDAP-NTPEYIEVGFERGDAVSI 234
                                       **********99875579**********************************999888.9***************** PP

                         TIGR00032 228 ngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYEapalllLikAhkdLetlvltkdvlefkeiveeky 304
                                       nge ++p +++ k+ne++g+hG+Gr+D vE R +g+KsR+iYE+p+ ++L++Ah+ +e+ +l++  +++k+    +y
  lcl|FitnessBrowser__Dino:3610091 235 NGEAMSPATVLTKLNELGGAHGIGRLDLVEGRFVGMKSRGIYETPGGTILLEAHRGIEQITLDRGAAHLKDELMPRY 311
                                       ***************************************************************************** PP

                         TIGR00032 305 seliYkGlwfdplaealdalikktqervtGtvrvklfkGnaivigrkseyslYdeelvsfek.dkefdqkdaiGfik 380
                                       +eliY+G+wf+p++e+l+a+i+ +q +vtGtvr+kl+kG+++++gr s++slY+e  v+fe    ++dqkda+Gfi+
  lcl|FitnessBrowser__Dino:3610091 312 AELIYNGFWFSPEREMLQAAIDASQAHVTGTVRLKLYKGSVRTVGRWSDHSLYSEAHVTFEDdAGAYDQKDAAGFIQ 388
                                       *************************************************************944589********** PP

                         TIGR00032 381 irglqikvyr 390
                                       +++l+ k  +
  lcl|FitnessBrowser__Dino:3610091 389 LNALRLKLLA 398
                                       ****999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (406 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: 00:00:00.01
# Mc/sec: 10.95
//
[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