GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argG in Caldicellulosiruptor kronotskyensis 2002

Align argininosuccinate synthase (EC 6.3.4.5) (characterized)
to candidate WP_013430408.1 CALKRO_RS07345 argininosuccinate synthase

Query= BRENDA::A4I066
         (418 letters)



>NCBI__GCF_000166775.1:WP_013430408.1
          Length = 403

 Score =  484 bits (1246), Expect = e-141
 Identities = 243/402 (60%), Positives = 300/402 (74%), Gaps = 2/402 (0%)

Query: 12  KKPRVVLAYSGGLDTSVIIPWLKENYDYEVIACCANVGQGAGEIDGLEEKAKKSGASKLY 71
           K  +VVLAYSGGLDTSVIIPWLKEN+D EVIA   +VGQ   + D ++EKA K+GASK+Y
Sbjct: 2   KLNKVVLAYSGGLDTSVIIPWLKENFDCEVIAVVVDVGQ-EDDFDAIKEKAYKTGASKVY 60

Query: 72  LLDLREEYVTDYIFPTLKAGATYEGKYMLGTSHARPLIAKHLVEVAHKEGAVAICHGATG 131
           + D +EE+V +YIFPTLKAGA YEGKY+LGTS ARPLIAK LV +A KE A AI HGATG
Sbjct: 61  IEDAKEEFVNEYIFPTLKAGAIYEGKYLLGTSMARPLIAKKLVNIAKKENADAIAHGATG 120

Query: 132 KGNDQVRFELAVMALDPSLKCVAPWREWNIKSREDAIDYAEAHGVPVPCTKSDLYSRDRN 191
           KGNDQVRFE+ + AL P +K +APWR WN+KSRED ++Y    G+ +P  K + YS D N
Sbjct: 121 KGNDQVRFEVTIKALMPQIKIIAPWRIWNLKSREDELNYLTQKGIDIPFKKEESYSMDGN 180

Query: 192 LWHISHEGMDLEDPANEPAYARLLRLCNTVEKAPDEAEYVTVQFEKGIPVAVNGRKMSSV 251
           +WH+SHEG+DLEDP N P + ++L++     K  D  E V ++FEKGIPV VNG++M  V
Sbjct: 181 IWHLSHEGLDLEDPWNMPDFDKVLKITKNPLKLADLPETVEIEFEKGIPVKVNGQQMGGV 240

Query: 252 ELVEELNALGGKHAIGIEDIVEDRLVGMKSRGVYETPAGTILYKALDMLESLCLDRDTQS 311
           EL++ LN +G  H IGI DIVE+RLVGMKSRGVYETP GTILY A   LE LCLDR T  
Sbjct: 241 ELLKTLNKIGSNHGIGIADIVENRLVGMKSRGVYETPGGTILYYAHRELEYLCLDRATLH 300

Query: 312 FKRQSAVRFSELVYDGKWFTPLRESMSAMFDQMAETVTGEATLKLYKGNLVPAGAQSPYS 371
           FK   A+RF+ELVYDG WF+PLRE++SA  D+  E V G   L LY+GN+  AG++SP S
Sbjct: 301 FKDMVAIRFAELVYDGLWFSPLREAISAFVDKTQEVVNGTVRLVLYRGNIYSAGSKSPNS 360

Query: 372 LYNKNIASFGDSQHLYNHHDAEGFIRLFGLPLRVRSMMKAKE 413
           LY K++A+F + Q +YN  DAEGFI LFGLPL+V  M+  KE
Sbjct: 361 LYIKDLATFEEDQ-MYNQKDAEGFINLFGLPLKVFGMVNRKE 401


Lambda     K      H
   0.317    0.134    0.397 

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: 489
Number of extensions: 15
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: 418
Length of database: 403
Length adjustment: 31
Effective length of query: 387
Effective length of database: 372
Effective search space:   143964
Effective search space used:   143964
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate WP_013430408.1 CALKRO_RS07345 (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.3133379.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.3e-159  516.3   0.0   3.8e-159  516.1   0.0    1.0  1  NCBI__GCF_000166775.1:WP_013430408.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000166775.1:WP_013430408.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  516.1   0.0  3.8e-159  3.8e-159       1     391 [.       5     396 ..       5     399 .. 0.98

  Alignments for each domain:
  == domain 1  score: 516.1 bits;  conditional E-value: 3.8e-159
                             TIGR00032   1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqpeedldaieekalklGaekayviDareefvkdylfaa 72 
                                           kvvlaysGGlDtsv++++l+e+  +eviav+vdvGq e+d+dai+eka k Ga k y+ Da+eefv++y+f++
  NCBI__GCF_000166775.1:WP_013430408.1   5 KVVLAYSGGLDTSVIIPWLKENfDCEVIAVVVDVGQ-EDDFDAIKEKAYKTGASKVYIEDAKEEFVNEYIFPT 76 
                                           8*********************99************.8*********************************** PP

                             TIGR00032  73 iqanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkviaPvrele 145
                                           ++a+a+yegkYll+t++aRpliakklv++akke+a+a+ahG+tgKGnDqvRFe++i++l p++k+iaP+r ++
  NCBI__GCF_000166775.1:WP_013430408.1  77 LKAGAIYEGKYLLGTSMARPLIAKKLVNIAKKENADAIAHGATGKGNDQVRFEVTIKALMPQIKIIAPWRIWN 149
                                           ************************************************************************* PP

                             TIGR00032 146 li.ReeeieyaaekGievpvekekaysiDenllgrsiEageLEdpstepp.ediyelvkdpiektedepevve 216
                                           l  Re+e++y+++kGi++p +ke+ ys+D n+++ s+E+ +LEdp+ +p  +++ +++k+p +   d pe+ve
  NCBI__GCF_000166775.1:WP_013430408.1 150 LKsREDELNYLTQKGIDIPFKKEESYSMDGNIWHLSHEGLDLEDPWNMPDfDKVLKITKNPLKLA-DLPETVE 221
                                           *88******************************************99986266789999999888.******* PP

                             TIGR00032 217 ieFekGvPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYEapalllLikAhkdLetlvl 289
                                           ieFekG+Pv++ng+++  vel++++n+i+ +hG+G  DivE+R++g+KsR++YE+p+ ++L  Ah++Le l l
  NCBI__GCF_000166775.1:WP_013430408.1 222 IEFEKGIPVKVNGQQMGGVELLKTLNKIGSNHGIGIADIVENRLVGMKSRGVYETPGGTILYYAHRELEYLCL 294
                                           ************************************************************************* PP

                             TIGR00032 290 tkdvlefkeiveekyseliYkGlwfdplaealdalikktqervtGtvrvklfkGnaivigrkseyslYdeelv 362
                                           ++ +l+fk++v  +++el+Y Glwf+pl+ea+ a+++ktqe v+Gtvr+ l++Gn +++g ks++slY ++l+
  NCBI__GCF_000166775.1:WP_013430408.1 295 DRATLHFKDMVAIRFAELVYDGLWFSPLREAISAFVDKTQEVVNGTVRLVLYRGNIYSAGSKSPNSLYIKDLA 367
                                           ************************************************************************* PP

                             TIGR00032 363 sfekdkefdqkdaiGfikirglqikvyre 391
                                           +fe+d+ ++qkda+Gfi++ gl+ kv+ +
  NCBI__GCF_000166775.1:WP_013430408.1 368 TFEEDQMYNQKDAEGFINLFGLPLKVFGM 396
                                           ************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (403 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: 00:00:00.00
# Mc/sec: 16.59
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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:

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:

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:

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:

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