GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Salinicoccus carnicancri Crm

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_017549340.1 C792_RS0110175 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000330705.1:WP_017549340.1
          Length = 491

 Score =  556 bits (1434), Expect = e-163
 Identities = 271/486 (55%), Positives = 367/486 (75%), Gaps = 1/486 (0%)

Query: 1   MSLFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDE 60
           M++ +  + EL + I  KEIK S++V   ++RI+A D+ + +FL +++E     A+ELD 
Sbjct: 1   MNIHELTVEELYEKIQAKEIKPSEVVGALFERIEASDETIGSFLFVNKEEGLKRAEELDR 60

Query: 61  AVDGRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIG 120
                   G LFG+P+G+KDNI TK + TTC+S++LE+F+P+YDATV+ +L +   V +G
Sbjct: 61  LQAEDRMDGALFGIPMGIKDNICTKDILTTCASRMLEDFNPVYDATVMDKLNEENPVMMG 120

Query: 121 KLNMDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIR 180
           K NMDEFAMG STENS +K  +NPW+   VPGGSSGGSAAAVAAG VPFSLGSDTGGS+R
Sbjct: 121 KQNMDEFAMGGSTENSYFKPARNPWDTKAVPGGSSGGSAAAVAAGYVPFSLGSDTGGSVR 180

Query: 181 QPASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTS 240
           QP++FCGVVG+KPTYGRVSRYGLVAFASSLDQIGPITR V DNA +L+ ISG    DSTS
Sbjct: 181 QPSAFCGVVGMKPTYGRVSRYGLVAFASSLDQIGPITRNVRDNAKILEIISGSHGKDSTS 240

Query: 241 ANVDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLP 300
                 +FL  +  D+ G+KIA+PKE++GEG+  E   SV  + ++ E LGAT +EVS+P
Sbjct: 241 MPGVEAEFLEGIDRDLSGMKIALPKEFIGEGIDDEVSASVRRSAEIFESLGATVDEVSIP 300

Query: 301 HSKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIM 360
           H+KY ++ YYL++SSEASANLARFDGIRYGY+ + A  L + YK+TR+EGFG+EVKRRI+
Sbjct: 301 HTKYGVSAYYLIASSEASANLARFDGIRYGYKAEGAQTLEEHYKKTRSEGFGSEVKRRIL 360

Query: 361 LGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLT 420
           LGTF LS+G+YD +Y +AQK+R+L++ + +++F +YD+I+GPTTPT A+ IGE ++D L 
Sbjct: 361 LGTFVLSAGHYDQHYIRAQKLRSLLEGEMKELFSEYDLIIGPTTPTAAYDIGEKSEDSLQ 420

Query: 421 MYANDILTIPVNLAGVPGISVPCGLA-DGLPLGLQIIGKHFDESTVYRVAHAFEQATDHH 479
           MY +DILT+P NL G+P +S+P GL+ DG P+GLQ+I  HFDE  +Y  A  FE+  + H
Sbjct: 421 MYKDDILTVPANLTGMPALSIPSGLSRDGRPIGLQLIANHFDEKKIYNAAFKFEEKFNLH 480

Query: 480 KAKPEL 485
           +   +L
Sbjct: 481 EELKKL 486


Lambda     K      H
   0.315    0.134    0.381 

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: 724
Number of extensions: 31
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: 485
Length of database: 491
Length adjustment: 34
Effective length of query: 451
Effective length of database: 457
Effective search space:   206107
Effective search space used:   206107
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: 52 (24.6 bits)

Align candidate WP_017549340.1 C792_RS0110175 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA)
to HMM TIGR00132 (gatA: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit (EC 6.3.5.-))

# 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/TIGR00132.hmm
# target sequence database:        /tmp/gapView.980619.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00132  [M=466]
Accession:   TIGR00132
Description: gatA: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-189  616.6   0.0   1.7e-189  616.4   0.0    1.0  1  NCBI__GCF_000330705.1:WP_017549340.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000330705.1:WP_017549340.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  616.4   0.0  1.7e-189  1.7e-189       3     465 ..      13     478 ..      11     479 .. 0.98

  Alignments for each domain:
  == domain 1  score: 616.4 bits;  conditional E-value: 1.7e-189
                             TIGR00132   3 ellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva..kek.klagipiavKdniavk 72 
                                           e++++ke++ +ev+ ++ eriea +++i +fl v+ke+ lk+a++ld+  a  + +  l+gip+++Kdni++k
  NCBI__GCF_000330705.1:WP_017549340.1  13 EKIQAKEIKPSEVVGALFERIEASDETIGSFLFVNKEEGLKRAEELDRLQAedRMDgALFGIPMGIKDNICTK 85 
                                           68999******************************************9877543356**************** PP

                             TIGR00132  73 diettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGSsgGs 145
                                           di ttcaS++Le+++++ydatV+ +l+e++ +++Gk N+DEFamG+ste+S+f++ +nP++++ vpGGSsgGs
  NCBI__GCF_000330705.1:WP_017549340.1  86 DILTTCASRMLEDFNPVYDATVMDKLNEENPVMMGKQNMDEFAMGGSTENSYFKPARNPWDTKAVPGGSSGGS 158
                                           ************************************************************************* PP

                             TIGR00132 146 aaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvis 218
                                           aaavaa+ vp++lgsDTGgS+RqP +fcgvvG+KPtYG+vSRyGlva+asSldqiG+++++v d a++l++is
  NCBI__GCF_000330705.1:WP_017549340.1 159 AAAVAAGYVPFSLGSDTGGSVRQPSAFCGVVGMKPTYGRVSRYGLVAFASSLDQIGPITRNVRDNAKILEIIS 231
                                           ************************************************************************* PP

                             TIGR00132 219 gkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelgaeivevslpsvkl 291
                                           g+  kDsts+   ++e+le + +dl g+k+++ ke+++e++d+ev++++++  e +e+lga++ evs+p+ k+
  NCBI__GCF_000330705.1:WP_017549340.1 232 GSHGKDSTSMPGVEAEFLEGIDRDLSGMKIALPKEFIGEGIDDEVSASVRRSAEIFESLGATVDEVSIPHTKY 304
                                           ************999********************************************************** PP

                             TIGR00132 292 alaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGayalskeyydkyykk 364
                                            +++Yy+i++sEas+nlar+dgiryG+++e ++ l+e y+ktRsegfg+evkrRi+lG+++ls++ yd++y++
  NCBI__GCF_000330705.1:WP_017549340.1 305 GVSAYYLIASSEASANLARFDGIRYGYKAEGAQTLEEHYKKTRSEGFGSEVKRRILLGTFVLSAGHYDQHYIR 377
                                           ************************************************************************* PP

                             TIGR00132 365 AqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvltvpanlaGlpaisvPlgkkekgl 437
                                           Aqk+r+l+  e+++lf+e+D+i++pt+pt a  +gek ed+l+my +D+ltvpanl+G+pa+s+P g +++g 
  NCBI__GCF_000330705.1:WP_017549340.1 378 AQKLRSLLEGEMKELFSEYDLIIGPTTPTAAYDIGEKSEDSLQMYKDDILTVPANLTGMPALSIPSGLSRDGR 450
                                           ************************************************************************* PP

                             TIGR00132 438 piGlqiigkafddkkllsvakaleqald 465
                                           piGlq+i+++fd+kk++++a ++e++++
  NCBI__GCF_000330705.1:WP_017549340.1 451 PIGLQLIANHFDEKKIYNAAFKFEEKFN 478
                                           ************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (491 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 31.60
//
[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