GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Herbaspirillum seropedicae SmR1

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate HSERO_RS23305 HSERO_RS23305 glutamyl-tRNA amidotransferase subunit A

Query= SwissProt::O06491
         (485 letters)



>FitnessBrowser__HerbieS:HSERO_RS23305
          Length = 488

 Score =  467 bits (1202), Expect = e-136
 Identities = 246/489 (50%), Positives = 329/489 (67%), Gaps = 14/489 (2%)

Query: 6   HKIT--ELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVD 63
           HK+T  EL   +  ++I  ++L      RI A D  + AFL +D E   A AK  D  + 
Sbjct: 2   HKLTLKELSAQLQARKISATELATLFLDRIDASD--LNAFLHVDRELTLAQAKVADSRLS 59

Query: 64  GRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLN 123
             +  G L G+PI  KD  VT+G RTT  S++L+N+   +DATVV++   A  VT+GKLN
Sbjct: 60  DNNA-GQLTGVPIAHKDIFVTRGWRTTAGSRMLDNYVSPFDATVVEQFNAAGMVTLGKLN 118

Query: 124 MDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPA 183
            DEFAMGS  ENS +  T NPW+   VPGGSSGGSAAAVAA   P +  +DTGGSIRQPA
Sbjct: 119 CDEFAMGSGNENSYFGPTLNPWDKRAVPGGSSGGSAAAVAARLAPAATATDTGGSIRQPA 178

Query: 184 SFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANV 243
           S CGV G+KPTYG VSRYG++AFASSLDQ GPI +T ED   LL A++G D+ DSTS   
Sbjct: 179 SLCGVTGIKPTYGSVSRYGMIAFASSLDQGGPIAKTAEDCGLLLNAMTGFDERDSTSLQR 238

Query: 244 DVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSK 303
              DF  SL   ++GL+I VPKE+ G G+  +   +V AAL   E LGA   E+SLP ++
Sbjct: 239 PKEDFTRSLNDSLQGLRIGVPKEFFGAGLAADVEAAVRAALSEFEKLGAQLVEISLPKTE 298

Query: 304 YALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGT 363
            ++  YY+++ +EAS+NL+RFDG+RYG+R  +  NL D+Y+++RAEGFG EVKRRI++G+
Sbjct: 299 LSIPVYYVIAPAEASSNLSRFDGVRYGHRAADYGNLDDMYRKSRAEGFGEEVKRRILVGS 358

Query: 364 FALSSGYYDAYYKKAQKVRTLIKKDFEDVF----EKYDVIVGPTTPTPAFKIGENTKDPL 419
           + LS GYYDAYY +AQK+R LI +DF++       + DVI+GP +PT A+ +G+ T DP+
Sbjct: 359 YVLSHGYYDAYYLQAQKIRRLIAQDFQNALAGANRQCDVIMGPVSPTVAWDLGDKTNDPV 418

Query: 420 TMYANDILTIPVNLAGVPGISVPCGLADG-----LPLGLQIIGKHFDESTVYRVAHAFEQ 474
             Y  DI T+  +LAG+PG+S+PCG   G      P+GLQIIG +FDE+ +  VAH F+Q
Sbjct: 419 ANYLADIFTLSTSLAGLPGMSIPCGFGQGEKNGKRPVGLQIIGNYFDEARLLNVAHQFQQ 478

Query: 475 ATDHHKAKP 483
           ATD H  +P
Sbjct: 479 ATDWHLREP 487


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: 583
Number of extensions: 31
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: 485
Length of database: 488
Length adjustment: 34
Effective length of query: 451
Effective length of database: 454
Effective search space:   204754
Effective search space used:   204754
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 HSERO_RS23305 HSERO_RS23305 (glutamyl-tRNA amidotransferase subunit A)
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.25852.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   8.4e-180  584.4   0.0   9.7e-180  584.2   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS23305  HSERO_RS23305 glutamyl-tRNA amid


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS23305  HSERO_RS23305 glutamyl-tRNA amidotransferase subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  584.2   0.0  9.7e-180  9.7e-180       3     465 ..      11     481 ..       9     482 .. 0.97

  Alignments for each domain:
  == domain 1  score: 584.2 bits;  conditional E-value: 9.7e-180
                                  TIGR00132   3 ellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdn 68 
                                                ++l+++++s++e+++ +l+ri+a +  +nafl+v++e +l++ak  d++++ ++  +l+g+pia Kd 
  lcl|FitnessBrowser__HerbieS:HSERO_RS23305  11 AQLQARKISATELATLFLDRIDASD--LNAFLHVDRELTLAQAKVADSRLSdNNaGQLTGVPIAHKDI 76 
                                                678999***************9865..6*********************9954435************ PP

                                  TIGR00132  69 iavkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneer 136
                                                +++++++tt++S++L+nyvsp+datVve+ ++ag++++Gk N DEFamGs+ e+S+fg+t nP++++ 
  lcl|FitnessBrowser__HerbieS:HSERO_RS23305  77 FVTRGWRTTAGSRMLDNYVSPFDATVVEQFNAAGMVTLGKLNCDEFAMGSGNENSYFGPTLNPWDKRA 144
                                                ******************************************************************** PP

                                  TIGR00132 137 vpGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGila 204
                                                vpGGSsgGsaaavaa l+p a ++DTGgSiRqPAs+cgv G+KPtYG vSRyG++a+asSldq G++a
  lcl|FitnessBrowser__HerbieS:HSERO_RS23305 145 VPGGSSGGSAAAVAARLAPAATATDTGGSIRQPASLCGVTGIKPTYGSVSRYGMIAFASSLDQGGPIA 212
                                                ******************************************************************** PP

                                  TIGR00132 205 kkvedialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfeklle 272
                                                k+ ed  l+l++++g D++Dstsl+ ++e+++++l++ l+gl++gv ke+++ +l  +v+++++++l 
  lcl|FitnessBrowser__HerbieS:HSERO_RS23305 213 KTAEDCGLLLNAMTGFDERDSTSLQRPKEDFTRSLNDSLQGLRIGVPKEFFGAGLAADVEAAVRAALS 280
                                                ******************************************************************** PP

                                  TIGR00132 273 kleelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfge 340
                                                ++e+lga++ve+slp+ +l++++Yy+i+p+Eassnl+r+dg+ryG+r+ ++ +l+++y k+R+egfge
  lcl|FitnessBrowser__HerbieS:HSERO_RS23305 281 EFEKLGAQLVEISLPKTELSIPVYYVIAPAEASSNLSRFDGVRYGHRAADYGNLDDMYRKSRAEGFGE 348
                                                ******************************************************************** PP

                                  TIGR00132 341 evkrRimlGayalskeyydkyykkAqkvrtliidefeklf....eevDvivsptaptlafklgekaed 404
                                                evkrRi++G+y+ls++yyd+yy++Aqk+r+li+++f++++    +++Dvi++p++pt+a  lg+k++d
  lcl|FitnessBrowser__HerbieS:HSERO_RS23305 349 EVKRRILVGSYVLSHGYYDAYYLQAQKIRRLIAQDFQNALaganRQCDVIMGPVSPTVAWDLGDKTND 416
                                                ***************************************9999899********************** PP

                                  TIGR00132 405 plemylsDvltvpanlaGlpaisvPlgkke....kglpiGlqiigkafddkkllsvakaleqald 465
                                                p+++yl+D++t+  +laGlp++s+P+g  +       p+Glqiig++fd+ +ll+va++++qa+d
  lcl|FitnessBrowser__HerbieS:HSERO_RS23305 417 PVANYLADIFTLSTSLAGLPGMSIPCGFGQgeknGKRPVGLQIIGNYFDEARLLNVAHQFQQATD 481
                                                **************************86432221568************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (488 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 6.90
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Links

Downloads

Related tools

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