Alignments for a candidate for gatA in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Herbaspirillum seropedicae SmR1

Align glutamyl-tRNA^Gln amidotransferase subunit A (EC 6.3.5.7) (characterized)
to candidate HSERO_RS23305 HSERO_RS23305 glutamyl-tRNA amidotransferase subunit A

Query= metacyc::MONOMER-13955
         (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.19895.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.92
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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