Alignments for a candidate for gatA in Thermomonospora curvata DSM 43183

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Thermomonospora curvata DSM 43183

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_052305694.1 TCUR_RS17540 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000024385.1:WP_052305694.1
          Length = 482

 Score =  455 bits (1171), Expect = e-132
 Identities = 251/462 (54%), Positives = 309/462 (66%), Gaps = 5/462 (1%)

Query: 19  EIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSEHGLLFGMPIGV 78
           ++   ++      RI  VD ++ AFL +D E A A A+ +D       E G L G+PI  
Sbjct: 5   QVSAVEVTQAHLDRIAEVDGRIGAFLHVDAEVALAQARAVDSRRAAGEELGPLAGVPIAH 64

Query: 79  KDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEFAMGSSTENSAY 138
           KD   T  + TT  SKILE + P YDATV  RL+ A  V +GK N+DEFAMGSSTENSAY
Sbjct: 65  KDVFTTVDMPTTAGSKILEGWRPPYDATVTARLRAAGLVILGKTNLDEFAMGSSTENSAY 124

Query: 139 KLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCGVVGLKPTYGRV 198
             T+NPW+L+ VPGGSSGGS+AAVA+ + P + G+DTGGSIRQPA+  G+VG KPTYG  
Sbjct: 125 GPTRNPWDLERVPGGSSGGSSAAVASYQAPLATGTDTGGSIRQPAAVTGIVGTKPTYGGS 184

Query: 199 SRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPDFL-SSLTGDIK 257
           SRYGL+AFASSLD  GP  RTV D A L +A SG D MDSTS +  VP  + ++   D+ 
Sbjct: 185 SRYGLIAFASSLDTPGPFGRTVLDAALLHEAFSGHDPMDSTSIDRPVPPVVEAARRADVA 244

Query: 258 GLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKYALATYYLLSSSEA 317
           GL+I V KE  GEG           A+++LE LGA   EVS PH  YAL  YYL++ SE 
Sbjct: 245 GLRIGVVKELGGEGYQPGVLARFNEAVELLESLGAKVAEVSCPHFAYALPAYYLIAPSEC 304

Query: 318 SANLARFDGIRYGYRT--DNADNLIDLYKQTRAEGFGNEVKRRIMLGTFALSSGYYDAYY 375
           S+NLARFD +RYG R   D   +  ++   TRA+GFG EVKRRIMLGT+ALSSGYYDAYY
Sbjct: 305 SSNLARFDAMRYGLRVGDDGTRSAEEVMALTRAQGFGPEVKRRIMLGTYALSSGYYDAYY 364

Query: 376 KKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYANDILTIPVNLAG 435
            KAQ+VRTLI +DFE  FE+ DV+V PTTPT AF +G+   DP+ MY  D+ TIP NLAG
Sbjct: 365 GKAQQVRTLIIRDFEAAFEQVDVLVSPTTPTTAFPLGDRVDDPMAMYLADLATIPSNLAG 424

Query: 436 VPGISVPCGLA--DGLPLGLQIIGKHFDESTVYRVAHAFEQA 475
            P ISVPCGLA  D LP+GLQ++     +  VYRV  A E+A
Sbjct: 425 TPAISVPCGLADEDDLPVGLQVMAPVLADDRVYRVGAAVERA 466


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: 597
Number of extensions: 25
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: 482
Length adjustment: 34
Effective length of query: 451
Effective length of database: 448
Effective search space:   202048
Effective search space used:   202048
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_052305694.1 TCUR_RS17540 (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.240434.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.5e-187  607.8   0.0   7.3e-187  607.7   0.0    1.0  1  NCBI__GCF_000024385.1:WP_052305694.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000024385.1:WP_052305694.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  607.7   0.0  7.3e-187  7.3e-187       8     464 ..       4     467 ..       1     469 [. 0.97

  Alignments for each domain:
  == domain 1  score: 607.7 bits;  conditional E-value: 7.3e-187
                             TIGR00132   8 kevsikevleeilerieavkdkinaflevtkekalkkakkldkkva..ke.kklagipiavKdniavkdiett 77 
                                            +vs++ev+++ l+ri +v+ +i afl+v++e al++a+++d++ a  +e  +lag+pia Kd++++ d++tt
  NCBI__GCF_000024385.1:WP_052305694.1   4 GQVSAVEVTQAHLDRIAEVDGRIGAFLHVDAEVALAQARAVDSRRAagEElGPLAGVPIAHKDVFTTVDMPTT 76 
                                           578999************************************9988876657********************* PP

                             TIGR00132  78 caSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGSsgGsaaava 150
                                           ++SkiLe++++pydatV+ rl++ag +i+GktNlDEFamGsste+Sa+g+t+nP++ ervpGGSsgGs+aava
  NCBI__GCF_000024385.1:WP_052305694.1  77 AGSKILEGWRPPYDATVTARLRAAGLVILGKTNLDEFAMGSSTENSAYGPTRNPWDLERVPGGSSGGSSAAVA 149
                                           ************************************************************************* PP

                             TIGR00132 151 adlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvisgkDkk 223
                                             ++pla g+DTGgSiRqPA+++g+vG KPtYG  SRyGl+a+asSld+ G++ ++v d+al++++ sg+D +
  NCBI__GCF_000024385.1:WP_052305694.1 150 SYQAPLATGTDTGGSIRQPAAVTGIVGTKPTYGGSSRYGLIAFASSLDTPGPFGRTVLDAALLHEAFSGHDPM 222
                                           ************************************************************************* PP

                             TIGR00132 224 Dstslevkveelleelkk.dlkglkvgvvkelseesldkevkekfekllekleelgaeivevslpsvklalai 295
                                           Dsts++ +v+ ++e++++ d+ gl++gvvkel +e+++ +v ++f++++e le+lga++ evs+p++ +al++
  NCBI__GCF_000024385.1:WP_052305694.1 223 DSTSIDRPVPPVVEAARRaDVAGLRIGVVKELGGEGYQPGVLARFNEAVELLESLGAKVAEVSCPHFAYALPA 295
                                           **********9999988879***************************************************** PP

                             TIGR00132 296 YyiispsEassnlarydgiryGkrveelks..lkelyaktRsegfgeevkrRimlGayalskeyydkyykkAq 366
                                           Yy+i+psE ssnlar+d++ryG rv ++    ++e++a tR++gfg evkrRimlG+yals++yyd+yy kAq
  NCBI__GCF_000024385.1:WP_052305694.1 296 YYLIAPSECSSNLARFDAMRYGLRVGDDGTrsAEEVMALTRAQGFGPEVKRRIMLGTYALSSGYYDAYYGKAQ 368
                                           *************************9987655999************************************** PP

                             TIGR00132 367 kvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvltvpanlaGlpaisvPlgkke.kglp 438
                                           +vrtlii++fe +fe+vDv+vspt+pt+af lg++ +dp++myl+D+ t+p nlaG+paisvP+g ++ ++lp
  NCBI__GCF_000024385.1:WP_052305694.1 369 QVRTLIIRDFEAAFEQVDVLVSPTTPTTAFPLGDRVDDPMAMYLADLATIPSNLAGTPAISVPCGLADeDDLP 441
                                           ****************************************************************9876599** PP

                             TIGR00132 439 iGlqiigkafddkkllsvakaleqal 464
                                           +Glq+++ +++d+++++v++a+e+al
  NCBI__GCF_000024385.1:WP_052305694.1 442 VGLQVMAPVLADDRVYRVGAAVERAL 467
                                           ***********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (482 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: 26.73
//
[ok]

This GapMind analysis is from Jul 25 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:

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