Alignments for a candidate for gatA in Haloechinothrix alba DSM 45207

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Haloechinothrix alba DSM 45207

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_089299957.1 CHB84_RS03180 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_900188115.1:WP_089299957.1
          Length = 500

 Score =  461 bits (1187), Expect = e-134
 Identities = 243/477 (50%), Positives = 323/477 (67%), Gaps = 9/477 (1%)

Query: 10  ELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELD-EAVDGRSEH 68
           EL   IH  E+   ++     +RI  VD ++ AFL ++ E A A A+++D +   GR   
Sbjct: 10  ELAAGIHSGELSSVEVTRSHLERIAKVDSEINAFLHVETEGALATAEKVDADIAAGRRPA 69

Query: 69  GLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEFA 128
             L G+P+G+KD + TKG+ TTC S+ LE + P YDATV ++L++A+ V +GK NMDEFA
Sbjct: 70  SPLAGVPLGLKDVLTTKGIPTTCGSRTLEGWIPPYDATVTRKLREADVVVLGKTNMDEFA 129

Query: 129 MGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCGV 188
           MGSSTENSAY  T+NPW+   VPGGSSGGSAAA+AA + P ++G+DTGGS+RQP +  G 
Sbjct: 130 MGSSTENSAYGPTRNPWDTTRVPGGSSGGSAAALAAFQAPVTVGTDTGGSVRQPGALTGT 189

Query: 189 VGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPDF 248
           VG+KPTYG VSRYGLVAF+SSLDQ GP  RTV D A L + I G D MDSTS N  VP  
Sbjct: 190 VGVKPTYGGVSRYGLVAFSSSLDQAGPCARTVLDAALLHEVIGGHDPMDSTSLNAPVPPV 249

Query: 249 LSS----LTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKY 304
           + +     +GD++GL++ V  E  GEG       S  AA+  L  LGA   EVS P+ +Y
Sbjct: 250 VEAARRGASGDLRGLRVGVVTELGGEGYQPGVLRSFAAAVDTLRELGAEVAEVSCPNFEY 309

Query: 305 ALATYYLLSSSEASANLARFDGIRYGYRT--DNADNLIDLYKQTRAEGFGNEVKRRIMLG 362
           AL+ YYL++ SE S+NLARFD +RYG R   D  +   D+   +R  GFG EVKRRI++G
Sbjct: 310 ALSAYYLIAPSECSSNLARFDAMRYGLRVADDGTNGADDVMSLSREAGFGAEVKRRIIIG 369

Query: 363 TFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMY 422
           T+ALS+GYYDAYY  AQKVR+L+ +DF+  +++ DV+V PT PT AF++GE   DP++MY
Sbjct: 370 TYALSAGYYDAYYGSAQKVRSLVTRDFDAAYDQVDVLVSPTAPTTAFRVGERVDDPMSMY 429

Query: 423 ANDILTIPVNLAGVPGISVPCGLA--DGLPLGLQIIGKHFDESTVYRVAHAFEQATD 477
             D+ TIP NLAG   +SVP GL+  DGLP+GLQI+     +  +Y V  A+E+A D
Sbjct: 430 RADLCTIPTNLAGTAAMSVPSGLSDEDGLPVGLQIMAPALADDRMYEVGAAYERARD 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: 627
Number of extensions: 26
Number of successful extensions: 5
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: 500
Length adjustment: 34
Effective length of query: 451
Effective length of database: 466
Effective search space:   210166
Effective search space used:   210166
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_089299957.1 CHB84_RS03180 (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.1018669.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     1e-188  613.8   0.0   1.2e-188  613.6   0.0    1.0  1  NCBI__GCF_900188115.1:WP_089299957.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900188115.1:WP_089299957.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  613.6   0.0  1.2e-188  1.2e-188       5     463 ..      15     484 ..      11     487 .. 0.97

  Alignments for each domain:
  == domain 1  score: 613.6 bits;  conditional E-value: 1.2e-188
                             TIGR00132   5 lkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva...ke.kklagipiavKdniavkd 73 
                                           +++ e+s++ev+++ leri +v+++inafl+v++e al++a+k+d+++a   +  ++lag+p+++Kd++++k+
  NCBI__GCF_900188115.1:WP_089299957.1  15 IHSGELSSVEVTRSHLERIAKVDSEINAFLHVETEGALATAEKVDADIAagrRPaSPLAGVPLGLKDVLTTKG 87 
                                           7788999*****************************************99854445***************** PP

                             TIGR00132  74 iettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGSsgGsa 146
                                           i+ttc+S++Le++++pydatV+++l+ea+++++GktN+DEFamGsste+Sa+g+t+nP++++rvpGGSsgGsa
  NCBI__GCF_900188115.1:WP_089299957.1  88 IPTTCGSRTLEGWIPPYDATVTRKLREADVVVLGKTNMDEFAMGSSTENSAYGPTRNPWDTTRVPGGSSGGSA 160
                                           ************************************************************************* PP

                             TIGR00132 147 aavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvisg 219
                                           aa+aa+++p+++g+DTGgS+RqP +++g+vG+KPtYG vSRyGlva++sSldq G++a++v d+al+++vi g
  NCBI__GCF_900188115.1:WP_089299957.1 161 AALAAFQAPVTVGTDTGGSVRQPGALTGTVGVKPTYGGVSRYGLVAFSSSLDQAGPCARTVLDAALLHEVIGG 233
                                           ************************************************************************* PP

                             TIGR00132 220 kDkkDstslevkveelleelkk....dlkglkvgvvkelseesldkevkekfekllekleelgaeivevslps 288
                                           +D +Dstsl+++v+ ++e++++    dl+gl+vgvv el +e+++ +v ++f++++++l+elgae+ evs+p+
  NCBI__GCF_900188115.1:WP_089299957.1 234 HDPMDSTSLNAPVPPVVEAARRgasgDLRGLRVGVVTELGGEGYQPGVLRSFAAAVDTLRELGAEVAEVSCPN 306
                                           **************9999998888889********************************************** PP

                             TIGR00132 289 vklalaiYyiispsEassnlarydgiryGkrveelks..lkelyaktRsegfgeevkrRimlGayalskeyyd 359
                                           +++al++Yy+i+psE ssnlar+d++ryG rv ++    ++++++ +R++gfg+evkrRi++G+yals++yyd
  NCBI__GCF_900188115.1:WP_089299957.1 307 FEYALSAYYLIAPSECSSNLARFDAMRYGLRVADDGTngADDVMSLSREAGFGAEVKRRIIIGTYALSAGYYD 379
                                           ********************************9987667999******************************* PP

                             TIGR00132 360 kyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvltvpanlaGlpaisvPlgk 432
                                           +yy  Aqkvr+l++++f+ ++++vDv+vsptapt+af++ge+ +dp++my +D++t+p nlaG+ a+svP g 
  NCBI__GCF_900188115.1:WP_089299957.1 380 AYYGSAQKVRSLVTRDFDAAYDQVDVLVSPTAPTTAFRVGERVDDPMSMYRADLCTIPTNLAGTAAMSVPSGL 452
                                           ***********************************************************************98 PP

                             TIGR00132 433 ke.kglpiGlqiigkafddkkllsvakaleqa 463
                                           ++ +glp+Glqi++ a++d+++++v++a+e+a
  NCBI__GCF_900188115.1:WP_089299957.1 453 SDeDGLPVGLQIMAPALADDRMYEVGAAYERA 484
                                           76599************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (500 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: 17.07
//
[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