Alignments for a candidate for gatA in Crocosphaera subtropica ATCC 51142

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Crocosphaera subtropica ATCC 51142

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_009545528.1 CCE_RS08085 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit A

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000017845.1:WP_009545528.1
          Length = 482

 Score =  552 bits (1423), Expect = e-162
 Identities = 283/479 (59%), Positives = 355/479 (74%), Gaps = 2/479 (0%)

Query: 8   ITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSE 67
           I EL Q +  KE    ++  E+ +RI AVD KV++FL +  + A   AK++DE +    E
Sbjct: 4   IRELHQQLVNKERSAVEITTEALERINAVDSKVKSFLQVTADHALETAKKVDEKIAKNEE 63

Query: 68  HGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEF 127
            GLL G+PIG+KDN+ T G++TTC SKIL NF P Y++TV Q+L+DA AV +GK N+DEF
Sbjct: 64  IGLLAGIPIGIKDNMCTTGIKTTCGSKILANFVPPYESTVTQKLKDAGAVMVGKTNLDEF 123

Query: 128 AMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCG 187
           AMGSSTENS Y++T NPW+L  VPGGSSGGSAAAVAA E   +LGSDTGGSIRQPAS CG
Sbjct: 124 AMGSSTENSGYQVTANPWDLSRVPGGSSGGSAAAVAASECVVALGSDTGGSIRQPASLCG 183

Query: 188 VVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPD 247
           VVGLKPTYG VSR+GLVA+ASSLDQIGP  R V+D A LL AI+G D  DSTS N  VPD
Sbjct: 184 VVGLKPTYGLVSRFGLVAYASSLDQIGPFARNVQDAAILLGAIAGYDPKDSTSINTPVPD 243

Query: 248 FLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKYALA 307
           +   L   ++GL I V +E  GEG+     ++V AA+  L+ LGA    VS P  +Y L 
Sbjct: 244 YTQFLKPSLEGLTIGVIEETFGEGLDPVVSKTVKAAIDHLKTLGAKVVNVSCPRFRYGLP 303

Query: 308 TYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFALS 367
            YY+++ SEAS+NLAR+D ++YG R D AD LID+Y +TRA GFGNEVKRRIM+GT+ LS
Sbjct: 304 AYYIIAPSEASSNLARYDAVKYGIRED-ADTLIDMYTKTRAVGFGNEVKRRIMIGTYTLS 362

Query: 368 SGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYANDIL 427
           +GYYDAYY KAQKVRTLIK+DF+  FEK DV+V PT+PT AFK GE T DPL+MY +D+ 
Sbjct: 363 AGYYDAYYLKAQKVRTLIKQDFDAGFEKVDVLVCPTSPTTAFKAGEKTSDPLSMYLSDLT 422

Query: 428 TIPVNLAGVPGISVPCGLAD-GLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKAKPEL 485
           TIPVNLAG+PG+S+PCG  D  LP+GLQ+IG   +E  +++VA+A+EQ+TD H   P L
Sbjct: 423 TIPVNLAGLPGMSIPCGFDDNNLPVGLQLIGNVLEEGKLFQVAYAYEQSTDWHNQVPPL 481


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: 622
Number of extensions: 23
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: 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_009545528.1 CCE_RS08085 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB 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.24493.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     6e-207  673.9   0.1   6.8e-207  673.7   0.1    1.0  1  lcl|NCBI__GCF_000017845.1:WP_009545528.1  CCE_RS08085 Asp-tRNA(Asn)/Glu-tR


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000017845.1:WP_009545528.1  CCE_RS08085 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  673.7   0.1  6.8e-207  6.8e-207       2     465 ..       8     473 ..       7     474 .. 0.98

  Alignments for each domain:
  == domain 1  score: 673.7 bits;  conditional E-value: 6.8e-207
                                 TIGR00132   2 kellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva..ke.kklagipiavKd 67 
                                               +++l++ke s++e+++e leri+av++k+++fl+vt+++al++akk+d+k+a  +e  +lagipi++Kd
  lcl|NCBI__GCF_000017845.1:WP_009545528.1   8 HQQLVNKERSAVEITTEALERINAVDSKVKSFLQVTADHALETAKKVDEKIAknEEiGLLAGIPIGIKD 76 
                                               78999**********************************************9754445*********** PP

                                 TIGR00132  68 niavkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneer 136
                                               n+++ +i+ttc+SkiL n+v+py++tV+++lk+aga+++GktNlDEFamGsste+S ++vt+nP++ +r
  lcl|NCBI__GCF_000017845.1:WP_009545528.1  77 NMCTTGIKTTCGSKILANFVPPYESTVTQKLKDAGAVMVGKTNLDEFAMGSSTENSGYQVTANPWDLSR 145
                                               ********************************************************************* PP

                                 TIGR00132 137 vpGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilak 205
                                               vpGGSsgGsaaavaa ++++algsDTGgSiRqPAs+cgvvGlKPtYGlvSR+GlvayasSldqiG++a+
  lcl|NCBI__GCF_000017845.1:WP_009545528.1 146 VPGGSSGGSAAAVAASECVVALGSDTGGSIRQPASLCGVVGLKPTYGLVSRFGLVAYASSLDQIGPFAR 214
                                               ********************************************************************* PP

                                 TIGR00132 206 kvedialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekl 274
                                               +v+d+a++l +i+g+D kDsts++++v+++++ lk  l gl +gv++e ++e+ld  v++++++++++l
  lcl|NCBI__GCF_000017845.1:WP_009545528.1 215 NVQDAAILLGAIAGYDPKDSTSINTPVPDYTQFLKPSLEGLTIGVIEETFGEGLDPVVSKTVKAAIDHL 283
                                               ********************************************************************* PP

                                 TIGR00132 275 eelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevk 343
                                               ++lga++v+vs+p++++ l++Yyii+psEassnlaryd+++yG r + ++ l ++y+ktR+ gfg+evk
  lcl|NCBI__GCF_000017845.1:WP_009545528.1 284 KTLGAKVVNVSCPRFRYGLPAYYIIAPSEASSNLARYDAVKYGIREDADT-LIDMYTKTRAVGFGNEVK 351
                                               *********************************************88877.****************** PP

                                 TIGR00132 344 rRimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsD 412
                                               rRim+G+y+ls++yyd+yy+kAqkvrtli+++f+  fe+vDv+v+pt+pt+afk gek++dpl+mylsD
  lcl|NCBI__GCF_000017845.1:WP_009545528.1 352 RRIMIGTYTLSAGYYDAYYLKAQKVRTLIKQDFDAGFEKVDVLVCPTSPTTAFKAGEKTSDPLSMYLSD 420
                                               ********************************************************************* PP

                                 TIGR00132 413 vltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqald 465
                                               ++t+p+nlaGlp++s+P+g ++++lp+Glq+ig+++++ kl++va+a+eq +d
  lcl|NCBI__GCF_000017845.1:WP_009545528.1 421 LTTIPVNLAGLPGMSIPCGFDDNNLPVGLQLIGNVLEEGKLFQVAYAYEQSTD 473
                                               *************************************************9987 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 12.49
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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