GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Phyllobacterium endophyticum PEPV15

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_106716872.1 CU100_RS12530 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_003010935.1:WP_106716872.1
          Length = 493

 Score =  459 bits (1180), Expect = e-133
 Identities = 245/483 (50%), Positives = 327/483 (67%), Gaps = 11/483 (2%)

Query: 8   ITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSE 67
           I E +  +  K I  ++L     + I+  ++ + A++    E+A A AK  D  +     
Sbjct: 9   IAEARDQLKAKTISAAELTGAYIEAIENANEALNAYIVTTPEKALAMAKASDARL-ASGN 67

Query: 68  HGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEF 127
            G L G+P+G+KD   T+G+ T  +S IL+ F P Y++TV   L    AV +GKLNMDEF
Sbjct: 68  AGALEGIPLGIKDLFGTEGIHTQAASHILDGFKPNYESTVTANLWADGAVMLGKLNMDEF 127

Query: 128 AMGSSTENSAYKLTKNPW-----NLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQP 182
           AMGSS E S Y   KNPW     N D VPGGSSGGSAAAVAA     +  +DTGGSIRQP
Sbjct: 128 AMGSSNETSYYGAVKNPWRARGSNADLVPGGSSGGSAAAVAARLCAGATATDTGGSIRQP 187

Query: 183 ASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSAN 242
           A+F G VG+KPTYGR SR+G+VAFASSLDQ GPI R V D A LL++++ VD  D+TS +
Sbjct: 188 AAFTGTVGIKPTYGRCSRWGIVAFASSLDQAGPIARDVRDAAILLKSMASVDVKDTTSVD 247

Query: 243 VDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHS 302
           V VPD+ +++   + GLKI +PKEY  +G+ +E        ++ L+  GA+  ++SLPH+
Sbjct: 248 VAVPDYEAAIGKPLAGLKIGIPKEYRVDGMPEEIERLWQQGIEWLKDAGASIVDISLPHT 307

Query: 303 KYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLG 362
           KYAL  YY+++ +EAS+NLAR+DG+RYG R    D ++++Y++TRA GFG EVKRRIM+G
Sbjct: 308 KYALPAYYIVAPAEASSNLARYDGVRYGLRVPGKD-IVEMYEKTRATGFGEEVKRRIMIG 366

Query: 363 TFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEK-YDVIVGPTTPTPAFKIGEN--TKDPL 419
           T+ LS+GYYDAYY +AQKVRTLIKKDFEDVF    D I+ P TP+ AF I +     DP+
Sbjct: 367 TYVLSAGYYDAYYLQAQKVRTLIKKDFEDVFHAGVDAILTPATPSAAFGIADQDMAADPV 426

Query: 420 TMYANDILTIPVNLAGVPGISVPCGL-ADGLPLGLQIIGKHFDESTVYRVAHAFEQATDH 478
            MY NDI T+ VN+AG+PGI+VP GL A GLPLGLQ+IG+ FDE T+++ A+  EQA   
Sbjct: 427 KMYLNDIFTVTVNMAGLPGIAVPAGLDARGLPLGLQLIGRPFDEETLFQTAYVIEQAAGK 486

Query: 479 HKA 481
             A
Sbjct: 487 FNA 489


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: 617
Number of extensions: 30
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: 493
Length adjustment: 34
Effective length of query: 451
Effective length of database: 459
Effective search space:   207009
Effective search space used:   207009
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_106716872.1 CU100_RS12530 (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.3324385.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.7e-174  566.9   0.0     2e-174  566.6   0.0    1.0  1  NCBI__GCF_003010935.1:WP_106716872.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010935.1:WP_106716872.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  566.6   0.0    2e-174    2e-174       2     463 ..      13     483 ..      12     486 .. 0.97

  Alignments for each domain:
  == domain 1  score: 566.6 bits;  conditional E-value: 2e-174
                             TIGR00132   2 kellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdniavk 72 
                                           +++lk+k++s+ e++ +++e+ie+ ++ +na++ +t+ekal++ak++d+++a  +   l gip+++Kd + ++
  NCBI__GCF_003010935.1:WP_106716872.1  13 RDQLKAKTISAAELTGAYIEAIENANEALNAYIVTTPEKALAMAKASDARLAsGNaGALEGIPLGIKDLFGTE 85 
                                           578999*********************************************975536**************** PP

                             TIGR00132  73 diettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknP.....eneervpGG 140
                                           +i+t +aS+iL+++++ y++tV+ +l ++ga+++Gk N+DEFamGss etS++g++knP      n + vpGG
  NCBI__GCF_003010935.1:WP_106716872.1  86 GIHTQAASHILDGFKPNYESTVTANLWADGAVMLGKLNMDEFAMGSSNETSYYGAVKNPwrargSNADLVPGG 158
                                           ***********************************************************666665899***** PP

                             TIGR00132 141 SsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialv 213
                                           SsgGsaaavaa l+  a ++DTGgSiRqPA+f+g+vG+KPtYG+ SR+G+va+asSldq G++a++v d+a++
  NCBI__GCF_003010935.1:WP_106716872.1 159 SSGGSAAAVAARLCAGATATDTGGSIRQPAAFTGTVGIKPTYGRCSRWGIVAFASSLDQAGPIARDVRDAAIL 231
                                           ************************************************************************* PP

                             TIGR00132 214 ldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelgaeivevsl 286
                                           l+ ++ +D kD+ts++v+v+++  ++ k l glk+g+ ke++ +++++e+++ +++ +e l++ ga iv++sl
  NCBI__GCF_003010935.1:WP_106716872.1 232 LKSMASVDVKDTTSVDVAVPDYEAAIGKPLAGLKIGIPKEYRVDGMPEEIERLWQQGIEWLKDAGASIVDISL 304
                                           ************************************************************************* PP

                             TIGR00132 287 psvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGayalskeyyd 359
                                           p+ k+al++Yyi++p+Eassnlarydg+ryG rv  ++ + e+y ktR+ gfgeevkrRim+G+y+ls++yyd
  NCBI__GCF_003010935.1:WP_106716872.1 305 PHTKYALPAYYIVAPAEASSNLARYDGVRYGLRVPGKD-IVEMYEKTRATGFGEEVKRRIMIGTYVLSAGYYD 376
                                           **********************************9998.********************************** PP

                             TIGR00132 360 kyykkAqkvrtliidefeklfe.evDvivsptaptlafklgek..aedplemylsDvltvpanlaGlpaisvP 429
                                           +yy++Aqkvrtli+++fe++f+  vD i++p++p  af ++++  a+dp++myl+D++tv++n+aGlp+i+vP
  NCBI__GCF_003010935.1:WP_106716872.1 377 AYYLQAQKVRTLIKKDFEDVFHaGVDAILTPATPSAAFGIADQdmAADPVKMYLNDIFTVTVNMAGLPGIAVP 449
                                           *********************637****************87622567************************* PP

                             TIGR00132 430 lgkkekglpiGlqiigkafddkkllsvakaleqa 463
                                           +g + +glp+Glq+ig+ fd+++l++ a+ +eqa
  NCBI__GCF_003010935.1:WP_106716872.1 450 AGLDARGLPLGLQLIGRPFDEETLFQTAYVIEQA 483
                                           ********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (493 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 28.12
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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