Alignments for a candidate for gatA in Methanococcus aeolicus Nankai-3

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Methanococcus aeolicus Nankai-3

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_011973717.1 MAEO_RS05075 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit A

Query= curated2:Q6LX43
         (431 letters)



>NCBI__GCF_000017185.1:WP_011973717.1
          Length = 434

 Score =  704 bits (1817), Expect = 0.0
 Identities = 343/432 (79%), Positives = 385/432 (89%), Gaps = 2/432 (0%)

Query: 2   ITDRVSDYLEKIEKSDVNAFIDVNGEKVLKEAEELEKNDTLKNKPLYGKIVAVKSNINVK 61
           I D+   Y+EKIEKSD+NA I ++ EKVL EA+ELE N+ LKNKPLYGKI+A+KSNINVK
Sbjct: 3   IIDKALKYIEKIEKSDINAIIQLDKEKVLNEAKELENNEKLKNKPLYGKIIAIKSNINVK 62

Query: 62  GYKISCASKTLEKYVGTYDATVVKKLRSQGALIVGMTNMDEFAGGSSGETSCYGPTKNPA 121
           GY ISCASKTLE Y+  YDATVVKK++SQG LI+GMTNMDEFA GSSGETS YG TKNP 
Sbjct: 63  GYNISCASKTLENYISAYDATVVKKIKSQGGLIIGMTNMDEFASGSSGETSYYGATKNPN 122

Query: 122 AMDRIPGGSSSGSAAAVAADLCDMAIGSDTGGSIRNPASHCGIVGFKPSYGVVSRQGLCD 181
           A  +IPGGSSSGSA+AVA DLCDMA+GSDTGGSIRNPASHCG+VGFKPSYGVVSRQGLCD
Sbjct: 123 AEGKIPGGSSSGSASAVAGDLCDMALGSDTGGSIRNPASHCGVVGFKPSYGVVSRQGLCD 182

Query: 182 LAMSFDQIGPLTKNAEDALVLTNAIKGIDRSDSTSLETPKFEK--KDISNYKIGVVKEFM 239
           LAMSFDQIGPLTK+AEDAL+LTN IKG D SDST++ETPKFEK  K +  YK+G+VKEFM
Sbjct: 183 LAMSFDQIGPLTKSAEDALLLTNIIKGKDLSDSTTVETPKFEKNEKQVKKYKVGIVKEFM 242

Query: 240 DVTDEKIRNEIEKGIEVFKDMGCKIVDLSYKYIDLALPTYYLINYVEFFSATRKYDGRRY 299
           +V+DEKIRN+IE+GIEVFKDMGCKIV+L+YKY DLALPTYYLINYVEFFSATRKYDGRRY
Sbjct: 243 EVSDEKIRNKIEEGIEVFKDMGCKIVELNYKYTDLALPTYYLINYVEFFSATRKYDGRRY 302

Query: 300 GEFIEEACGEEVLRRILIGKHISEQEFSGKYYKKALQARKSMKKEMLGLFNSADLIVGPT 359
           G  IEE CGEEVLRRILIGKHISEQEFSGKYYKKAL  RK MK EML LFN  D+IV PT
Sbjct: 303 GYPIEEVCGEEVLRRILIGKHISEQEFSGKYYKKALYTRKLMKNEMLKLFNDVDIIVSPT 362

Query: 360 VPKLPHKLGEDVSPMEMYAYDVLTVPTNICGICSGVVRCGNISGVPVGLQIQGAPLEDEK 419
           VPKLPH +G++++PMEMY+YDVLTVPTNICGIC+GVV+CGNI+G PVGLQIQG P +DEK
Sbjct: 363 VPKLPHNIGKELTPMEMYSYDVLTVPTNICGICAGVVKCGNIAGNPVGLQIQGKPFDDEK 422

Query: 420 VLSAMIEFEKNY 431
           VL+AMIEFEK Y
Sbjct: 423 VLNAMIEFEKQY 434


Lambda     K      H
   0.315    0.135    0.383 

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: 734
Number of extensions: 31
Number of successful extensions: 2
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: 431
Length of database: 434
Length adjustment: 32
Effective length of query: 399
Effective length of database: 402
Effective search space:   160398
Effective search space used:   160398
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: 42 (22.0 bits)
S2: 51 (24.3 bits)

Align candidate WP_011973717.1 MAEO_RS05075 (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.2406.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.6e-172  559.2   4.7   4.1e-172  559.0   4.7    1.0  1  lcl|NCBI__GCF_000017185.1:WP_011973717.1  MAEO_RS05075 Asp-tRNA(Asn)/Glu-t


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000017185.1:WP_011973717.1  MAEO_RS05075 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 !  559.0   4.7  4.1e-172  4.1e-172      16     463 ..       4     433 ..       1     434 [] 0.97

  Alignments for each domain:
  == domain 1  score: 559.0 bits;  conditional E-value: 4.1e-172
                                 TIGR00132  16 leeilerieavkd.kinaflevtkekalkkakkldkkva.kekklagipiavKdniavkdiettcaSki 82 
                                               +++ l+ ie++++ +ina+++++kek+l++ak+l+++ + k+k+l+g +ia+K+ni+vk+++++caSk+
  lcl|NCBI__GCF_000017185.1:WP_011973717.1   4 IDKALKYIEKIEKsDINAIIQLDKEKVLNEAKELENNEKlKNKPLYGKIIAIKSNINVKGYNISCASKT 72 
                                               5666677777765489********************9997779************************** PP

                                 TIGR00132  83 LenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGSsgGsaaavaa 151
                                               Leny+s ydatVv+++k++g liiG+tN+DEFa Gss+etS++g+tknP++e ++pGGSs+Gsa ava 
  lcl|NCBI__GCF_000017185.1:WP_011973717.1  73 LENYISAYDATVVKKIKSQGGLIIGMTNMDEFASGSSGETSYYGATKNPNAEGKIPGGSSSGSASAVAG 141
                                               ********************************************************************* PP

                                 TIGR00132 152 dlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvisgk 220
                                               dl+++algsDTGgSiR+PAs+cgvvG+KP+YG+vSR+Gl+++a+S+dqiG+l+k+ ed+ l++++i+gk
  lcl|NCBI__GCF_000017185.1:WP_011973717.1 142 DLCDMALGSDTGGSIRNPASHCGVVGFKPSYGVVSRQGLCDLAMSFDQIGPLTKSAEDALLLTNIIKGK 210
                                               ********************************************************************* PP

                                 TIGR00132 221 DkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelgaeivevslpsv 289
                                               D  Dst++e+++  + e+++k++k+ kvg+vke++e+  d+++++k+e+ +e+++++g++ive+++++ 
  lcl|NCBI__GCF_000017185.1:WP_011973717.1 211 DLSDSTTVETPK--F-EKNEKQVKKYKVGIVKEFMEV-SDEKIRNKIEEGIEVFKDMGCKIVELNYKYT 275
                                               ********9965..5.555555***************.9****************************** PP

                                 TIGR00132 290 klalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGayalskeyy 358
                                               +lal++Yy+i+++E++s++++ydg+ryG+ +ee++              geev rRi++G++++++e +
  lcl|NCBI__GCF_000017185.1:WP_011973717.1 276 DLALPTYYLINYVEFFSATRKYDGRRYGYPIEEVC--------------GEEVLRRILIGKHISEQEFS 330
                                               ***********************************..............******************** PP

                                 TIGR00132 359 dkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvltvpanlaGlpais 427
                                               +kyykkA   r+l+++e+ klf++vD+ivspt+p+l++++g++ + p+emy +Dvltvp n++G++a +
  lcl|NCBI__GCF_000017185.1:WP_011973717.1 331 GKYYKKALYTRKLMKNEMLKLFNDVDIIVSPTVPKLPHNIGKELT-PMEMYSYDVLTVPTNICGICAGV 398
                                               *********************************************.*********************** PP

                                 TIGR00132 428 vPlgkkekglpiGlqiigkafddkkllsvakaleqa 463
                                               v +g+   g p+Glqi+gk fdd+k+l+++ ++e++
  lcl|NCBI__GCF_000017185.1:WP_011973717.1 399 VKCGNI-AGNPVGLQIQGKPFDDEKVLNAMIEFEKQ 433
                                               ******.7***********************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (434 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: 00:00:00.02
# Mc/sec: 9.95
//
[ok]

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