Alignments for a candidate for gatE in Methanosarcina acetivorans C2A

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatE in Methanosarcina acetivorans C2A

Align glutamyl-tRNA(Gln) amidotransferase subunit E (EC 6.3.5.7) (characterized)
to candidate WP_011022814.1 MA_RS15025 Glu-tRNA(Gln) amidotransferase subunit GatE

Query= metacyc::MONOMER-14999
         (619 letters)



>NCBI__GCF_000007345.1:WP_011022814.1
          Length = 633

 Score =  561 bits (1446), Expect = e-164
 Identities = 301/625 (48%), Positives = 427/625 (68%), Gaps = 14/625 (2%)

Query: 2   DWEKVGLKMGLEIHQQLDTESKLFCPCRTELTD-SEPDHDIVRNLRPTQSELGKFDRAAF 60
           D+ ++GLK GLEIHQQLD++ KLFC C T + D  + D +  R LR T+SE+G+ DRAA 
Sbjct: 5   DYSELGLKAGLEIHQQLDSKEKLFCRCPTLIRDIGDSDFEFFRYLRATESEMGEKDRAAV 64

Query: 61  EEAMRKLHFHYENYHEETCLVEADEEPPHPLNPEALEIAVTIALLLNMRVVDEFHTMRKQ 120
           E+   +  + Y+ Y + TCL+E DEEPP  LN EAL+I++ ++ L NM+ VD+ H MRK 
Sbjct: 65  EQTKIRRKYIYKAY-DTTCLIENDEEPPRELNKEALDISLGVSKLFNMKPVDQMHVMRKI 123

Query: 121 VIDGSNTGGFQRTGLVATDGHLETPQGTVKIENLCLEEDAARRIRETGDGVVFRLDRLGI 180
           V+DGSNT GFQRT  +A+DG++ET +G   I++LC+EE+AA++I E GD +V+ LDRLGI
Sbjct: 124 VVDGSNTSGFQRTAFLASDGYIETSEGRCGIDSLCVEEEAAQKIEEKGDSIVYSLDRLGI 183

Query: 181 PLVEITTDPSMSDPQQLREVAYQIGQILRST-RVKRGLGTIRQDLNISIRDGARVEVKGV 239
           PLVEI T P +  P+  REVA  IG +LRST +VKRGLGTIRQD+NISI  G RVE+KGV
Sbjct: 184 PLVEIATAPDIRSPRHAREVAEYIGMVLRSTGKVKRGLGTIRQDVNISIARGERVEIKGV 243

Query: 240 QDLDLIPEIVEREVKRQLSLVEIRDTLQERGAVVEDKIFDVSEVFADTESRIISSAE--- 296
           Q LDLI +IV REV+RQL+L+ IR  L ER A V ++I+DV+ +F DT+S+++       
Sbjct: 244 QALDLIEDIVRREVERQLNLLFIRQELLERKAFVCEEIYDVTGLFMDTKSKVLQKGVKKG 303

Query: 297 SVLAVKLRGFDGLIGVEIQPGRRLGTEMADYAKKRGVSGIFHTDELPAYGITEEEVRGLR 356
           S+LA  L+ F+ L+G E+QPGRRLGTE +D AK  GV G+FHTDELP YGITE+EV+ ++
Sbjct: 304 SILAALLKKFNRLVGKEVQPGRRLGTEFSDRAKTAGVGGLFHTDELPNYGITEKEVQAVK 363

Query: 357 DAVGASQGDAVVMVAHERVTAENALREVIRRAEMAIQGVPEETRKALPDGNTQYLRPLPT 416
           DA+GA   DA VMVA E   A  A+  VI RA+ AI+G+PEETRKALPDGNT Y+RPLP 
Sbjct: 364 DAIGAGPEDAFVMVADEPEKARLAIEAVINRAKEAIEGIPEETRKALPDGNTAYMRPLPG 423

Query: 417 SSRMYLETDIPLFRIEDDLLEGIRRNLPELPSEKKERIMRDYGLSEDLASQLVKRNLVDE 476
           ++RMY ETD+P   I  +  + I+   PEL +++ +R   + GL+++LA ++     +  
Sbjct: 424 AARMYPETDVPQIEISQEYFDSIKP--PELLTKRAKRFASESGLNKELAEKVAYSRYLPL 481

Query: 477 FEALTE-----FRVDTTVIASLLAYTLRELRREGHDVDGLGLDELRDAIKLLEVGKISKD 531
           FE L E       V++T+IA  L   + E+RR G + D L  +  +     +   +I+K+
Sbjct: 482 FEILLETYTKDANVNSTLIARTLVGIVPEIRRNGVETDNLTDEHFKGLFAAISNQEIAKE 541

Query: 532 ALRDIVACMADE-GLAAEDAARKLNLLLLAEDEIESIIQEIVEGNLDMISERGMGAMGPL 590
           A++D++  +A E  L  ++A  KL L     +E+E+ I+++V    D I ++G  A+GPL
Sbjct: 542 AIQDLLTALAKEPELTVQEAISKLGLSAFDPEEVENFIKQMVMEKGDFIKDKGPSALGPL 601

Query: 591 MGQAMGRLRGRADGKVVNRILREKI 615
           MG  M   RG  DGK+++ +L+++I
Sbjct: 602 MGIVMKEYRGTVDGKILSHMLKKEI 626


Lambda     K      H
   0.318    0.137    0.380 

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: 995
Number of extensions: 54
Number of successful extensions: 8
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: 619
Length of database: 633
Length adjustment: 38
Effective length of query: 581
Effective length of database: 595
Effective search space:   345695
Effective search space used:   345695
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 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate WP_011022814.1 MA_RS15025 (Glu-tRNA(Gln) amidotransferase subunit GatE)
to HMM TIGR00134 (gatE: glutamyl-tRNA(Gln) amidotransferase, subunit E (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/TIGR00134.hmm
# target sequence database:        /tmp/gapView.3700375.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00134  [M=622]
Accession:   TIGR00134
Description: gatE_arch: glutamyl-tRNA(Gln) amidotransferase, subunit E
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-262  858.8   8.1   1.1e-262  858.6   8.1    1.0  1  NCBI__GCF_000007345.1:WP_011022814.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000007345.1:WP_011022814.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  858.6   8.1  1.1e-262  1.1e-262       3     620 ..       5     628 ..       3     630 .. 0.97

  Alignments for each domain:
  == domain 1  score: 858.6 bits;  conditional E-value: 1.1e-262
                             TIGR00134   3 dyekvGlkvGleihqqldtkrklfclcptllrdsee.dfeivrvlrpkrselGevdraaleeaerkkkfiyky 74 
                                           dy  +Glk Gleihqqld+k+klfc+cptl+rd  + dfe++r+lr ++se+Ge draa+e+++ ++k+iyk 
  NCBI__GCF_000007345.1:WP_011022814.1   5 DYSELGLKAGLEIHQQLDSKEKLFCRCPTLIRDIGDsDFEFFRYLRATESEMGEKDRAAVEQTKIRRKYIYKA 77 
                                           9********************************9877************************************ PP

                             TIGR00134  75 yndttclveadeepprelneealeiavevalllnmevvdevhtmrkividGsntsGfqrtalvatdGyletde 147
                                           y dttcl+e deeppreln+eal i++ v++l+nm+ vd++h+mrkiv+dGsntsGfqrta++a dGy+et+e
  NCBI__GCF_000007345.1:WP_011022814.1  78 Y-DTTCLIENDEEPPRELNKEALDISLGVSKLFNMKPVDQMHVMRKIVVDGSNTSGFQRTAFLASDGYIETSE 149
                                           *.*********************************************************************** PP

                             TIGR00134 148 gkvgieslcleedaarkiedrgdavvysldrlGiplveistepdikspkmakevaariGeilrstgkvkrGlG 220
                                           g+ gi+slc+ee+aa+kie++gd++vysldrlGiplvei+t+pdi sp+ a+eva+ iG++lrstgkvkrGlG
  NCBI__GCF_000007345.1:WP_011022814.1 150 GRCGIDSLCVEEEAAQKIEEKGDSIVYSLDRLGIPLVEIATAPDIRSPRHAREVAEYIGMVLRSTGKVKRGLG 222
                                           ************************************************************************* PP

                             TIGR00134 221 tirqdvnisirdGarvevkGvqdldliekiverevlrqlnllkirdelkergaeveekifdvtevfkdtkski 293
                                           tirqdvnisi  G rve+kGvq ldlie+iv rev rqlnll ir+el er a v e i+dvt +f dtksk+
  NCBI__GCF_000007345.1:WP_011022814.1 223 TIRQDVNISIARGERVEIKGVQALDLIEDIVRREVERQLNLLFIRQELLERKAFVCEEIYDVTGLFMDTKSKV 295
                                           ************************************************************************* PP

                             TIGR00134 294 irnaek...vkavllrGfdGlvGkeiqpGrrlGteladiakkiGvgGvfhtdelpayGiteeevkklrdavga 363
                                           +++  k   ++a ll+ f+ lvGke+qpGrrlGte++d+ak+ GvgG+fhtdelp+yGite+ev+ ++da+ga
  NCBI__GCF_000007345.1:WP_011022814.1 296 LQKGVKkgsILAALLKKFNRLVGKEVQPGRRLGTEFSDRAKTAGVGGLFHTDELPNYGITEKEVQAVKDAIGA 368
                                           **9777677**************************************************************** PP

                             TIGR00134 364 eegdavvlvadeevkveralrevierakealvGvpeetrkaledGntaylrplpgaarmypetdippvvikee 436
                                             +da v+vade  k+  a+++vi+rakea+ G+peetrkal+dGntay+rplpgaarmypetd+p + i +e
  NCBI__GCF_000007345.1:WP_011022814.1 369 GPEDAFVMVADEPEKARLAIEAVINRAKEAIEGIPEETRKALPDGNTAYMRPLPGAARMYPETDVPQIEISQE 441
                                           ************************************************************************* PP

                             TIGR00134 437 lleeiranlpelpeekaerlkkeyklsedlakklvksnyvdvfe....elskklkvdptviasvleltlkelr 505
                                            +++i+   pel  ++a+r+  e +l+++la+k++ s y+ +fe     ++k+ +v++t+ia++l + + e+r
  NCBI__GCF_000007345.1:WP_011022814.1 442 YFDSIK--PPELLTKRAKRFASESGLNKELAEKVAYSRYLPLFEilleTYTKDANVNSTLIARTLVGIVPEIR 512
                                           ***776..6*******************************999633326788889****************** PP

                             TIGR00134 506 reGvdidkleerelrevlklleeGkiakegleevlkllaeepdka.edearklklkllakeeiekiieeiiee 577
                                           r+Gv+ d+l +++++  + ++++ +iake+++++l +la+ep+ + ++++ kl l     ee+e++i++++ e
  NCBI__GCF_000007345.1:WP_011022814.1 513 RNGVETDNLTDEHFKGLFAAISNQEIAKEAIQDLLTALAKEPELTvQEAISKLGLSAFDPEEVENFIKQMVME 585
                                           ******************************************8761567899********************* PP

                             TIGR00134 578 kldlikerGegafgplmGrvmkklrGkadGkvvneilrkklke 620
                                           k d+ik++G  a+gplmG vmk++rG +dGk+++++l+k++ +
  NCBI__GCF_000007345.1:WP_011022814.1 586 KGDFIKDKGPSALGPLMGIVMKEYRGTVDGKILSHMLKKEIDN 628
                                           ***************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (622 nodes)
Target sequences:                          1  (633 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# 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