Alignments for a candidate for gatA in Dehalococcoides mccartyi 195

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Dehalococcoides mccartyi 195

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_010937023.1 DET_RS06835 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit A

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000011905.1:WP_010937023.1
          Length = 486

 Score =  534 bits (1376), Expect = e-156
 Identities = 272/479 (56%), Positives = 346/479 (72%), Gaps = 2/479 (0%)

Query: 8   ITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSE 67
           I +  +L+ ++++  ++L      RI+ ++ +++AF+ +  E A A AK  DEA+  +  
Sbjct: 9   IAQSHKLLKERKLSSAELTRAHLDRIEKLEPEIKAFMTVCPESALAQAKAADEAIK-QGH 67

Query: 68  HGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEF 127
              L G+P+ +KD + TKG+RTTCSS++LENF P Y+A VV +L +  AV +GK NMDEF
Sbjct: 68  IRPLTGIPMALKDVLCTKGIRTTCSSRMLENFVPPYNAHVVDKLAEEGAVLLGKTNMDEF 127

Query: 128 AMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCG 187
           AMGSSTENSA+  T NPWN   VPGGSSGGSAA VAA E  FSLGSDTGGSIRQPASFC 
Sbjct: 128 AMGSSTENSAFFTTHNPWNTAKVPGGSSGGSAACVAASEAVFSLGSDTGGSIRQPASFCS 187

Query: 188 VVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPD 247
           V GLKP+YG VSRYGLVAFASSLDQIGP T+ V D A ++ AI+G D  DSTS     PD
Sbjct: 188 VTGLKPSYGMVSRYGLVAFASSLDQIGPFTKDVLDCALVMNAIAGFDDRDSTSVPQTAPD 247

Query: 248 FLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWE-EVSLPHSKYAL 306
           F S L GDIKG K+ VPKEY    +  +  E +  AL VL GLGA+ + EVSLPH+ YAL
Sbjct: 248 FSSCLDGDIKGFKLGVPKEYFSHNMRADIAEKINDALGVLSGLGASVDREVSLPHTPYAL 307

Query: 307 ATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFAL 366
           A YY+L+ SEASANL+R+DG++YGY  +  +N+ +  ++TRA+GFG EVKRRIM+GT+AL
Sbjct: 308 AVYYILAPSEASANLSRYDGVKYGYSYNQTENMWEAMEKTRAKGFGPEVKRRIMIGTYAL 367

Query: 367 SSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYANDI 426
           S+GYYDA+Y KAQKVRTLI ++F + FEKYD ++ PTTP   F IGE   DP  MY  D 
Sbjct: 368 SAGYYDAWYVKAQKVRTLISQEFNNAFEKYDALITPTTPNLPFSIGEKLSDPFEMYMCDT 427

Query: 427 LTIPVNLAGVPGISVPCGLADGLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKAKPEL 485
            TIP+N+AG+P IS+P G  DGLP+GLQIIGK F + T+ R+AHAF+ AT  HK  P L
Sbjct: 428 CTIPINIAGLPAISIPAGFVDGLPVGLQIIGKPFADQTIMRIAHAFQCATAWHKETPRL 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: 632
Number of extensions: 25
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: 486
Length adjustment: 34
Effective length of query: 451
Effective length of database: 452
Effective search space:   203852
Effective search space used:   203852
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_010937023.1 DET_RS06835 (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.957.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.7e-194  632.2   0.0   3.2e-194  631.9   0.0    1.0  1  lcl|NCBI__GCF_000011905.1:WP_010937023.1  DET_RS06835 Asp-tRNA(Asn)/Glu-tR


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000011905.1:WP_010937023.1  DET_RS06835 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 !  631.9   0.0  3.2e-194  3.2e-194       3     463 ..      14     476 ..      12     479 .. 0.98

  Alignments for each domain:
  == domain 1  score: 631.9 bits;  conditional E-value: 3.2e-194
                                 TIGR00132   3 ellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdni 69 
                                               +llk++++s+ e++++ l+rie+ + +i+af++v++e+al++ak+ d++++  + ++l+gip+a+Kd++
  lcl|NCBI__GCF_000011905.1:WP_010937023.1  14 KLLKERKLSSAELTRAHLDRIEKLEPEIKAFMTVCPESALAQAKAADEAIKqGHiRPLTGIPMALKDVL 82 
                                               67899*********************************************964456************* PP

                                 TIGR00132  70 avkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervp 138
                                               ++k+i+ttc+S++Len+v+py+a+Vv +l e+ga+++GktN+DEFamGsste+Saf  t+nP+n+++vp
  lcl|NCBI__GCF_000011905.1:WP_010937023.1  83 CTKGIRTTCSSRMLENFVPPYNAHVVDKLAEEGAVLLGKTNMDEFAMGSSTENSAFFTTHNPWNTAKVP 151
                                               ********************************************************************* PP

                                 TIGR00132 139 GGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkv 207
                                               GGSsgGsaa vaa +++++lgsDTGgSiRqPAsfc+v GlKP+YG+vSRyGlva+asSldqiG+++k+v
  lcl|NCBI__GCF_000011905.1:WP_010937023.1 152 GGSSGGSAACVAASEAVFSLGSDTGGSIRQPASFCSVTGLKPSYGMVSRYGLVAFASSLDQIGPFTKDV 220
                                               ********************************************************************* PP

                                 TIGR00132 208 edialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfeklleklee 276
                                                d alv+++i+g D +Dsts+  + +++ + l  d+kg+k+gv ke++ +++  +++ek++++l +l  
  lcl|NCBI__GCF_000011905.1:WP_010937023.1 221 LDCALVMNAIAGFDDRDSTSVPQTAPDFSSCLDGDIKGFKLGVPKEYFSHNMRADIAEKINDALGVLSG 289
                                               ********************************************************************* PP

                                 TIGR00132 277 lgaei.vevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkr 344
                                               lga +  evslp+  +ala+Yyi++psEas+nl+rydg++yG+  ++++++ e + ktR++gfg evkr
  lcl|NCBI__GCF_000011905.1:WP_010937023.1 290 LGASVdREVSLPHTPYALAVYYILAPSEASANLSRYDGVKYGYSYNQTENMWEAMEKTRAKGFGPEVKR 358
                                               ****9559************************************************************* PP

                                 TIGR00132 345 RimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDv 413
                                               Rim+G+yals++yyd++y kAqkvrtli +ef+++fe++D +++pt+p l+f++gek +dp+emy+ D 
  lcl|NCBI__GCF_000011905.1:WP_010937023.1 359 RIMIGTYALSAGYYDAWYVKAQKVRTLISQEFNNAFEKYDALITPTTPNLPFSIGEKLSDPFEMYMCDT 427
                                               ********************************************************************* PP

                                 TIGR00132 414 ltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqa 463
                                               +t+p+n+aGlpais+P+g   +glp+Glqiigk f+d++++++a+a++ a
  lcl|NCBI__GCF_000011905.1:WP_010937023.1 428 CTIPINIAGLPAISIPAGFV-DGLPVGLQIIGKPFADQTIMRIAHAFQCA 476
                                               ********************.7***********************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (486 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: 7.72
//
[ok]

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

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

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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