Alignments for a candidate for gatB in Nocardiopsis lucentensis DSM 44048

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Nocardiopsis lucentensis DSM 44048

Align Glutamyl-tRNA(Gln) amidotransferase subunit B, chloroplastic/mitochondrial; Glu-AdT subunit B; EC 6.3.5.- (characterized)
to candidate WP_017598149.1 D471_RS0108090 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

Query= SwissProt::Q9FV81
         (550 letters)



>NCBI__GCF_000341125.1:WP_017598149.1
          Length = 498

 Score =  382 bits (981), Expect = e-110
 Identities = 203/498 (40%), Positives = 309/498 (62%), Gaps = 15/498 (3%)

Query: 64  DEILRDYEAVIGIETHVQLSTLTKAFCSCSNNYGSYPNTSICPVCMGLPGALPVLNSKVV 123
           ++ L  YE V+G+ETH++L T +K FCSC   +G+ PNT +CPVC+ LPG+LPV+N K V
Sbjct: 4   EQALAKYEPVLGLETHIELGTASKMFCSCPTAFGARPNTQVCPVCLALPGSLPVVNRKAV 63

Query: 124 EFGVRLGLALNCDLSLKSKFDRKQYFYPDLPKGYQISQFDIPIASGGYVDVDIPLEFGGG 183
           E  +RLGLALNC ++   +F RK YFYPD+PK YQISQ+D PI   G++DV +    G  
Sbjct: 64  EGAIRLGLALNCSIAPWGRFARKNYFYPDMPKNYQISQYDEPICVDGHLDVTVDTPEGPR 123

Query: 184 HRRFGITRVHMEEDAGKLLH--SDTG-----DYSQVDLNRAGVPLLEIVSEPDMRSG--- 233
             R  I RVHMEED GK  H    TG     DYS VD NRAG+PLLEIV++P   +G   
Sbjct: 124 VFRVDIERVHMEEDTGKTSHVGGATGRIHGADYSIVDYNRAGIPLLEIVTKPITGTGELA 183

Query: 234 -IEAAEYACEMQRIARYLGVSNGNMQEGSLRCDVNISIRPIGQAEFGTKVEIKNLNAFSA 292
            + A  YA E++ + R LG+S+  M+EGS+RCDVN+SI   G  E+GT+ E KN+N+  +
Sbjct: 184 PLVARAYAAELRDLVRSLGISDVRMEEGSMRCDVNVSINERGADEWGTRSETKNVNSLRS 243

Query: 293 ISRAIDFEISRQALLYNQGKADQIVTETRLWEEGAQKTVTMRKKEGLADYRYFPEPDLPE 352
           + RA+  EI RQA + + G+  ++V ETR ++E   ++++ R KE   DYRYFP+PDL  
Sbjct: 244 VERAVRSEIERQAGVLDDGQ--KVVQETRHFQENTGRSISGRSKEEAQDYRYFPDPDLVP 301

Query: 353 VILTQEYVDSIRASLPELPEAKRRRYEA-MGLGMQDVLFLANDVSVAEYFDAVIGKGAEV 411
           V  +QE+++ +RA+LPELP AKR R  A   L   ++  L N     +  +A +  GA  
Sbjct: 302 VAPSQEWIEELRATLPELPAAKRARVRAEWDLTDTELRDLVN-ADAIDLVEATVAAGAPS 360

Query: 412 KLAANWIMSDIAAYLKNEKLSINDIKLTPQELAELIAAIKDGTISGKIGKEILFELLAKG 471
             A    +++++     +++ +  + +TP ++A +IA + +GT++ K+ ++++  +LA  
Sbjct: 361 AEARKLWLNELSRRATEQEVELASLPITPGQVARIIALVAEGTLTNKLARQVVEGVLAGE 420

Query: 472 GTVKGMIKAKDLVQITDPAEIEKMVIQVVSENPKQLEQYRSGKTKLQGYFAGQVMKMSKG 531
           G    ++ A+ L  ++D   +   V + ++ NP   E+ R GK    G   G VMK ++G
Sbjct: 421 GEPDAVVDARGLKVVSDDGALGAAVDEAIAGNPDVAEKVRGGKVAAAGALVGAVMKATRG 480

Query: 532 KANPGLLNKILLEKLNAK 549
           +A+ G   +++LEKL AK
Sbjct: 481 QADAGRARELILEKLGAK 498


Lambda     K      H
   0.317    0.134    0.379 

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: 666
Number of extensions: 28
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: 550
Length of database: 498
Length adjustment: 35
Effective length of query: 515
Effective length of database: 463
Effective search space:   238445
Effective search space used:   238445
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_017598149.1 D471_RS0108090 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB)
to HMM TIGR00133 (gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B 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/TIGR00133.hmm
# target sequence database:        /tmp/gapView.8267.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00133  [M=481]
Accession:   TIGR00133
Description: gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B 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-148  479.2   0.0   6.9e-148  479.0   0.0    1.0  1  lcl|NCBI__GCF_000341125.1:WP_017598149.1  D471_RS0108090 Asp-tRNA(Asn)/Glu


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000341125.1:WP_017598149.1  D471_RS0108090 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  479.0   0.0  6.9e-148  6.9e-148       3     480 ..       9     495 ..       7     496 .. 0.95

  Alignments for each domain:
  == domain 1  score: 479.0 bits;  conditional E-value: 6.9e-148
                                 TIGR00133   3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnsk 71 
                                               +ye v+GlE+H+ l+t+sK+Fc+c++ +    pNt+vcpvcl+lPG+lPv+N++av+ A+ l+laln+ 
  lcl|NCBI__GCF_000341125.1:WP_017598149.1   9 KYEPVLGLETHIELGTASKMFCSCPTAFGA-RPNTQVCPVCLALPGSLPVVNRKAVEGAIRLGLALNCS 76 
                                               7999************************99.************************************** PP

                                 TIGR00133  72 ivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke....keigierlhlEeDtgksqyk 136
                                                +++   F+RK+YfYpD+Pk+yqi+q+d Pi+ dG+l++ +++ e     ++ ier+h+EeDtgk+++ 
  lcl|NCBI__GCF_000341125.1:WP_017598149.1  77 -IAPWGRFARKNYFYPDMPKNYQISQYDEPICVDGHLDVTVDTPEgprvFRVDIERVHMEEDTGKTSHV 144
                                               .668********************************999888877777789*****************9 PP

                                 TIGR00133 137 esdk.....dkqslvDfNRsgvPLlEiVtkPdlksak....earaflkklrqilryleisdgdleeGsm 196
                                               +  +     +++s+vD+NR+g+PLlEiVtkP   +++     ara+  +lr ++r l+isd  +eeGsm
  lcl|NCBI__GCF_000341125.1:WP_017598149.1 145 GGATgrihgADYSIVDYNRAGIPLLEIVTKPITGTGElaplVARAYAAELRDLVRSLGISDVRMEEGSM 213
                                               87766687899*********************999883333479************************* PP

                                 TIGR00133 197 RvDvNvsirlkGqekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvsl 265
                                               R+DvNvsi+ +G ++ gtr E KN+nsl+s+e+a+  EieRq  +l +g++v+qetr+f+e++ + +s 
  lcl|NCBI__GCF_000341125.1:WP_017598149.1 214 RCDVNVSINERGADEWGTRSETKNVNSLRSVERAVRSEIERQAGVLDDGQKVVQETRHFQENTGRSISG 282
                                               ********************************************************************* PP

                                 TIGR00133 266 RkKeeseDYRYfpePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlellda 334
                                               R+Kee++DYRYfp+Pdl+p+  ++e+++e ++++lpelP akr+r+  e +l +++ + lv+ ++ +d 
  lcl|NCBI__GCF_000341125.1:WP_017598149.1 283 RSKEEAQDYRYFPDPDLVPVAPSQEWIEE-LRATLPELPAAKRARVRAEWDLTDTELRDLVN-ADAIDL 349
                                               *****************************.****************************9996.566788 PP

                                 TIGR00133 335 feevvklikepklavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleelle 403
                                                e  v + +++ +a +  l+el ++  +++++la   ++p ++a++i+l+ eg++++k a++++e +l 
  lcl|NCBI__GCF_000341125.1:WP_017598149.1 350 VEATVAAGAPSAEARKLWLNELSRRATEQEVELASLPITPGQVARIIALVAEGTLTNKLARQVVEGVLA 418
                                               88888777777666655569************************************************* PP

                                 TIGR00133 404 nkkdpkklieklgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkev 472
                                                +++p+++++++gl  +sd+ +l ++v+e+i+ np+  ek + gk +a + lvG vmk t+g+ad+ ++
  lcl|NCBI__GCF_000341125.1:WP_017598149.1 419 GEGEPDAVVDARGLKVVSDDGALGAAVDEAIAGNPDVAEKVRGGKVAAAGALVGAVMKATRGQADAGRA 487
                                               ********************************************************************* PP

                                 TIGR00133 473 ekllkell 480
                                                +l+ e+l
  lcl|NCBI__GCF_000341125.1:WP_017598149.1 488 RELILEKL 495
                                               ****9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (498 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: 9.46
//
[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