Alignments for a candidate for gatB in Desulfuromusa kysingii DSM 7343

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Desulfuromusa kysingii DSM 7343

Align Glutamyl-tRNA(Gln) amidotransferase subunit B, chloroplastic/mitochondrial; Glu-AdT subunit B; EC 6.3.5.- (characterized)
to candidate WP_092350518.1 BLU87_RS15575 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

Query= SwissProt::Q9FV81
         (550 letters)



>NCBI__GCF_900107645.1:WP_092350518.1
          Length = 477

 Score =  478 bits (1229), Expect = e-139
 Identities = 239/478 (50%), Positives = 333/478 (69%), Gaps = 7/478 (1%)

Query: 70  YEAVIGIETHVQLSTLTKAFCSCSNNYGSYPNTSICPVCMGLPGALPVLNSKVVEFGVRL 129
           YE VIG+E HVQL+T TK FC CS  +G  PN+  CPVC+GLPGALPVLN +VV+  ++ 
Sbjct: 5   YEVVIGLEVHVQLTTKTKIFCGCSTEFGQTPNSQTCPVCLGLPGALPVLNQQVVDDAIKA 64

Query: 130 GLALNCDLSLKSKFDRKQYFYPDLPKGYQISQFDIPIASGGYVDVDIPLEFGGGHRRFGI 189
           GLA NC ++  S F RK YFYPDLPKGYQISQF++PI   G++D++       G +R GI
Sbjct: 65  GLATNCQIAPHSIFARKNYFYPDLPKGYQISQFELPICEHGWMDIETE---ELGKKRIGI 121

Query: 190 TRVHMEEDAGKLLHSDTGDYSQVDLNRAGVPLLEIVSEPDMRSGIEAAEYACEMQRIARY 249
           TR+HMEEDAGKLLH++ G  S VDLNRA  PLLE+VSEPDMRS  EA  Y  ++ +I  Y
Sbjct: 122 TRIHMEEDAGKLLHNE-GSSSFVDLNRACTPLLEVVSEPDMRSSDEAIAYLKQLHQIVVY 180

Query: 250 LGVSNGNMQEGSLRCDVNISIRPIGQAEFGTKVEIKNLNAFSAISRAIDFEISRQALLYN 309
           LG+ +GN++EGS RCD N+SIRP GQ E GT+ E+KNLN+F  I +AI++E+ RQ  + +
Sbjct: 181 LGICDGNLEEGSFRCDANVSIRPWGQKELGTRSELKNLNSFRFIKQAIEYEVERQIDVID 240

Query: 310 QGKADQIVTETRLWEEGAQKTVTMRKKEGLADYRYFPEPDLPEVILTQEYVDSIRASLPE 369
            G  +++V ETRL++  A  + +MR KE   DYRYFP+PDL  + ++ E+V+ +R+ LPE
Sbjct: 241 AG--EEVVQETRLFDPDAGVSRSMRGKEEAHDYRYFPDPDLLPLQVSDEWVEKVRSCLPE 298

Query: 370 LPEAKRRRY-EAMGLGMQDVLFLANDVSVAEYFDAVIGKGAEVKLAANWIMSDIAAYLKN 428
           LP  K +RY + MGL   D   ++++  +AEYF+A++G+  + K+ +NW+M ++   LK 
Sbjct: 299 LPGVKLQRYQDEMGLPAYDAGVISSERPLAEYFEALVGRYDKPKICSNWVMGEVLGALKE 358

Query: 429 EKLSINDIKLTPQELAELIAAIKDGTISGKIGKEILFELLAKGGTVKGMIKAKDLVQITD 488
             L+I+   +TP+ LA ++  I D TISGKI K +  E+   G T   +I  K L Q+TD
Sbjct: 359 HNLTIDQCPVTPELLAGILQRIDDATISGKIAKTVFEEVWNSGKTADEVIAEKGLKQVTD 418

Query: 489 PAEIEKMVIQVVSENPKQLEQYRSGKTKLQGYFAGQVMKMSKGKANPGLLNKILLEKL 546
              IE +V +V++ NP Q+ +Y  GK K+ G+F GQVMK SKGKANPG++N++L +KL
Sbjct: 419 TGAIESIVNEVIAANPSQVAEYLGGKEKMLGFFVGQVMKASKGKANPGMVNQLLKKKL 476


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: 736
Number of extensions: 32
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: 477
Length adjustment: 35
Effective length of query: 515
Effective length of database: 442
Effective search space:   227630
Effective search space used:   227630
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_092350518.1 BLU87_RS15575 (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.12009.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.4e-188  610.8   0.0   8.5e-188  610.6   0.0    1.0  1  lcl|NCBI__GCF_900107645.1:WP_092350518.1  BLU87_RS15575 Asp-tRNA(Asn)/Glu-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900107645.1:WP_092350518.1  BLU87_RS15575 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 !  610.6   0.0  8.5e-188  8.5e-188       3     480 ..       4     476 ..       2     477 .] 0.98

  Alignments for each domain:
  == domain 1  score: 610.6 bits;  conditional E-value: 8.5e-188
                                 TIGR00133   3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnsk 71 
                                                ye+viGlEvHvql tk+K+Fc cs+e+ + +pN+++cpvclglPGalPvlN+++v  A+k +la+n++
  lcl|NCBI__GCF_900107645.1:WP_092350518.1   4 RYEVVIGLEVHVQLTTKTKIFCGCSTEFGQ-TPNSQTCPVCLGLPGALPVLNQQVVDDAIKAGLATNCQ 71 
                                               69***************************9.************************************** PP

                                 TIGR00133  72 ivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleielee.kekeigierlhlEeDtgksqykesd 139
                                                +++ s+F+RK+YfYpDlPkgyqi+q++lPi+e+G ++ie+ee ++k+igi+r+h+EeD+gk+ ++e  
  lcl|NCBI__GCF_900107645.1:WP_092350518.1  72 -IAPHSIFARKNYFYPDLPKGYQISQFELPICEHGWMDIETEElGKKRIGITRIHMEEDAGKLLHNEG- 138
                                               .668************************************9873679******************966. PP

                                 TIGR00133 140 kdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkG 208
                                                 + s+vD+NR+++PLlE+V++Pd++s++ea a+lk+l+qi+ yl+i dg+leeGs+R+D+Nvsir+ G
  lcl|NCBI__GCF_900107645.1:WP_092350518.1 139 --SSSFVDLNRACTPLLEVVSEPDMRSSDEAIAYLKQLHQIVVYLGICDGNLEEGSFRCDANVSIRPWG 205
                                               ..58***************************************************************** PP

                                 TIGR00133 209 qekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYf 277
                                               q++ gtr E+KNlns++ i++aieyE+eRq++++  geev+qetr fd    +  s+R Kee++DYRYf
  lcl|NCBI__GCF_900107645.1:WP_092350518.1 206 QKELGTRSELKNLNSFRFIKQAIEYEVERQIDVIDAGEEVVQETRLFDPDAGVSRSMRGKEEAHDYRYF 274
                                               ********************************************************************* PP

                                 TIGR00133 278 pePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepk 346
                                               p+Pdl p+++++e+v++ v+  lpelP  k +r++ e+gl ++da v+ s++ l+++fe +v   ++pk
  lcl|NCBI__GCF_900107645.1:WP_092350518.1 275 PDPDLLPLQVSDEWVEK-VRSCLPELPGVKLQRYQDEMGLPAYDAGVISSERPLAEYFEALVGRYDKPK 342
                                               ****************9.*************************************************** PP

                                 TIGR00133 347 lavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkkliekl 415
                                                  nW++ e+lg L+++++++ ++ ++pe la +++ i++++is+k+ak+++ee+ + +k ++++i ++
  lcl|NCBI__GCF_900107645.1:WP_092350518.1 343 ICSNWVMGEVLGALKEHNLTIDQCPVTPELLAGILQRIDDATISGKIAKTVFEEVWNSGKTADEVIAEK 411
                                               ********************************************************************* PP

                                 TIGR00133 416 gliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                               gl q++d+ ++ +iv+evi+ np +v +y+ gkek+l+f+vGqvmk +kg+a+p  v++llk++l
  lcl|NCBI__GCF_900107645.1:WP_092350518.1 412 GLKQVTDTGAIESIVNEVIAANPSQVAEYLGGKEKMLGFFVGQVMKASKGKANPGMVNQLLKKKL 476
                                               **************************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (477 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: 9.58
//
[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