GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gltX in Dinoroseobacter shibae DFL-12

Align glutamyl-tRNA(Glx) synthetase (EC 6.1.1.24) (characterized)
to candidate 3608405 Dshi_1805 glutamyl-tRNA synthetase (RefSeq)

Query= reanno::Caulo:CCNA_01982
         (470 letters)



>FitnessBrowser__Dino:3608405
          Length = 471

 Score =  456 bits (1173), Expect = e-133
 Identities = 247/471 (52%), Positives = 307/471 (65%), Gaps = 9/471 (1%)

Query: 1   MSNPTPTGVVTRFAPSPTGFLHIGGARTALFNWLYARHTGGKFLIRVEDTDRERSTEAAV 60
           MS    + VVTRFAPSPTG+LHIGGARTALFNWLYAR  GGKFL+R+EDTD+ RST  A 
Sbjct: 1   MSPTDASPVVTRFAPSPTGYLHIGGARTALFNWLYARGRGGKFLLRIEDTDKARSTAEAT 60

Query: 61  AAIFEGLDWLGLKSDDEVIFQHTRAPRHVEVVHELLAKGRAYRCWMSIEELEVAREKARA 120
            AIF GL WLGL  D + + Q   A RH +V   L   G+AY+C+ + +E+   RE ARA
Sbjct: 61  EAIFAGLRWLGLDWDGDAVSQAEGAARHAQVARALQEAGKAYKCFTTQDEIAAFREAARA 120

Query: 121 EGRA--IRSPWRDA-PEGDLSAPHVIRFKGPLDGETLVNDLVKGPVTFKNIELDDLVLLR 177
           EGR+   RSPWRDA P     AP+VIR K P +G T++ D V+G V  +N +LDD++LLR
Sbjct: 121 EGRSTLFRSPWRDADPASHPDAPYVIRIKAPQEGTTVIADQVQGDVRIRNDQLDDMILLR 180

Query: 178 ADGAPTYNLAVVVDDHDMGVTHVIRGDDHLNNAARQTLIYQAMDWAVPAFAHIPLIHGPD 237
           +DG+P Y LAVVVDDHDMGVTHVIRGDDHLNNAARQ +IY AM W +P FAHIPLIHGPD
Sbjct: 181 SDGSPVYMLAVVVDDHDMGVTHVIRGDDHLNNAARQMMIYDAMGWDMPVFAHIPLIHGPD 240

Query: 238 GAKLSKRHGAQAVGEFADLGYIPEGMRNYLARLGWGHGDDEVFTDEQAISWFDVADVVKA 297
           G KLSKRHGA  V E+  +GY  + MRNYLARLGW HGDDE F D QA +WFD+  + K+
Sbjct: 241 GKKLSKRHGALGVEEYQAMGYPAQAMRNYLARLGWSHGDDEFFGDAQAQAWFDLDGIGKS 300

Query: 298 PARLDWAKLNHINAQHLRKADDARLTALALAAAETRGEPLPADAAER-IARTVPEVKEGA 356
           PARLD  KL++++ QHL    D  + A A       G P   +A E  ++R +  +K+ A
Sbjct: 301 PARLDLKKLDNLSGQHLGVMADEAIVAGAQGYLAATGAPPLTEAQETGLSRAMYCLKDRA 360

Query: 357 KTILELVDHCAFALKTRPLALEEKTQKQLTEETVER--LKRLRDQLAAAPDFDAATLETV 414
           K   +L++   F L +RP+  + K  K L  +TV R  L  L  QL  A  +   TLE V
Sbjct: 361 KKFPDLLEKAHFILASRPIDPDPKAAKSL--DTVSRGILAELTPQLQNA-SWTRDTLEGV 417

Query: 415 LKSFAESEGVGFGKFGPALRGVLTGGAQAPDLNKTMAALSRDEAIGRLDDA 465
           +   AE+ G+G GK    LR  L G +  P +   M  L RDE + RL DA
Sbjct: 418 VGGLAEAHGLGLGKLAAPLRAALAGRSATPSVFDMMLVLGRDETLARLSDA 468


Lambda     K      H
   0.319    0.135    0.405 

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: 710
Number of extensions: 34
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: 470
Length of database: 471
Length adjustment: 33
Effective length of query: 437
Effective length of database: 438
Effective search space:   191406
Effective search space used:   191406
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Apr 09 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:

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:

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:

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:

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