GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gltX in Shewanella loihica PV-4

Align Glutamate--tRNA ligase; EC 6.1.1.17 (characterized, see rationale)
to candidate 5208954 Shew_1449 glutamyl-tRNA synthetase (RefSeq)

Query= uniprot:A0A0H3C8P5_CAUVN
         (470 letters)



>FitnessBrowser__PV4:5208954
          Length = 469

 Score =  337 bits (863), Expect = 7e-97
 Identities = 184/460 (40%), Positives = 267/460 (58%), Gaps = 4/460 (0%)

Query: 9   VVTRFAPSPTGFLHIGGARTALFNWLYARHTGGKFLIRVEDTDRERSTEAAVAAIFEGLD 68
           + TRFAPSPTGFLH+GGARTAL++WLYAR   G+F++R+EDTD ERST  A AAI EG++
Sbjct: 3   IKTRFAPSPTGFLHVGGARTALYSWLYARANQGEFVLRIEDTDLERSTPEACAAILEGME 62

Query: 69  WLGLKSDDEVIFQHTRAPRHVEVVHELLAKGRAYRCWMSIEELEVAREKARAEGRAIRSP 128
           WLGL  D+   +Q  R  R+ E++ ++L +G AY+C+ S E +E  RE+  A+G   +  
Sbjct: 63  WLGLNWDEGPYYQTKRFDRYNEIIAQMLEQGTAYKCYCSRERIEAMREEQAAKGEQQKYD 122

Query: 129 W--RDAPEGDLSAPHVIRFKGPLDGETLVNDLVKGPVTFKNIELDDLVLLRADGAPTYNL 186
              RD    D   P V+RFK P +G  + +D V+G +   N  LDDL++ R DG PTYN 
Sbjct: 123 GCCRDKAPRDTDEPFVVRFKNPTEGSVVFDDHVRGRIEISNELLDDLIIARTDGTPTYNF 182

Query: 187 AVVVDDHDMGVTHVIRGDDHLNNAARQTLIYQAMDWAVPAFAHIPLIHGPDGAKLSKRHG 246
            VVVDD DMG+T V+RG+DH+NN  RQ  I +A++  VP +AH+ +I G DGAKLSKRHG
Sbjct: 183 CVVVDDWDMGITCVVRGEDHINNTPRQINILKALNAPVPEYAHVAMILGDDGAKLSKRHG 242

Query: 247 AQAVGEFADLGYIPEGMRNYLARLGWGHGDDEVFTDEQAISWFDVADVVKAPARLDWAKL 306
           A  V ++ D GY+PE + NYL RLGW HGD EVF+ E+   +F + D+ KA +  +  KL
Sbjct: 243 AVGVMQYRDDGYLPEALLNYLVRLGWSHGDQEVFSIEEMKQYFKLDDINKAASAFNTEKL 302

Query: 307 NHINAQHLRKADDARLTALALAAAETRGEPLPADAAERIARTVPEVKEGAKTILELVDHC 366
             +N QH  K       A  L     + + +       +A  V  + E AKT+ EL    
Sbjct: 303 IWLN-QHYMKELAPEYVAKHL-EWHMQDQNIDTANGPALAEVVSALAERAKTLKELAASS 360

Query: 367 AFALKTRPLALEEKTQKQLTEETVERLKRLRDQLAAAPDFDAATLETVLKSFAESEGVGF 426
            +  +      E   +K L    +E L+ L+ + A   +++   +   +++ A    +G 
Sbjct: 361 RYFYEDFAEFDETAAKKHLRGVALEPLQLLQKKFAELSEWNVEAIHQAIEATAAELELGM 420

Query: 427 GKFGPALRGVLTGGAQAPDLNKTMAALSRDEAIGRLDDAL 466
           GK G  LR  +TG   +P ++ T   + +     R+  A+
Sbjct: 421 GKVGMPLRVAVTGAGMSPAVDLTAFLVGKARCEQRISKAI 460


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: 642
Number of extensions: 31
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: 470
Length of database: 469
Length adjustment: 33
Effective length of query: 437
Effective length of database: 436
Effective search space:   190532
Effective search space used:   190532
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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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