GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gltX in Phyllobacterium endophyticum PEPV15

Align glutamyl-tRNA(Glx) synthetase (EC 6.1.1.24) (characterized)
to candidate WP_106716609.1 CU100_RS10940 glutamate--tRNA ligase

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



>NCBI__GCF_003010935.1:WP_106716609.1
          Length = 474

 Score =  483 bits (1244), Expect = e-141
 Identities = 249/473 (52%), Positives = 317/473 (67%), Gaps = 16/473 (3%)

Query: 7   TGVVTRFAPSPTGFLHIGGARTALFNWLYARHTGGKFLIRVEDTDRERSTEAAVAAIFEG 66
           + VVTRFAPSPTG+LHIGGARTALFNWLYA+HTGGK L+R+EDTDRERS+EAAV AI +G
Sbjct: 3   SSVVTRFAPSPTGYLHIGGARTALFNWLYAKHTGGKMLLRIEDTDRERSSEAAVTAILDG 62

Query: 67  LDWLGLKSDDEVIFQHTRAPRHVEVVHELLAKGRAYRCWMSIEELEVAREKARAEGRAIR 126
           L WLGL+ D + + Q+ RAPRH  V  EL++KG+AY C+ S  ELE  REKARAEGR  R
Sbjct: 63  LRWLGLEWDGDAVSQYERAPRHRAVAEELVSKGKAYYCYASQAELEEVREKARAEGRPPR 122

Query: 127 --SPWRD-----APEGDLSAPHVIRFKGPLDGETLVNDLVKGPVTFKNIELDDLVLLRAD 179
               WRD     APEG      VIR K P +GETLV D V+G V F N +LDD ++LR+D
Sbjct: 123 YDGRWRDRDPSEAPEG---VKPVIRIKAPQEGETLVRDQVQGDVRFPNKDLDDFIILRSD 179

Query: 180 GAPTYNLAVVVDDHDMGVTHVIRGDDHLNNAARQTLIYQAMDWAVPAFAHIPLIHGPDGA 239
           G PTY  AVVVDDHDMGVTH+IRGDDHL NAARQT+IY AM W VP   HIPLIHG DGA
Sbjct: 180 GNPTYMHAVVVDDHDMGVTHIIRGDDHLTNAARQTVIYDAMGWEVPVMGHIPLIHGADGA 239

Query: 240 KLSKRHGAQAVGEFADLGYIPEGMRNYLARLGWGHGDDEVFTDEQAISWFDVADVVKAPA 299
           KLSKRHGA  V  +  +GY+P  +RNYL RLGW HGDDE+ +DEQ I WF+++D+ +  A
Sbjct: 240 KLSKRHGALGVEAYRAMGYLPAALRNYLVRLGWSHGDDEIMSDEQMIQWFEISDINRGAA 299

Query: 300 RLDWAKLNHINAQHLRKADDARLT-ALALAAAETRG-----EPLPADAAERIARTVPEVK 353
           R D+ KL  IN  ++R +DDA L  A+     E  G       L  +  +++   +P +K
Sbjct: 300 RFDFQKLEAINGHYMRMSDDAGLVQAMVDILPEIEGGAEMLSRLDGNTKKQLLAAMPGLK 359

Query: 354 EGAKTILELVDHCAFALKTRPLALEEKTQKQLTEETVERLKRLRDQLAAAPDFDAATLET 413
           E AKT++EL D   +    RPL+L+EK    L EE    L  +  QLA+   ++   L+ 
Sbjct: 360 ERAKTLVELADSAKYLFAQRPLSLDEKAYGLLNEEGRSILSGVLPQLASVEQWEPGPLDA 419

Query: 414 VLKSFAESEGVGFGKFGPALRGVLTGGAQAPDLNKTMAALSRDEAIGRLDDAL 466
            ++++AE  G+  GK    LR  LTG A +P +   +A L R+E++GR+ D +
Sbjct: 420 AVRAYAEETGLKLGKIAQPLRAALTGKATSPGVFDVLAVLGREESLGRIKDQI 472


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: 693
Number of extensions: 37
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: 474
Length adjustment: 33
Effective length of query: 437
Effective length of database: 441
Effective search space:   192717
Effective search space used:   192717
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 Jul 26 2024. The underlying query database was built on Jul 25 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