Alignments for a candidate for gltX in Trichormus variabilis ATCC 29413

GapMind for Amino acid biosynthesis

Alignments for a candidate for gltX in Trichormus variabilis ATCC 29413

Align Glutamate--tRNA ligase; Glutamyl-tRNA synthetase; GluRS; EC 6.1.1.17 (characterized)
to candidate WP_011321519.1 AVA_RS24665 glutamate--tRNA ligase

Query= SwissProt::Q8DLI5
         (485 letters)



>NCBI__GCF_000204075.1:WP_011321519.1
          Length = 481

 Score =  627 bits (1616), Expect = 0.0
 Identities = 307/478 (64%), Positives = 366/478 (76%), Gaps = 1/478 (0%)

Query: 1   MTVRVRLAPSPTGNLHIGTARTAVFNWLYARHRGGKFILRIEDTDRERSRPEYTENILEG 60
           MTVRVR+APSPTGNLHIGTARTAVFNWL+ARH GG FILRIEDTD ERSRPEYTENI+ G
Sbjct: 1   MTVRVRIAPSPTGNLHIGTARTAVFNWLFARHHGGTFILRIEDTDLERSRPEYTENIMTG 60

Query: 61  LQWLGLTWDEGPYFQSDRLDLYRQAIQTLLDKGLAYYCYCTPEELEALRAEQKAKGQAPR 120
           L+WLGL WDEGP+FQS RLDLY++A++ LLD+GLAY CY T EELEALR  QKAKG+APR
Sbjct: 61  LRWLGLNWDEGPFFQSQRLDLYQKAVKQLLDQGLAYRCYTTSEELEALREAQKAKGEAPR 120

Query: 121 YDNRHRHLTPEEQAAFEAAGRTPVIRFKIEDDRQIEWQDLVRGRVSWQGADLGGDMVIAR 180
           YDNRHRHLTPE++A F+A GR+ VIRFKI+D+R+I W DLVRG++SW+G+DLGGDMVIAR
Sbjct: 121 YDNRHRHLTPEQEAEFKAQGRSFVIRFKIDDEREIVWNDLVRGKMSWRGSDLGGDMVIAR 180

Query: 181 AAPRGEIGYPLYNLVVVVDDIAMGITDVIRGEDHIGNTPKQILLYEALGATPPNFAHTPL 240
           A+   + G PLYN VVV+DDI M I+ VIRGEDHI NT KQILLYEA GA  P FAHTPL
Sbjct: 181 AS-ENDTGQPLYNFVVVIDDIDMQISHVIRGEDHIANTAKQILLYEAFGAKIPEFAHTPL 239

Query: 241 ILNSTGQKLSKRDGVTSISDFRAMGYLAPALANYMTLLGWSPPEGVGELFTLDLAAKHFS 300
           ILN  G+KLSKRDGVTSISDF+ MG+ +  L NYMTLLGWSPP+   E+FTL+ AAK F+
Sbjct: 240 ILNMEGRKLSKRDGVTSISDFQQMGFTSEGLVNYMTLLGWSPPDSTQEIFTLEAAAKEFT 299

Query: 301 FERINKAGARFDWDKLNWLNRQYIQQLEPEEFLAELIPLWQGAGYAFDEERDRPWLFDLA 360
           FER+NKAGA+FDW KL+WLN QYI     ++    LIP W+ AGY+F   RDRPWL  L 
Sbjct: 300 FERVNKAGAKFDWAKLDWLNSQYIHNTPVDQLTDLLIPYWEAAGYSFAGGRDRPWLEQLV 359

Query: 361 QLLQPGLNTLREAIDQGAVFFIPSVTFDSEAMAQLGQPQSATILAYLLEHLPAEPALTVA 420
            LL   L  L +A+D   +FF  +V    E   QL Q  S  +L  ++  L A+  LT  
Sbjct: 360 GLLSASLTRLTDAVDMSKLFFSETVELSEEGSKQLQQEGSKAVLEAIIAALEAQTQLTEN 419

Query: 421 MGQQLIQQAAKAAGVKKGATMRTLRAALTGAVHGPDLMAAWQILHQRGWDEPRLAAAL 478
             Q +I+Q  KA  VKKG  MR+LR ALTG VHGPDL+ +W +L+Q G D+PRL+ A+
Sbjct: 420 AAQDIIKQVVKAQNVKKGLVMRSLRVALTGDVHGPDLIQSWLLLNQIGLDKPRLSQAI 477


Lambda     K      H
   0.320    0.136    0.418 

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: 735
Number of extensions: 25
Number of successful extensions: 2
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: 485
Length of database: 481
Length adjustment: 34
Effective length of query: 451
Effective length of database: 447
Effective search space:   201597
Effective search space used:   201597
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 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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