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

GapMind for Amino acid biosynthesis

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

Align glutamine-tRNA ligase (EC 6.1.1.18); glutamate-tRNAGln ligase (EC 6.1.1.24) (characterized)
to candidate 5210072 Shew_2516 glutaminyl-tRNA synthetase (RefSeq)

Query= BRENDA::P00962
         (554 letters)



>FitnessBrowser__PV4:5210072
          Length = 556

 Score =  830 bits (2144), Expect = 0.0
 Identities = 400/550 (72%), Positives = 456/550 (82%), Gaps = 4/550 (0%)

Query: 3   EAEARPTNFIRQIIDEDLASGKHTTVHTRFPPEPNGYLHIGHAKSICLNFGIAQDYKGQC 62
           + E RP+NFIR IIDEDL SGKHT VHTRFPPEPNGYLHIGHAKSICLNFG+AQDYKG C
Sbjct: 5   DTEVRPSNFIRNIIDEDLESGKHTRVHTRFPPEPNGYLHIGHAKSICLNFGLAQDYKGLC 64

Query: 63  NLRFDDTNPVKEDIEYVESIKNDVEWLGFHWSGNVRYSSDYFDQLHAYAIELINKGLAYV 122
           NLRFDDTNP KEDI+YV SI+ DV WLGF W G +RYSS+YFDQLH YA+ELINKGLAYV
Sbjct: 65  NLRFDDTNPEKEDIDYVNSIQADVHWLGFQWDGEIRYSSNYFDQLHQYAVELINKGLAYV 124

Query: 123 DELTPEQIREYRGTLTQPGKNSPYRDRSVEENLALFEKMRAGGFEEGKACLRAKIDMASP 182
             L  EQ REYRGTL +PGKNSPYRD  VEENL LFEKMR G F+EG+  LRAKIDMASP
Sbjct: 125 CFLNGEQTREYRGTLKEPGKNSPYRDTFVEENLELFEKMRKGEFKEGECALRAKIDMASP 184

Query: 183 FIVMRDPVLYRIKFAEHHQTGNKWCIYPMYDFTHCISDALEGITHSLCTLEFQDNRRLYD 242
           F+ MRDPV+YRI+FA HHQTG+KWCIYPMYDFTHCISDALE ITHSLCTLEFQDNRRLYD
Sbjct: 185 FMCMRDPVIYRIRFAHHHQTGDKWCIYPMYDFTHCISDALEDITHSLCTLEFQDNRRLYD 244

Query: 243 WVLDNI---TIPVHPRQYEFSRLNLEYTVMSKRKLNLLVTDKHVEGWDDPRMPTISGLRR 299
           WVLDN+     P   RQYEFSRLNLEYT+MSKRKLN LV    V GWDDPRMPTI+GLRR
Sbjct: 245 WVLDNLDDFQAPNRTRQYEFSRLNLEYTLMSKRKLNDLVVRGLVSGWDDPRMPTIAGLRR 304

Query: 300 RGYTAASIREFCKRIGVTKQDNTIEMASLESCIREDLNENAPRAMAVIDPVKLVIENY-Q 358
           RGYT A+IREFC+RIGVTKQ+N +E++ L++CIRE+LNE+APRAMAVI+PVK++IENY +
Sbjct: 305 RGYTPAAIREFCRRIGVTKQENMVEVSMLDACIREELNEHAPRAMAVINPVKVIIENYPE 364

Query: 359 GEGEMVTMPNHPNKPEMGSRQVPFSGEIWIDRADFREEANKQYKRLVLGKEVRLRNAYVI 418
           G+ E ++ P HP    MG R++ F  E++ID  DFREEANK+YKRL+ GKEVRLRNAYVI
Sbjct: 365 GQVEKLSAPAHPTIESMGERELVFGRELYIDADDFREEANKKYKRLIQGKEVRLRNAYVI 424

Query: 419 KAERVEKDAEGNITTIFCTYDADTLSKDPADGRKVKGVIHWVSAAHALPVEIRLYDRLFS 478
           KAER +KD  GN+TTI+CTYD  TL K+PADGRKVKGVIHWV A  A+P E RLYDRLF+
Sbjct: 425 KAERCDKDEAGNVTTIYCTYDDQTLGKNPADGRKVKGVIHWVEATSAVPAEFRLYDRLFN 484

Query: 479 VPNPGAADDFLSVINPESLVIKQGFAEPSLKDAVAGKAFQFEREGYFCLDSRHSTAEKPV 538
            PNP AA+    V+NP+SLV+K G  EP L +A A KA+QFEREGYFC DS+ S+ E  V
Sbjct: 485 QPNPAAAETVDEVLNPKSLVVKHGLVEPGLVNAEAEKAYQFEREGYFCADSKDSSPEHLV 544

Query: 539 FNRTVGLRDT 548
           FN TV LRD+
Sbjct: 545 FNLTVALRDS 554


Lambda     K      H
   0.319    0.137    0.416 

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: 1078
Number of extensions: 40
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: 554
Length of database: 556
Length adjustment: 36
Effective length of query: 518
Effective length of database: 520
Effective search space:   269360
Effective search space used:   269360
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: 53 (25.0 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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, or view the source code, or see 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