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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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