GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gltX in Desulfovibrio vulgaris Hildenborough

Align glutamine-tRNA ligase (EC 6.1.1.18); glutamate-tRNAGln ligase (EC 6.1.1.24) (characterized)
to candidate 208462 DVU2951 glutaminyl-tRNA synthetase

Query= BRENDA::P00962
         (554 letters)



>MicrobesOnline__882:208462
          Length = 570

 Score =  654 bits (1687), Expect = 0.0
 Identities = 328/554 (59%), Positives = 398/554 (71%), Gaps = 8/554 (1%)

Query: 5   EARP-TNFIRQIIDEDLASGKHT-TVHTRFPPEPNGYLHIGHAKSICLNFGIAQDYKGQC 62
           EA P  +F+R  +  D  +G+    VHTRFPPEPNGYLHIGHAKSICLNFGIA +Y G+C
Sbjct: 14  EATPGLDFVRSRVVADNRTGRFDGRVHTRFPPEPNGYLHIGHAKSICLNFGIANEYGGKC 73

Query: 63  NLRFDDTNPVKEDIEYVESIKNDVEWLGFHWSGNVRYSSDYFDQLHAYAIELINKGLAYV 122
           NLRFDDTNPVKE  EYV+SI+ DV W+GF W     Y+S+YF+QL+ +A +LI  G AYV
Sbjct: 74  NLRFDDTNPVKESREYVDSIRTDVAWMGFSWDDREFYASNYFEQLYQFAEQLIMAGKAYV 133

Query: 123 DELTPEQIREYRGTLTQPGKNSPYRDRSVEENLALFEKMRAGGFEEGKACLRAKIDMASP 182
           D L+ E+IR +RGTLTQPG  SPYR+RSVEENL LF +MRAG F +G   LRAKIDMASP
Sbjct: 134 DSLSAEEIRAHRGTLTQPGTESPYRNRSVEENLDLFRRMRAGEFADGTHVLRAKIDMASP 193

Query: 183 FIVMRDPVLYRIKFAEHHQTGNKWCIYPMYDFTHCISDALEGITHSLCTLEFQDNRRLYD 242
            +VMRDP LYRI+ A HH+TG+ WCIYPMYDFTHCISD+LEGITHS+CTLEF++NR LYD
Sbjct: 194 NVVMRDPTLYRIRHAHHHRTGDAWCIYPMYDFTHCISDSLEGITHSICTLEFENNRELYD 253

Query: 243 WVLDNITIPVHPRQYEFSRLNLEYTVMSKRKLNLLVTDKHVEGWDDPRMPTISGLRRRGY 302
           W LD + +  HP+Q EF+RLNL YTV+SKRKL  LV    V+GWDDPRMPTISGLRRRG 
Sbjct: 254 WTLDALGV-YHPQQIEFARLNLTYTVLSKRKLIQLVEGGFVKGWDDPRMPTISGLRRRGV 312

Query: 303 TAASIREFCKRIGVTKQDNTIEMASLESCIREDLNENAPRAMAVIDPVKLVIENY-QGEG 361
              ++REFC RIGV K D+T++    E CIRE LN   PR M V+DP+++VIENY +G+ 
Sbjct: 313 PPEALREFCARIGVAKADSTVDYGLFEFCIRERLNATTPRVMGVLDPIRVVIENYPEGQV 372

Query: 362 EMVTMPNHPNKPEMGSRQVPFSGEIWIDRADFREEANKQYKRLVLGKEVRLRNAYVIKAE 421
           E   MP HP     GSR VPFS  ++I+R DFRE+  K++ RL  G EVRLR AY I   
Sbjct: 373 EEFDMPYHPEDASFGSRIVPFSRVLYIERDDFREDPPKKFFRLAPGAEVRLRYAYYITCR 432

Query: 422 RVEKDAEGNITTIFCTYDADTLSKDPADGRKVKGVIHWVSAAHALPVEIRLYDRLFSVPN 481
            V KD  GNI  + CTYD ++      DGRKVKG +HWVSAAHA+  E+RLY++LF+V +
Sbjct: 433 EVVKDEAGNIVELRCTYDPESRGGSSPDGRKVKGTLHWVSAAHAVESEVRLYEQLFAVSD 492

Query: 482 PGAADD---FLSVINPESLVIKQGFAEPSLKDAVAGKAFQFEREGYFCLDSRHSTAEKPV 538
           P    +   F   +NP+SL + +   EPSL     G   QFER GYFC D   S    PV
Sbjct: 493 PDDVPEGGVFTDNLNPDSLKVVRAMLEPSLGGIEPGTKVQFERMGYFCADP-DSVPGAPV 551

Query: 539 FNRTVGLRDTWAKV 552
           FNRTV L+DTWAK+
Sbjct: 552 FNRTVTLKDTWAKL 565


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: 1019
Number of extensions: 45
Number of successful extensions: 5
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: 570
Length adjustment: 36
Effective length of query: 518
Effective length of database: 534
Effective search space:   276612
Effective search space used:   276612
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