GapMind for Amino acid biosynthesis

 

Aligments for a candidate for gltX in Desulfovibrio vulgaris Miyazaki F

Align glutamine-tRNA ligase (EC 6.1.1.18); glutamate-tRNAGln ligase (EC 6.1.1.24) (characterized)
to candidate 8500742 DvMF_1485 glutaminyl-tRNA synthetase (RefSeq)

Query= BRENDA::P00962
         (554 letters)



>lcl|FitnessBrowser__Miya:8500742 DvMF_1485 glutaminyl-tRNA
           synthetase (RefSeq)
          Length = 569

 Score =  684 bits (1765), Expect = 0.0
 Identities = 337/548 (61%), Positives = 410/548 (74%), Gaps = 7/548 (1%)

Query: 10  NFIRQIIDEDLASGKHTT-VHTRFPPEPNGYLHIGHAKSICLNFGIAQDYKGQCNLRFDD 68
           +FIR +I  D A+G+  + VHTRFPPEPNGYLHIGHAKSICLNFG+A+++ G+CNLRFDD
Sbjct: 18  DFIRALITADNANGRFDSRVHTRFPPEPNGYLHIGHAKSICLNFGVAREFGGKCNLRFDD 77

Query: 69  TNPVKEDIEYVESIKNDVEWLGFHWSGNVRYSSDYFDQLHAYAIELINKGLAYVDELTPE 128
           TNP+KE  EYV+SI+ DV+WLG  W G   Y+SDYF+QL+ YA +LI  G AYVD L+ +
Sbjct: 78  TNPLKESQEYVDSIREDVKWLGGDWQGREFYASDYFEQLYQYAEQLILAGKAYVDSLSAD 137

Query: 129 QIREYRGTLTQPGKNSPYRDRSVEENLALFEKMRAGGFEEGKACLRAKIDMASPFIVMRD 188
           +IRE+RGTLT PGK SPYR+RSVEENL LF +MRAG F++G+  LRAKIDMASP +VMRD
Sbjct: 138 EIREHRGTLTAPGKESPYRNRSVEENLDLFRRMRAGEFKDGEHVLRAKIDMASPNVVMRD 197

Query: 189 PVLYRIKFAEHHQTGNKWCIYPMYDFTHCISDALEGITHSLCTLEFQDNRRLYDWVLDNI 248
           P LYRI+ A HH+TG+ WCIYPMYD+THCISD++EGITHS+CTLEF +NR LYDW LD +
Sbjct: 198 PTLYRIRHAHHHRTGDAWCIYPMYDYTHCISDSIEGITHSICTLEFVNNRELYDWTLDTL 257

Query: 249 TIPVHPRQYEFSRLNLEYTVMSKRKLNLLVTDKHVEGWDDPRMPTISGLRRRGYTAASIR 308
            +  HP+Q EF+RLNL YTV+SKRKL  LV   +V GWDDPRMPTISGLRRRG T  +++
Sbjct: 258 GV-YHPQQLEFARLNLTYTVLSKRKLIQLVEGGYVNGWDDPRMPTISGLRRRGVTPEALQ 316

Query: 309 EFCKRIGVTKQDNTIEMASLESCIREDLNENAPRAMAVIDPVKLVIENY-QGEGEMVTMP 367
           +FC RIGV K D+ ++ + LE C+RE LN  APR M V+DP+K+VIENY   + E   MP
Sbjct: 317 DFCARIGVAKADSVVDFSLLEFCMREHLNAVAPRVMGVLDPIKVVIENYPDDQVETFDMP 376

Query: 368 NHPNKPEMGSRQVPFSGEIWIDRADFREEANKQYKRLVLGKEVRLRNAYVIKAERVEKDA 427
            HP     GSR VPFS  ++I+R DFRE+  K+Y RL  G EVRLR AY I    V KDA
Sbjct: 377 YHPEDTSHGSRTVPFSKVLYIERDDFREDPPKKYHRLAPGAEVRLRYAYYITCREVVKDA 436

Query: 428 EGNITTIFCTYDADTLSKDPADGRKVKGVIHWVSAAHALPVEIRLYDRLFSVPNPGAADD 487
           +GNIT + CTYD  T      DGRKVKG IHWVSAAHAL  E+RLY+ LFSV NP AA++
Sbjct: 437 DGNITELRCTYDPATKGGWSQDGRKVKGTIHWVSAAHALHAEVRLYEHLFSVENPNAAEE 496

Query: 488 ---FLSVINPESLVIKQGFAEPSLKDAVAGKAFQFEREGYFCLDSRHSTAEKPVFNRTVG 544
              F+  +NP+SL       EP+L D   G   QFER GYFC D +  T  KPVFNRTVG
Sbjct: 497 GKTFVDYLNPDSLKTVTAMLEPALADVAPGTRVQFERIGYFCAD-KDGTPGKPVFNRTVG 555

Query: 545 LRDTWAKV 552
           LRD+WAK+
Sbjct: 556 LRDSWAKI 563


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: 1050
Number of extensions: 49
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: 569
Length adjustment: 36
Effective length of query: 518
Effective length of database: 533
Effective search space:   276094
Effective search space used:   276094
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, 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