Alignments for a candidate for glnA in Desulfovibrio vulgaris Miyazaki F

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Desulfovibrio vulgaris Miyazaki F

Align glutamine synthetase type III subunit (EC 6.3.1.2) (characterized)
to candidate 8500852 DvMF_1590 glutamine synthetase catalytic region (RefSeq)

Query= metacyc::SYNPCC7942_0169-MONOMER
         (723 letters)



>FitnessBrowser__Miya:8500852
          Length = 726

 Score =  854 bits (2207), Expect = 0.0
 Identities = 427/730 (58%), Positives = 537/730 (73%), Gaps = 11/730 (1%)

Query: 1   MSGNAARVNAVHQITNREPLPSKPPMSLEA-----IWAENVFDLSKMQARLPKAVFKSIK 55
           MSG  AR+NA+  ITN +P  S  PM+        ++  NVF+   M+ RLPK V+KS+K
Sbjct: 1   MSGIQARLNAISAITNYKP--SAAPMNFAETKPTELFGCNVFNDKVMKDRLPKTVYKSLK 58

Query: 56  NTIVTGQKLDPSVADAVATAMKDWAMSKGALYYAHVFYPMTNVTAEKHDGFISVQGDGKV 115
            TI  G+KLDPS+AD VA AMKDWA+ KGA ++ HVFYP+T +TAEKHD F+   G G  
Sbjct: 59  KTIELGEKLDPSIADVVANAMKDWAIEKGATHFTHVFYPLTGLTAEKHDAFLVPDGKGGA 118

Query: 116 ISEFSGKVLVQGEPDGSSFPNGGIRDTFEARGYTGWDVTSPAYIMETDNGSTLCIPTVFV 175
           +SEFSGK+L+QGEPD SSFP+GG+R TFEARGYT WDVTSPAY++E  NG+ LCIPT FV
Sbjct: 119 LSEFSGKLLIQGEPDASSFPSGGLRATFEARGYTAWDVTSPAYLLENPNGTFLCIPTAFV 178

Query: 176 SWTGEALDKKVPLLRSIAAMDKAARKVLTLLGNTEVSQVNSSCGAEQEYFLVDANFAAQR 235
           SWTGEALDKK PLLR+  A++K A++VL L G      + S  G EQEYFL+D NFA  R
Sbjct: 179 SWTGEALDKKTPLLRANQALNKQAQRVLKLFGTETKLPLVSYAGPEQEYFLIDRNFAFAR 238

Query: 236 PDLLLAGRTLFGRPSAKGQEFDDHYFGAIPERVQVFMQDVEETLYKLGIPAKTRHNEVAP 295
           PDL + GR+LFG   AKGQEF+D YFG IP RV  FM +VE  L+KLG+P KTRHNEVAP
Sbjct: 239 PDLHICGRSLFGAKPAKGQEFEDQYFGVIPRRVLSFMMEVERELFKLGVPVKTRHNEVAP 298

Query: 296 GQFEIAPFFEAANVASDHQQLIMTVLKQTAKKHGFMCLLHEKPFAGINGSGKHVNWSVGN 355
            Q+EIAP FE +N+A+DH QLIMTVL+  AK++G +CLLHEKPFAGINGSGKH+N+S+GN
Sbjct: 299 SQYEIAPIFETSNLATDHNQLIMTVLRSVAKRYGMVCLLHEKPFAGINGSGKHLNYSIGN 358

Query: 356 ATQGNLLDPGDSPHDNAQFLVFCGAVIRGVHKYGPLMRAAIATASNDHRLGANEAPPAIM 415
           A  G+L DPG+SPH+NAQFLVFC A IR VHKYG L+RA +A+ASNDHRLGANEAPPAIM
Sbjct: 359 ADLGSLFDPGESPHENAQFLVFCAAAIRAVHKYGALLRATVASASNDHRLGANEAPPAIM 418

Query: 416 SVYLGTQLEEVFEQIKTGTVTESKQKGIMDLGVDVLPYLTKDAGDRNRTSPFAFTGNRFE 475
           SVYLG QL +VFEQIKTG V   K+  +M++GVDVLP L  D GDRNRTSPFAFTGNRFE
Sbjct: 419 SVYLGEQLTDVFEQIKTGKVNGCKKACVMNIGVDVLPPLPMDPGDRNRTSPFAFTGNRFE 478

Query: 476 FRAVGASQSVSGPLIVLNTILADSLDWIGNRLESELAKG--LDLNTAILTVLKEVMEEHG 533
           FRAVG+S S++GP + LNT++A+SLD+I   LE +  KG    LN A+  +L+++M+EH 
Sbjct: 479 FRAVGSSMSIAGPQVALNTMMAESLDYIATELE-KATKGDPAKLNEAVQKLLQKIMKEHD 537

Query: 534 NVIFGGNGYSEEWHREAVEKRGLANLPTTADALPVLKEEYIEDLFKKTGVLTPVELESRF 593
            VIF G+GYSEEWH+EA E+RGL NL TT DALPVL    +  LF   GV +  E++SR 
Sbjct: 538 KVIFNGDGYSEEWHKEA-ERRGLPNLKTTPDALPVLSSPEVVKLFTSYGVFSEAEVKSRE 596

Query: 594 EVYAEQYILSIEVEAKLAVSIAKTIIYPAAVEYLAKLSGTIASLSGLGIDFEKESARKIA 653
           E+Y EQY  +++ EA L + +A+TII+PAA+ Y  +L+ T A+L   G D++  +   + 
Sbjct: 597 EIYLEQYCKTVKTEANLVIRMARTIIFPAAMRYQGELAATCANLKAAGHDYKVVTLEDVT 656

Query: 654 ELTSSLVGAATQLSEALEHESSDTVEHLQYCAKTLRPLMDNVRTYADALEAEVADSFWPL 713
               ++  A  +L + L+HE++ T    ++    + P M  VR YADALEA VAD  W L
Sbjct: 657 TKLRAMQAAVGELEKKLDHEAASTHAEAKHMCDVILPAMLKVREYADALEAVVADDLWAL 716

Query: 714 PTYQEMLFIK 723
           P+YQEMLFIK
Sbjct: 717 PSYQEMLFIK 726


Lambda     K      H
   0.316    0.133    0.383 

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: 1243
Number of extensions: 35
Number of successful extensions: 4
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: 723
Length of database: 726
Length adjustment: 40
Effective length of query: 683
Effective length of database: 686
Effective search space:   468538
Effective search space used:   468538
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)

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

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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