Alignments for a candidate for glnA in Maridesulfovibrio bastinii DSM 16055

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Maridesulfovibrio bastinii DSM 16055

Align glutamine synthetase type III subunit (EC 6.3.1.2) (characterized)
to candidate WP_027180554.1 G496_RS0118300 glutamine synthetase III

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



>NCBI__GCF_000429985.1:WP_027180554.1
          Length = 727

 Score =  840 bits (2170), Expect = 0.0
 Identities = 426/735 (57%), Positives = 535/735 (72%), Gaps = 20/735 (2%)

Query: 1   MSGNAARVNAVHQITNRE----PL--PSKPPMSLEAIWAENVFDLSKMQARLPKAVFKSI 54
           MSG  +R NA++ + N +    PL     PP     ++  NVF    M+  LPK +FKSI
Sbjct: 1   MSGYQSRQNAINAVNNYKRTTAPLNFTETPPTE---VFGSNVFSEKVMRKMLPKDIFKSI 57

Query: 55  KNTIVTGQKLDPSVADAVATAMKDWAMSKGALYYAHVFYPMTNVTAEKHDGFISVQGDGK 114
           K TI  G KLDP+VAD VA AMK+WA+SKGA +Y HVFYP+T +TAEKHDGF+S  G+G 
Sbjct: 58  KKTIKHGTKLDPAVADYVAAAMKEWAVSKGATHYTHVFYPLTGLTAEKHDGFLSPDGEGG 117

Query: 115 VISEFSGKVLVQGEPDGSSFPNGGIRDTFEARGYTGWDVTSPAYIMETDNGSTLCIPTVF 174
            I+EFSGK+L+QGEPD SSFPNGGIR TFEARGYT WDVT+PAYI+E  NG+ LCIPT F
Sbjct: 118 AIAEFSGKLLIQGEPDASSFPNGGIRTTFEARGYTAWDVTNPAYILENPNGTFLCIPTCF 177

Query: 175 VSWTGEALDKKVPLLRSIAAMDKAARKVLTLLGNTEVSQVNSSCGAEQEYFLVDANFAAQ 234
           VSWTGEALDKK PL+RS  AM+K A+++L L GN     V S+ G EQEYFL+D NF   
Sbjct: 178 VSWTGEALDKKTPLMRSSQAMNKQAQRILKLFGNDNGELVVSNAGPEQEYFLIDRNFFFS 237

Query: 235 RPDLLLAGRTLFGRPSAKGQEFDDHYFGAIPERVQVFMQDVEETLYKLGIPAKTRHNEVA 294
           RPDLL++GRT+FG   AKGQEFDDHYFGAIP RV  FM DVE  LYKLG+P KTRHNEVA
Sbjct: 238 RPDLLVSGRTVFGSKPAKGQEFDDHYFGAIPRRVLSFMMDVEHELYKLGVPIKTRHNEVA 297

Query: 295 PGQFEIAPFFEAANVASDHQQLIMTVLKQTAKKHGFMCLLHEKPFAGINGSGKHVNWSVG 354
           PGQFEIAP +E +N+A+DH Q++MT LK  AKKHG  CLLHEKPFAGINGSGKH+N+S+ 
Sbjct: 298 PGQFEIAPLYEQSNLATDHNQMVMTTLKTVAKKHGMACLLHEKPFAGINGSGKHLNYSLS 357

Query: 355 NATQGNLLDPGDSPHDNAQFLVFCGAVIRGVHKYGPLMRAAIATASNDHRLGANEAPPAI 414
             + G+L DPGD+PH+NAQFL+ C A IR VHKYG L+RA +A+A NDHRLGANEAPPAI
Sbjct: 358 TPSLGSLYDPGDTPHENAQFLLVCAATIRAVHKYGKLLRAVVASAGNDHRLGANEAPPAI 417

Query: 415 MSVYLGTQLEEVFEQIKTGTVTESKQKGIMDLGVDVLPYLTKDAGDRNRTSPFAFTGNRF 474
           +SVYLG QL  +  QIK G V+ESK K  + +GVD +P L +DAGDRNRTSPFAFTGNRF
Sbjct: 418 LSVYLGDQLTSILNQIKEGKVSESKCKENLKIGVDTIPPLPRDAGDRNRTSPFAFTGNRF 477

Query: 475 EFRAVGASQSVSGPLIVLNTILADSLDWIGNRLESELAKG--LDLNTAILTVLKEVMEEH 532
           EFRAVG++ S++GP + LNT++A+SLD+   ++E E+  G    L+ A+  V++++M+EH
Sbjct: 478 EFRAVGSNMSIAGPQVALNTMVAESLDYCATKIE-EITGGDCKKLHDAVEQVIRDIMKEH 536

Query: 533 GNVIFGGNGYSEEWHREAVEKRGLANLPTTADALPVLKEEYIEDLFKKTGVLTPVELESR 592
             V+F G+GYSEEWH+EA EKRGL NL  +A+ALPVL +  + +LF K  V T  EL+SR
Sbjct: 537 EAVVFNGDGYSEEWHKEA-EKRGLPNLRNSAEALPVLNDPEVIELFTKYEVFTERELDSR 595

Query: 593 FEVYAEQYILSIEVEAKLAVSIAKTIIYPAAVEYLAKLSGTIASLSGLGIDFEKESARKI 652
            E+Y EQY  ++  EA + + +  T I+PAAV Y  +L+ T A+L  +G D     +  +
Sbjct: 596 REIYLEQYSQTLRTEAAVCIKMGTTQIFPAAVRYQNELAQTCANLKAIGKD---SVSLTL 652

Query: 653 AELTSSLVGAATQLSE----ALEHESSDTVEHLQYCAKTLRPLMDNVRTYADALEAEVAD 708
            ++T+ L G  T L+E      + + +D +E  +Y   TL P M  VR YADALE  VAD
Sbjct: 653 DDVTAKLRGLQTSLTELESILAKEDFADALEEAKYLCYTLLPAMGKVREYADALEEVVAD 712

Query: 709 SFWPLPTYQEMLFIK 723
             WPLP+YQEMLFIK
Sbjct: 713 DLWPLPSYQEMLFIK 727


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: 1255
Number of extensions: 47
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: 727
Length adjustment: 40
Effective length of query: 683
Effective length of database: 687
Effective search space:   469221
Effective search space used:   469221
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 Jul 25 2024. The underlying query database was built on Jul 25 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