Alignments for a candidate for glnA in Mycolicibacterium vanbaalenii PYR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Mycolicibacterium vanbaalenii PYR-1

Align glutamine synthetase type III subunit (EC 6.3.1.2) (characterized)
to candidate WP_011781186.1 MVAN_RS20190 glutamine synthetase

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



>NCBI__GCF_000015305.1:WP_011781186.1
          Length = 725

 Score =  859 bits (2220), Expect = 0.0
 Identities = 428/725 (59%), Positives = 535/725 (73%), Gaps = 4/725 (0%)

Query: 1   MSGNAARVNAVHQITNREP--LPSKPPMSLEAIWAENVFDLSKMQARLPKAVFKSIKNTI 58
           MSGNA R+ A++ +    P  +   P  +   I+  NVF  ++MQ RLPK+V+KS+  TI
Sbjct: 1   MSGNAVRLQAINNVEAYVPPAISFDPTEAPGQIFGSNVFTKAEMQLRLPKSVYKSVVATI 60

Query: 59  VTGQKLDPSVADAVATAMKDWAMSKGALYYAHVFYPMTNVTAEKHDGFISVQGDGKVISE 118
             G KLDP++ADAVA+AMKDWA+SKGA +YAHVFYPMT +TAEKHD F+    DG+ ++E
Sbjct: 61  EKGAKLDPAIADAVASAMKDWALSKGATHYAHVFYPMTGLTAEKHDSFLEPISDGETLAE 120

Query: 119 FSGKVLVQGEPDGSSFPNGGIRDTFEARGYTGWDVTSPAYIMETDNGSTLCIPTVFVSWT 178
           F+GK L+QGEPD SSFP+GG+R TFEARGYTGWDVTSPAYI+E  NG+TLCIPTVFVS T
Sbjct: 121 FAGKTLIQGEPDASSFPSGGLRSTFEARGYTGWDVTSPAYILENPNGNTLCIPTVFVSMT 180

Query: 179 GEALDKKVPLLRSIAAMDKAARKVLTLLGNTEVSQVNSSCGAEQEYFLVDANFAAQRPDL 238
           GEALD K PLLRS  AM   A ++L L G+  + +V S CG EQEYFLVD +F   RPDL
Sbjct: 181 GEALDYKTPLLRSQQAMGVHAERILALFGHDNLQKVVSFCGPEQEYFLVDRHFFLARPDL 240

Query: 239 LLAGRTLFGRPSAKGQEFDDHYFGAIPERVQVFMQDVEETLYKLGIPAKTRHNEVAPGQF 298
           + AGRTLFG    KGQEFDDHYFGA+PERV  FM D E  L+KLGIPAKTRHNEVAP QF
Sbjct: 241 VNAGRTLFGAKPPKGQEFDDHYFGAVPERVLGFMMDTERELFKLGIPAKTRHNEVAPAQF 300

Query: 299 EIAPFFEAANVASDHQQLIMTVLKQTAKKHGFMCLLHEKPFAGINGSGKHVNWSVGNATQ 358
           E+AP FE AN+ASDHQQL+MTV K  AKKHG  CL HEKPFAG+NGSGKHVN+SVGNA  
Sbjct: 301 EVAPMFERANIASDHQQLLMTVFKTVAKKHGMECLFHEKPFAGVNGSGKHVNFSVGNADL 360

Query: 359 GNLLDPGDSPHDNAQFLVFCGAVIRGVHKYGPLMRAAIATASNDHRLGANEAPPAIMSVY 418
           G+LL PGD+PH+NAQFLVFC A+IR VHK+G L+R ++A+A+NDHRLGANEAPPAI+S++
Sbjct: 361 GSLLVPGDTPHENAQFLVFCAAIIRAVHKFGGLLRVSVASATNDHRLGANEAPPAIISIF 420

Query: 419 LGTQLEEVFEQIKTGTVTESKQKGIMDLGVDVLPYLTKDAGDRNRTSPFAFTGNRFEFRA 478
           LG QL +VF+QI  G  T SK KG+M +GVD LP L  D GDRNRTSPFAFTGNRFEFRA
Sbjct: 421 LGEQLADVFDQIAKGAATSSKGKGVMHIGVDTLPTLPTDPGDRNRTSPFAFTGNRFEFRA 480

Query: 479 VGASQSVSGPLIVLNTILADSLDWIGNRLESELAKGLDLNTAILTVLKEVMEEHGNVIFG 538
            G+ Q+V+ P+I+LNTI+ADS D++   LE  +A G+D ++A+ T+L E++ EHG V+F 
Sbjct: 481 PGSGQTVAVPMIILNTIMADSFDYMATALEKAVAGGVDFDSAVQTLLTEIITEHGAVVFN 540

Query: 539 GNGYSEEWHREAVEKRGLANLPTTADALPVLKEEYIEDLFKKTGVLTPVELESRFEVYAE 598
           G+GYSE W  EA E RGL NL TT DA+P L +    ++F++ GV +  EL SR+EV  E
Sbjct: 541 GDGYSENWQIEAAE-RGLPNLKTTLDAIPELIKPAAVEVFERYGVFSERELHSRYEVRLE 599

Query: 599 QYILSIEVEAKLAVSIAKTIIYPAAVEYLAKLSGTIASLSGLGIDFEKESARKIAELTSS 658
           QY L+I VEAKLA+ +  T+I PAA+ Y  +L+  +A+L   G+D +    + ++   + 
Sbjct: 600 QYALTIAVEAKLALELGTTVILPAAIRYQTELAQNVATLKAAGMDADTTLLQAVSAPIAE 659

Query: 659 LVGAATQLSEALEHESSDT-VEHLQYCAKTLRPLMDNVRTYADALEAEVADSFWPLPTYQ 717
           L  A   L  AL   S +T ++   +  + L P M+ VRT AD LE  VAD  WPLPTYQ
Sbjct: 660 LTTALGALKAALSGHSGETALDEATHAQQALLPAMEAVRTAADTLETVVADDLWPLPTYQ 719

Query: 718 EMLFI 722
           EML+I
Sbjct: 720 EMLYI 724


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: 1366
Number of extensions: 53
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: 723
Length of database: 725
Length adjustment: 40
Effective length of query: 683
Effective length of database: 685
Effective search space:   467855
Effective search space used:   467855
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 10 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