GapMind for Amino acid biosynthesis

 

Alignments for a candidate for glnA in Lacinutrix algicola AKS293

Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_055435843.1 ASC41_RS06575 glutamine synthetase

Query= BRENDA::Q5LGP1
         (729 letters)



>NCBI__GCF_001418085.1:WP_055435843.1
          Length = 728

 Score =  873 bits (2255), Expect = 0.0
 Identities = 426/730 (58%), Positives = 556/730 (76%), Gaps = 5/730 (0%)

Query: 1   MSKMRFFALQELSNRKPLEITTPSNKLSDYYASHVFDRKKMQEYLPKEAYKAVVDATEKG 60
           MS +RFFA++E  NRKP+ IT    + S+ +  +V+D KKM++ L  +A+ ++ +A EKG
Sbjct: 1   MSTLRFFAIKETLNRKPVVITEEKRR-SEIFGQNVYDSKKMRQTLTSDAFVSLTNAIEKG 59

Query: 61  TPISREMADLIANGMKSWAKSLNVTHYTHWFQPLTDGTAEKHDGFIEFGEDGEVIERFSG 120
             I R +AD IA+ MK WA S  VTHYTHWFQPLT  TAEKHD F E  E+   IE+F G
Sbjct: 60  GKIDRTIADQIASAMKDWALSKGVTHYTHWFQPLTGATAEKHDAFFETIENNGAIEKFGG 119

Query: 121 KLLIQQEPDASSFPNGGIRNTFEARGYTAWDVSSPAFVVDTTLCIPTIFISYTGEALDYK 180
             L+QQEPDASSFPNGGIRNTFEARGYTAWD +SPAF+  TTLCIPT+F++YTGEALDYK
Sbjct: 120 TQLVQQEPDASSFPNGGIRNTFEARGYTAWDPTSPAFIYGTTLCIPTVFVAYTGEALDYK 179

Query: 181 TPLLKALAAVDKAATEVCQLFDKNITRVFTNLGWEQEYFLVDTSLYNARPDLRLTGRTLM 240
           TPLL+AL AVD AA  VC+ FDKN+ +V  +LGWEQEYFL+D++L ++RPD++LTGRTL+
Sbjct: 180 TPLLRALQAVDNAAVAVCKYFDKNVKKVNASLGWEQEYFLIDSALVSSRPDIQLTGRTLL 239

Query: 241 GHSSAKDQQLEDHYFGSIPPRVTAFMKELEIECHKLGIPVKTRHNEVAPNQFELAPIFEN 300
           GH+SAK QQL+DHYFG+IP R  ++M++LE EC  LGIPVKTRHNEVAPNQFELAPI+E 
Sbjct: 240 GHASAKGQQLDDHYFGTIPNRAMSYMRDLETECMLLGIPVKTRHNEVAPNQFELAPIYEE 299

Query: 301 CNLANDHNQLVMDLMKRIARKHHFAVLFHEKPYNGVNGSGKHNNWSLCTDTGINLFAPGK 360
            NLA DHN L+MD+M ++A +H+F VLFHEKP+ G+NGSGKHNNWSL TDTG+NL +PGK
Sbjct: 300 ANLAVDHNALLMDVMDKVAERHNFKVLFHEKPFRGINGSGKHNNWSLSTDTGVNLLSPGK 359

Query: 361 NPKGNMLFLTFLVNVLMMVHKNQDLLRASIMSAGNSHRLGANEAPPAILSIFLGSQLSAT 420
            P  N+ FLTF +N +  V+ N++LLRA+I SA N HRLGANEAPPAI+S+F+G QL+  
Sbjct: 360 TPMSNLQFLTFFINTIKAVNDNEELLRAAIASASNDHRLGANEAPPAIISVFIGEQLTHV 419

Query: 421 LDEIVRQVTNSKMTPEEKTTLKLG-IGRIPEILLDTTDRNRTSPFAFTGNRFEFRAAGSS 479
           L+E+   VTN K++P+EKT LKL  +G+IPEILLD TDRNRTSPFAFTGN+FEFRA GS 
Sbjct: 420 LNEL-ENVTNGKLSPQEKTDLKLNVVGKIPEILLDNTDRNRTSPFAFTGNKFEFRAVGSK 478

Query: 480 ANCAAAMIAINAAMANQLNEFKASVDKLM-EEGIGKDEAIFRILKENIIASEPIRFEGDG 538
           ANCA  M  +N+ +A QL +FK  VD L+ ++ + KDEA+F IL+E I  S+ + FEG+G
Sbjct: 479 ANCANPMTLLNSIVAKQLIDFKVEVDALIAKKDLKKDEAVFNILREYIKKSKAVLFEGNG 538

Query: 539 YSEEWKQEAARRGLTNICHVPEALMHYMDNQSRAVLIGERIFNETELACRLEVELEKYTM 598
           Y E W++EA +RGL+N    PEAL   +  ++ ++     + NETE+  R E+ELE Y M
Sbjct: 539 YGEAWEKEAKKRGLSNNKSTPEALKVKVSKKALSLYKDLGVMNETEVVARYEIELEDYIM 598

Query: 599 KVQIESRVLGDLAINHIVPIAVSYQNRLLENLCRMKEIFSEEEYEVMSADRKELIKEISH 658
           ++QIE RVLGDLA NH+VP AV YQN L+EN+  +KEI+ E++++ +S  + ELI+EIS 
Sbjct: 599 RIQIEGRVLGDLARNHVVPTAVKYQNILIENVKGLKEIY-EKDFKKVSKAQLELIEEISK 657

Query: 659 RVSAIKVLVRDMTEARKVANHKENFKEKAFAYEETVRPYLESIRDHIDHLEMEIDDEIWP 718
            + +I  LV +MT+ R+ +N  ++ ++K+  Y   V+P  E IR H D LE+ +DDE+WP
Sbjct: 658 HIESINKLVTNMTDIRRKSNLIKSLEDKSIVYCNKVKPLFEEIRYHCDKLELLVDDELWP 717

Query: 719 LPKYRELLFT 728
           L KYRELLFT
Sbjct: 718 LTKYRELLFT 727


Lambda     K      H
   0.319    0.134    0.390 

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: 1262
Number of extensions: 46
Number of successful extensions: 6
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: 729
Length of database: 728
Length adjustment: 40
Effective length of query: 689
Effective length of database: 688
Effective search space:   474032
Effective search space used:   474032
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 (21.7 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

Links

Downloads

Related tools

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