Align Glutamine synthetase; GS; EC 6.3.1.2; Glutamate--ammonia ligase (uncharacterized)
to candidate GFF1448 PS417_07365 glutamine synthetase
Query= curated2:P23794 (471 letters) >FitnessBrowser__WCS417:GFF1448 Length = 456 Score = 109 bits (273), Expect = 2e-28 Identities = 106/399 (26%), Positives = 158/399 (39%), Gaps = 33/399 (8%) Query: 73 PVPETMTLIPWSP-GVARVLCKVFWGGGKGRFERDPRFIAEEAEKYQTEQGYTSYYGPEL 131 P+ ++ +PW A V + G DPR + + GY EL Sbjct: 86 PISGSLQRMPWRLIPTAAVQVSMHLTEGLPATVADPRHLLAKVIDALKADGYYPVMAAEL 145 Query: 132 EFFMFDKVKLDVSAPQSGTGYKIYAREAPWSDSGTFVIRFKEGYYPAPPVDQLMDVRVEI 191 EF++ D+ PQ AR+ + + Y ++Q+ ++ Sbjct: 146 EFYLLDQKPDSNGRPQP-------ARDVDGGRPRSTQV------YGLRELEQIEPFLADL 192 Query: 192 VDTLVKYFGYTIEATHHEVATAGQGEIDFRF-STLVDTADKVQTLKYVAKNIAAKHGLVV 250 K G E A GQ EI S + D+ K + K +A +HG+ Sbjct: 193 YSAC-KLQGIPARTAISEYAP-GQVEITLEHRSDALQAMDEAVRYKRLVKGVAHQHGMTA 250 Query: 251 TFMPKPIYGDNGTGMHTHLSLWTKDGKKNLMYDPNDEYAEISQFGRYVIGGLLTHARALS 310 FM KP GTGMH H+SL D + N ++ E + + R +GG+L+ Sbjct: 251 CFMAKPFDDLAGTGMHMHVSL--ADAQGNNLF--ASEATDGTPLLRQAVGGMLSTLLDSL 306 Query: 311 AIVSPTVNSYRRLIPGFEAPVYIAWSKGNRSAVIRVPAYYRGMEKAKRIEYRPPDPSTNP 370 + P NSYRR AP+ W NR+ +RVP G ++ IE+R NP Sbjct: 307 LMFCPNANSYRRFQTNSYAPLAATWGVDNRTVSLRVPG---GPANSRHIEHRICGADANP 363 Query: 371 YLAFAALLMAALDGVNKKIDPGDPVDENIYHLTPEKRRQLGIKELPRSLNEALDELESDK 430 YLA AA+L G+ ++ DPG PV+ N Y LP L LE Sbjct: 364 YLAAAAILAGIHRGIREQRDPGAPVEGNGY--------AQATALLPTDWLTTLRALEG-S 414 Query: 431 EFLKPVFNSSILDTYIDLKRDEARSLQGYPHPMELYYYL 469 + + F + LD Y+ +KR E R G + +YL Sbjct: 415 SWAREAFGTEFLDVYLAVKRAEYRQFMGEVGAQDWRWYL 453 Lambda K H 0.318 0.138 0.415 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: 515 Number of extensions: 23 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 471 Length of database: 456 Length adjustment: 33 Effective length of query: 438 Effective length of database: 423 Effective search space: 185274 Effective search space used: 185274 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 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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:
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