Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate Pf6N2E2_2177 Glutamine synthetase (EC 6.3.1.2), putative
Query= BRENDA::F2RM17 (446 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2177 Length = 451 Score = 159 bits (402), Expect = 2e-43 Identities = 119/369 (32%), Positives = 181/369 (49%), Gaps = 18/369 (4%) Query: 70 AVGEVRLVPDRSTFRVLDHEDSVAA-----VCCSLYEIDDQTPWAADPRSALSGFISTLA 124 A G++RLVPD S+ +++ A + C + E D + PW+A PR+ L + Sbjct: 69 AYGDLRLVPDLSSRVTVNNGPDAQAPVLDFIHCDVRETDGR-PWSACPRTLLQDEVERYR 127 Query: 125 DD-DVVPSTALESEFHFYTSEDGDDEPHGTRGLYATASMREFNDIVLETIDALEAQQINV 183 + + A E EF+ + D ++ + R+ + + AL A + Sbjct: 128 VELGLQVFAAFEHEFNLVATPAQPDCL-----AFSLQAQRQQAEFAGWLLSALRAGGVEP 182 Query: 184 KKHCPEYAAGQHELVTKHREGLTPVDDYVFLRETVAAIAESHGFETTFLPFPFETAT-NG 242 + PEY Q+E+ + G+ D V +RE IA G + +F P E A NG Sbjct: 183 EMFLPEYGQHQYEITCRPTLGVAAADRAVNVREITREIARQMGLDVSFAPKVSEHAVCNG 242 Query: 243 CHINLSLWNDTN--LFAPTDSDRALSSTGRHFVGGVLAHLPALLALTSPTVNSYARLQPQ 300 H++LSL + + + S LSS G+H+ GVL +LPAL ALT+PT SY RLQP Sbjct: 243 VHLHLSLQDLSADPVLHDAASSNGLSSLGQHWAAGVLHYLPALCALTAPTPVSYERLQPH 302 Query: 301 SGAAAFGCWGIGNREAAIRV-PEVPTNKRETATR--IEFRPADNTANPYLSLLGLLAAGW 357 +A++ C G NREAA+R+ P + + A + +EFR D TA+P+L++ LL AG Sbjct: 303 HWSASYACLGQRNREAALRICPTASLSGKPLANQYNLEFRAMDATASPHLAMAALLIAGR 362 Query: 358 DGVQNEIDPGRPLDEDPGNCSDELLDERGIERLPQTLGEALDALEKNEVLREALGEQLFD 417 G+Q + D+ P + RGI LP TL +ALD L + L E L L + Sbjct: 363 LGIQQRLALNAVTDQIPDELDEAQRRARGIIALPTTLAQALDCLRHSGALLETLPGPLVE 422 Query: 418 SYLTVKRHE 426 +Y +K E Sbjct: 423 TYFALKAQE 431 Lambda K H 0.317 0.134 0.402 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: 469 Number of extensions: 24 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: 446 Length of database: 451 Length adjustment: 33 Effective length of query: 413 Effective length of database: 418 Effective search space: 172634 Effective search space used: 172634 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: 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