Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_012406835.1 NPUN_RS00025 glutamine synthetase
Query= BRENDA::P36687 (439 letters) >NCBI__GCF_000020025.1:WP_012406835.1 Length = 496 Score = 182 bits (461), Expect = 3e-50 Identities = 138/408 (33%), Positives = 197/408 (48%), Gaps = 44/408 (10%) Query: 63 DLVFKADPDTYVEVPWDNVARVYGFI-----YKDNKPYGADPRGILKRALEELEKEGYKA 117 +LV DPDT+ VPW A+ GFI +++ +P RGIL+++L +L + G + Sbjct: 101 NLVAVPDPDTFKIVPW---AKRTGFILCDEYFQNGQPMPFSSRGILRQSLIDLHQRGLEH 157 Query: 118 YIGPEPEFYLFKKNGTWELEIPDVGGY---------------FDILTLD---KARDIRRE 159 +G E E+YL K L I +VG F L + +D+ Sbjct: 158 IVGLEVEWYLAKLEDPM-LAIANVGSSGKPGEPAKVSAVDHSFQYLLESHNPEIQDLLGL 216 Query: 160 IAEYMPSFGLIPEVLHHEVGKAQHEIDFRYDEALKTADNIVSFKYITKAVAEMHGLYATF 219 +AE + L + +E G Q E F AL+ AD ++ F+ TK + G A+F Sbjct: 217 LAENLVEMKLPLRSVENEGGVGQFEFTFDPIPALQAADTMMIFRMATKQICRQQGYIASF 276 Query: 220 MPKP-LFGFPGNGMHLHISLSK--DGENVFMGEEG---LSEIALHFIGGILKHAKALIAV 273 M +P L G NG HLH SL GEN FM S++A HF+GG+LKHA A Sbjct: 277 MCRPGLQGSSSNGWHLHQSLVDLTTGENAFMSANSQTLTSDLAKHFVGGLLKHANAASVF 336 Query: 274 TNPTVNSYKRLVPGYEAPVYISWGYRNRSALIRVP-AFWGKGARIEYRCPDPSANPYFAF 332 T PT+N YKR P AP WG NR A+IR+ F IE R +P+ANPY Sbjct: 337 TTPTINGYKRFRPYSLAPDRAGWGLENRGAMIRLQGGFDDPSTHIENRVGEPAANPYLYM 396 Query: 333 AAVLKAGLDGIKHKIDPFAYVEENVYEMSEEKRKELGIETLPGSLGEALEELEKDKVVKE 392 A+ L +GLDG+ K+DP + EE + LP SL EA+ L + ++ + Sbjct: 397 ASQLISGLDGVDCKLDPGSPTEEPYTTEN---------PILPKSLSEAISYLSQSELFPQ 447 Query: 393 ALGDAYKNF-INYKWKEWESYLEYLEEKHMPKDTKKVTEWELERYFFL 439 +G + NF I K E +L+ + ++ + K+VT WE YF L Sbjct: 448 KMGQQFINFIIKMKESEINRFLQSVADQPPEEYLKQVTNWEQREYFEL 495 Lambda K H 0.318 0.139 0.419 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: 574 Number of extensions: 28 Number of successful extensions: 5 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: 439 Length of database: 496 Length adjustment: 33 Effective length of query: 406 Effective length of database: 463 Effective search space: 187978 Effective search space used: 187978 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 10 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