Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate H281DRAFT_03844 H281DRAFT_03844 L-glutamine synthetase (EC 6.3.1.2)
Query= BRENDA::P12425 (444 letters) >FitnessBrowser__Burk376:H281DRAFT_03844 Length = 478 Score = 187 bits (476), Expect = 5e-52 Identities = 137/467 (29%), Positives = 214/467 (45%), Gaps = 48/467 (10%) Query: 13 VKEENVKYIRLQFTDILGTIKNVEIPVSQLGKALDNKVMFDGSSIE-------------- 58 +KE V+ +R F D G ++ + V+ KA ++ V + + Sbjct: 25 LKESAVQVVRFSFPDQHGLLRGKTLVVADAIKAFESGVTLTSTLLAKDTSHRTVFPVFTA 84 Query: 59 --GFVRIEES---DMYLYPDLNTFVIFPWTAEKGKVARFICDIYNPDGTPFEGDPRNNLK 113 GF E D + D TF I PW G V +CD+Y P+G P R+ + Sbjct: 85 GGGFGMPEMQGACDTLMIADPQTFRILPWAPHTGWV---LCDLYFPNGRPVPFGTRHLFR 141 Query: 114 RILKEMEDLGFSDFNLGPEPEFFLFKL-------DEKGEPTL----ELNDKG-GYFDLAP 161 R L+ + + GF + G E EF +FKL + G+P L EL G Y Sbjct: 142 RALERLANQGF-ELVSGLEVEFHVFKLTNPNMKPEHSGQPGLPPDVELLSHGYQYLTELR 200 Query: 162 TDLGENCRRDIVLELEEMGFEIEASHHEVAPGQHEIDFKYAGAVRSCDDIQTFKLVVKTI 221 D ++ + ++ + + + E P Q E F ++S DD+ F+ VK I Sbjct: 201 YDAVDHVMEMLRNGIDGLELPVRSLEVEYGPSQFEFTFAPTKGIKSADDMILFRSAVKQI 260 Query: 222 ARKHGLHATFMPKPLF-GVNGSGMHCNLSL--FKNGVNAFFDENADLQLSETAKHFIAGI 278 +++G HATFM +P V SG H + SL NG NAF +A LS + ++AG+ Sbjct: 261 CQRNGYHATFMCRPRIPNVVSSGWHLHQSLVHIDNGSNAFMPSDATAPLSSVGQAYLAGL 320 Query: 279 VKHATSFTAVTNPTVNSYKRLVPGYEAPCYVAWSAQNRSPLIRI-PASRGISTRVEVRSV 337 + HA + TA++ PT+N Y+R P AP W NR ++R+ +TRVE R Sbjct: 321 LAHAQAATALSTPTINGYRRYRPYSNAPDRANWGCDNRGVMLRVLGGPNDPATRVENRVG 380 Query: 338 DPAANPYLALSVLLAAGLDGIKNKLEAPAPIDRNIYVMSKEERMENGIVDLPATLAEALE 397 +P ANPYL + +GLDG++ KLE P S + E LP +L +AL+ Sbjct: 381 EPTANPYLYFGSQVLSGLDGLQRKLELPP---------SADTPYETEAQSLPRSLGDALD 431 Query: 398 EFKSNEVMVKALGEHLFEHFIEAKEIEWDMFRTQVHPWEREQYMSQY 444 +++E + + G ++F + KE E + F +V WE +Y + Sbjct: 432 ALRADECLREGFGSAFIDYFCKLKEAEINRFNLEVTDWEHREYFETF 478 Lambda K H 0.319 0.137 0.406 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: 499 Number of extensions: 28 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: 444 Length of database: 478 Length adjustment: 33 Effective length of query: 411 Effective length of database: 445 Effective search space: 182895 Effective search space used: 182895 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: 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