Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate 6937000 Sama_1174 glutamate--ammonia ligase (RefSeq)
Query= BRENDA::O33342 (457 letters) >FitnessBrowser__SB2B:6937000 Length = 455 Score = 171 bits (434), Expect = 3e-47 Identities = 147/438 (33%), Positives = 201/438 (45%), Gaps = 20/438 (4%) Query: 23 VDTVIVAFTDMQGRLAGKRISGRHFVDDIATRGVECCSYLLAVDVDLNTVPGYAMASWDT 82 V V V D G GK + R V + G S +L + V + V + W+ Sbjct: 19 VQHVEVFIIDPNGIPRGKLLH-RQEVLSMYRHGRPLPSTILGLTVQGDDVEDTGLV-WEV 76 Query: 83 GYGDMVMTPDLSTLRLIPW-LPGTALVIADLVWADGSEVAVS-PRSILRRQLDRLKARGL 140 G D + P L + PW TA V + G AV+ PR +L + +D L+A G Sbjct: 77 GDADCLAFPIEGGLLMQPWRAQPTAQVHLTMHPEAGMPAAVADPRLVLSKVIDSLQADGF 136 Query: 141 VADVATELEFIVFDQPYRQAWASGYRGLTPASDYNID-----YAILASSRMEPLLRDIRL 195 +A ELEF + DQ + A+G SD + Y IL R++P L D+ Sbjct: 137 YPVMAAELEFFLLDQRFD---ANGRPQPAMQSDGHRPHQTQVYGILELERLQPFLDDLYH 193 Query: 196 GMAGAGLRFEAVKGECNMGQQEIGFRYD-EALVTCDNHAIYKNGAKEIADQHGKSLTFMA 254 G+ E GQ EI + +AL D YK K +A +HG FMA Sbjct: 194 ACEVQGIPARTAISEYAPGQVEITLEHRFDALQAMDEAVRYKRLVKGVAAKHGMQACFMA 253 Query: 255 K-YDEREGNSCHIHVSLRGTDGSAVFADSNGPHGMSSMFRSFVAGQLATLREFTLCYAPT 313 K + E G+ H+HVSL DG+ FA N P G + +S +AG +ATL + L + P Sbjct: 254 KPFGELAGSGMHMHVSLADADGNNRFASDN-PEGTPELTQS-IAGMMATLEDAQLLFCPN 311 Query: 314 INSYKRFADSSFAPTALAWGLDNRTCALRVVGHGQNIR-VECRVPGGDVNQYLAVAALIA 372 NS++RF +S+AP A WG++NRT + RV G R VE R+ G D N YLA AA++A Sbjct: 312 ANSFRRFQSASYAPIAKTWGVNNRTVSFRVPGGPAPSRHVEHRICGADANPYLAAAAILA 371 Query: 373 GGLYGIERGLQLPEPCVGNAYQGADVERLPVTLADAAVLFEDSALVREAFGEDVVAHYLN 432 +GI L + VGN Y+G + LP A FE S ++ GED Y Sbjct: 372 ACHHGIRNQLSPGQAIVGNGYEGKH-QTLPTDWLSALTNFERSEWMKSVLGEDFHRIYGR 430 Query: 433 NARVELAAFNAAV--TDW 448 R E F A V DW Sbjct: 431 IKRAEYQEFMAEVGQQDW 448 Lambda K H 0.321 0.137 0.417 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: 531 Number of extensions: 29 Number of successful extensions: 7 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: 457 Length of database: 455 Length adjustment: 33 Effective length of query: 424 Effective length of database: 422 Effective search space: 178928 Effective search space used: 178928 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 (21.9 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