Align Glutamate--putrescine ligase (EC 6.3.1.11) (characterized)
to candidate 6938541 Sama_2644 glutamate--ammonia ligase (RefSeq)
Query= reanno::MR1:200446 (451 letters) >FitnessBrowser__SB2B:6938541 Length = 451 Score = 791 bits (2044), Expect = 0.0 Identities = 383/451 (84%), Positives = 419/451 (92%) Query: 1 MNKLIAFLKERKITEVECVICDMTGIARGKIAPVDKFLDEKGMRLPESVLLQTVTGDFVD 60 M KLIAFLKE+KITEVECVI DMTGIARGKIAPVDKF+ E+GMRLPESVLLQTVTGD+V+ Sbjct: 1 MEKLIAFLKEKKITEVECVISDMTGIARGKIAPVDKFIAEQGMRLPESVLLQTVTGDYVN 60 Query: 61 DDIYYSLLDDADIDFVCVPDENAVFMLPWTIEATAQVIHDCYDRMGNPIELSPRNVLKKV 120 DD YY LL++AD+DF+CVPDENAVF LPW +EATAQVIHD YDRMGNPIELSPRNVLKKV Sbjct: 61 DDTYYELLNEADVDFLCVPDENAVFELPWCVEATAQVIHDVYDRMGNPIELSPRNVLKKV 120 Query: 121 LSLYDEKGWEPVIAPEMEFYLTSRSDDHDLPLKPPIGRSGRPEAGRQSFSIDAANEYDPL 180 L LY+EKGWEPV+APEMEFYL +R+ D DLPL PP+GRSG PEAGRQSFSIDAANEYDPL Sbjct: 121 LKLYEEKGWEPVVAPEMEFYLVARNGDPDLPLNPPLGRSGLPEAGRQSFSIDAANEYDPL 180 Query: 181 FEDMYDWCEIQGLDIDTLIHEDGPAQMEINFSHGNPLSLADQVFVFKRTLREAALKHNVC 240 FEDMY+WCE QGL IDTLIHEDGPAQMEINFSHGN LSLADQVFVFKRTLREAALKHNVC Sbjct: 181 FEDMYEWCEAQGLFIDTLIHEDGPAQMEINFSHGNALSLADQVFVFKRTLREAALKHNVC 240 Query: 241 ATFMAKPVTDEPGSAMHIHQSVINKETGKNIFTNEDGTQSALFLSYIAGLQKYIPEFLPL 300 ATFMAKPVT+EPGSAMHIHQSV++K+TGKNIFT EDGT+SA FL YIAGLQ++IPEFLPL Sbjct: 241 ATFMAKPVTNEPGSAMHIHQSVVDKKTGKNIFTKEDGTKSANFLGYIAGLQQFIPEFLPL 300 Query: 301 MAPNANSFRRFLPGTSAPVNLEWGIENRTCGLRIPESSPQNRRIENRIPGADANCYLAFA 360 MAP+ NSFRRFLPGTSAPVNLEWG ENRTCGLRIPESSPQNRRIENRIPGADANCYLA A Sbjct: 301 MAPSVNSFRRFLPGTSAPVNLEWGEENRTCGLRIPESSPQNRRIENRIPGADANCYLAIA 360 Query: 361 AGLLCGYIGMVEGLKPSTPVQGKANESRSNNPHCLPLTLEEALVAMEESDACKEYLGESF 420 A LL GYIGMVEGLKP+ P G+ANESR+ + +CLPLTLEEAL AM+ESDA ++YLG++F Sbjct: 361 ASLLAGYIGMVEGLKPTNPALGRANESRTADTNCLPLTLEEALTAMDESDAARKYLGDAF 420 Query: 421 TTGFVAVKQAELENFRRVVSSWEREFLLLSV 451 TTGFVAVKQAELENFRRVVS+WEREFLLL+V Sbjct: 421 TTGFVAVKQAELENFRRVVSAWEREFLLLTV 451 Lambda K H 0.319 0.137 0.414 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: 788 Number of extensions: 21 Number of successful extensions: 1 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: 451 Length of database: 451 Length adjustment: 33 Effective length of query: 418 Effective length of database: 418 Effective search space: 174724 Effective search space used: 174724 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 Sep 17 2021. The underlying query database was built on Sep 17 2021.
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