Align arginase (EC 3.5.3.1) (characterized)
to candidate GFF1960 PGA1_c19930 agmatinase SpeB
Query= BRENDA::Q61176 (323 letters) >FitnessBrowser__Phaeo:GFF1960 Length = 322 Score = 89.0 bits (219), Expect = 1e-22 Identities = 85/294 (28%), Positives = 127/294 (43%), Gaps = 56/294 (19%) Query: 8 LEIIGAPFSKGQP-RGGVEKGPAALRKAGLLEKLKE---------TEYDVRDHGDLAF-- 55 + + G PF + R G GP A+R+A L+ E + + D+GDLAF Sbjct: 48 IAVTGVPFDQAVTNRPGTRLGPRAIREASCLQSPDEPYGWPHKPLSTLAIADYGDLAFDH 107 Query: 56 VDVPNDSSFQIVKNPRSVGKANEELAGVVAEVQKNGRVSVVLGGDHSLAVGSISGHARVH 115 DVP + + + G++A SVVLGGDH ++ + +A H Sbjct: 108 ADVPAFPA-----------ALTDHIRGILA----TETASVVLGGDHYISFPILKAYAEKH 152 Query: 116 PDLCVIWVDAHTDINTPLTTSSGNLHGQPVSFLLKELKGKFPDVPGFSWVTPCISAKDIV 175 + ++ DAHTD P HG + K +K + K V Sbjct: 153 GPISLLQFDAHTD-TWPDDNMDRIDHG---TMFYKAVK------------MGLVDPKTSV 196 Query: 176 YIGLRDVDPGEHYIIKTLGIKYFSMTEVDKLGIGKVMEETFSYLLGRKKRPIHLSFDVDG 235 +G+R + TLG+ V +G + + +LG RP +L+FD+D Sbjct: 197 QVGIRTTND------DTLGVNIIDAPTVHDIGPVETAKR-IKAILG--DRPTYLTFDIDC 247 Query: 236 LDPAFTPATGTPVLGGLSYREGLYITEEIYKTGLLSGLDIMEVNP---TLGKTA 286 LDPA+ P TGTPV GGL+ + I EI + G D++EV+P T G TA Sbjct: 248 LDPAYAPGTGTPVWGGLTSAQASRILREIAGINIKGG-DVVEVSPPFDTTGATA 300 Lambda K H 0.316 0.137 0.403 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: 323 Number of extensions: 22 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 323 Length of database: 322 Length adjustment: 28 Effective length of query: 295 Effective length of database: 294 Effective search space: 86730 Effective search space used: 86730 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: 42 (22.0 bits) S2: 48 (23.1 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