Align agmatine deiminase (EC 3.5.3.12) (characterized)
to candidate Synpcc7942_2402 Synpcc7942_2402 hypothetical protein
Query= BRENDA::Q9PAQ3 (363 letters) >FitnessBrowser__SynE:Synpcc7942_2402 Length = 376 Score = 333 bits (854), Expect = 4e-96 Identities = 167/342 (48%), Positives = 226/342 (66%), Gaps = 7/342 (2%) Query: 24 RFPAEWEPQSAILIAWPHANTDWSAHLADVEETYIALVAAITRFQMVIICVLDDDLQTYT 83 RFPAEWE Q +LIAWPHA++DW + L V+ Y L A+TRF+ ++I + D Sbjct: 38 RFPAEWEAQDGVLIAWPHADSDWRSLLDQVDRVYRDLAEAVTRFEQLLIVTPEPDR---V 94 Query: 84 EARLRSASVAMQQVRFTVASYNDTWLRDSGPITLIGTNRDFRLLDFRFTGWGGKFEAKAD 143 +L + +++ NDTW RD GP+T + T RLLD+ F GWG KF A D Sbjct: 95 AEQLAQTTANCDRIQIVELPTNDTWSRDFGPLT-VETPAGLRLLDWGFNGWGLKFAANHD 153 Query: 144 DQLVSVLHANGLFKNTQMHSINFALEGGAIETDGAGTLLTTWRCLHE--RHPQRTRKTLD 201 +Q+ L G+F T + ++ EGG+IE+DG GTLLTT +CL E R+P +R+ + Sbjct: 154 NQVTRRLWQQGIFGTTPLETVPLIFEGGSIESDGRGTLLTTSQCLLEANRNPGLSREAIA 213 Query: 202 ANLTAWLAQNRVLWLEHGYLEGDDTDAHIDTLARFASTDSIVYQSCDNTTDSHYAELQAM 261 + L +R+LWLEHG+LEGDDTDAHIDTL R A D+++Y +CD+ +DSH AEL A+ Sbjct: 214 QIIQRQLGGDRLLWLEHGHLEGDDTDAHIDTLVRIAPNDTLIYVACDDPSDSHAAELTAL 273 Query: 262 ANELTALRTTEGRAYRLFPLPWTKPILDQD-RRLPASYANFLIIEGAVLMPTYDDPADTI 320 EL ALR +G+ Y L PLPW +P D D +RLP +YAN+L+I GAVL+PTY+DPAD Sbjct: 274 EAELKALRAADGQPYHLIPLPWPQPCFDADGQRLPTTYANYLVINGAVLVPTYNDPADEA 333 Query: 321 AQSVLAEAFPTREIVPVPCRPLIWQNGSLHCITMQIPAGLLA 362 A + +A AFP R + + CRPL+ Q+GSLHCITMQ+PAGLL+ Sbjct: 334 AIAAIAAAFPDRLAIGINCRPLLEQHGSLHCITMQLPAGLLS 375 Lambda K H 0.322 0.134 0.423 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: 497 Number of extensions: 21 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: 363 Length of database: 376 Length adjustment: 30 Effective length of query: 333 Effective length of database: 346 Effective search space: 115218 Effective search space used: 115218 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: 49 (23.5 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