Align agmatine deiminase (EC 3.5.3.12) (characterized)
to candidate WP_057506685.1 ABB28_RS00175 agmatine deiminase family protein
Query= BRENDA::Q9PAQ3 (363 letters) >NCBI__GCF_001431535.1:WP_057506685.1 Length = 346 Score = 507 bits (1306), Expect = e-148 Identities = 244/339 (71%), Positives = 277/339 (81%) Query: 24 RFPAEWEPQSAILIAWPHANTDWSAHLADVEETYIALVAAITRFQMVIICVLDDDLQTYT 83 RFPAEWE QS +LIAWP A+TDW+ L VEETYIALVAAITRFQ V+ICV DDD++TY Sbjct: 6 RFPAEWEAQSGVLIAWPTADTDWADRLGQVEETYIALVAAITRFQPVLICVADDDVETYA 65 Query: 84 EARLRSASVAMQQVRFTVASYNDTWLRDSGPITLIGTNRDFRLLDFRFTGWGGKFEAKAD 143 E RLRS + MQ+VRF A+Y+DTWLRDSGPITL + F+LLDFRFTGWGGKF+A D Sbjct: 66 EMRLRSNRIDMQRVRFVTAAYDDTWLRDSGPITLQRKDGGFQLLDFRFTGWGGKFDATLD 125 Query: 144 DQLVSVLHANGLFKNTQMHSINFALEGGAIETDGAGTLLTTWRCLHERHPQRTRKTLDAN 203 DQLV VL A +F + + SI FALEGG IETDG GTLLTTW+CLHERHP R R +L A+ Sbjct: 126 DQLVGVLDAARVFNDAPVRSIAFALEGGGIETDGQGTLLTTWKCLHERHPDRDRASLSAD 185 Query: 204 LTAWLAQNRVLWLEHGYLEGDDTDAHIDTLARFASTDSIVYQSCDNTTDSHYAELQAMAN 263 L WL Q+RVLWL+HGYLEGDDTDAHIDTLARFAS DSIVYQ+CD+ +DSH+AELQAM Sbjct: 186 LADWLQQDRVLWLDHGYLEGDDTDAHIDTLARFASADSIVYQACDDASDSHHAELQAMGA 245 Query: 264 ELTALRTTEGRAYRLFPLPWTKPILDQDRRLPASYANFLIIEGAVLMPTYDDPADTIAQS 323 EL ALRT +G+ YRLFPLPW +P+LD+ RRL ASYANFLI+ GAVLMP Y D AD A+ Sbjct: 246 ELAALRTADGQPYRLFPLPWPQPVLDEGRRLAASYANFLIVNGAVLMPAYGDAADEAARD 305 Query: 324 VLAEAFPTREIVPVPCRPLIWQNGSLHCITMQIPAGLLA 362 VLA AFP REIV VPCR LIWQNGSLHCITMQ+PAGLLA Sbjct: 306 VLAAAFPDREIVQVPCRSLIWQNGSLHCITMQLPAGLLA 344 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: 551 Number of extensions: 18 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: 363 Length of database: 346 Length adjustment: 29 Effective length of query: 334 Effective length of database: 317 Effective search space: 105878 Effective search space used: 105878 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 24 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