Align Putative agmatine deiminase; EC 3.5.3.12; Agmatine iminohydrolase (uncharacterized)
to candidate Synpcc7942_2461 Synpcc7942_2461 hypothetical protein
Query= curated2:A6VVD9 (369 letters) >FitnessBrowser__SynE:Synpcc7942_2461 Length = 477 Score = 168 bits (426), Expect = 2e-46 Identities = 121/395 (30%), Positives = 191/395 (48%), Gaps = 56/395 (14%) Query: 14 FRMPAEHEPQEQVWMAWPTREDNWREKGKHAQAEFVAVATAIAQSTKVTFIVDAKHYEQA 73 FRMPAE EP +WMA+PT E+ + G +Q A+ AIA + K+ F+++ + Sbjct: 65 FRMPAEFEPITSIWMAYPTYEN---QAGYPSQTVQKAMVKAIAPTVKIDFLLNEPEEKVI 121 Query: 74 ------RLALP-DQIRVIEIPSDDCWMRDIGATYVVNDQGERRANSWQFNAWGGELDGLY 126 +P Q+R +P +D W+RD+G + VN + + + FNAW L Sbjct: 122 INGWLKTAGIPASQVRYHLVPHEDLWIRDMGPIFAVNAD-QTQVVDFGFNAWS-YLAATD 179 Query: 127 DSWEQDNAVAEKMAAVTGDYVYHAPLILEGGSIHVDGEGTLYTTEECLLHPSRNPHLSKE 186 + D V K+A + + LI EGG+ +G+GTL TE L RNP L+KE Sbjct: 180 PAAMTDEQVDRKVAGDLDLPILRSSLISEGGNREFNGKGTLMLTEAVELQ--RNPGLTKE 237 Query: 187 DIEDLLKVYLNVEKIIWLKDGLYNDE----------------TNGHVDNIMHVIRPGVVA 230 IE LK N++K+IWL++G+ +DE T GH+D + + Sbjct: 238 KIETELKRVFNLKKVIWLQEGVIDDELSYRGKLPDGSLTVLATGGHIDEYARFVDSNTIL 297 Query: 231 LTDC---EDSNDPQYAIS----KAAIKVLSQAIDAKGRTLEIIKLPMPGPLFVS---EDE 280 L + E ++DP AI+ + +K+L A D G+ I+++P P++V+ ED Sbjct: 298 LAEVTAEERASDPLAAINYQRLEENLKILQAATDQDGKPFRIVRIPAAKPIYVNMTKEDA 357 Query: 281 AKNLLKSDSM--------NRQVGERLAASYANFLITNNSIVFPTFG--------EKTDEQ 324 L+ + + Q+ LAASY NF+I N+ ++ P + ++ D+ Sbjct: 358 VFQALQELTFEDGTVIQDDDQIKTILAASYLNFVIANDVVIVPRYWQPDRNLEYQQKDQA 417 Query: 325 AKEILQKAFPEHKVIGVYARNILLGGGNIHCITQQ 359 A Q FP K++ + NI GGG +HCI QQ Sbjct: 418 ALAAFQSVFPNKKIVAINPENINAGGGGMHCIVQQ 452 Lambda K H 0.316 0.134 0.402 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: 436 Number of extensions: 28 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: 369 Length of database: 477 Length adjustment: 32 Effective length of query: 337 Effective length of database: 445 Effective search space: 149965 Effective search space used: 149965 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: 41 (21.6 bits) S2: 50 (23.9 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