Align arginine deiminase (EC 3.5.3.6) (characterized)
to candidate CA265_RS10475 CA265_RS10475 amidinotransferase
Query= reanno::pseudo3_N2E3:AO353_25635 (311 letters) >FitnessBrowser__Pedo557:CA265_RS10475 Length = 304 Score = 300 bits (768), Expect = 3e-86 Identities = 155/305 (50%), Positives = 208/305 (68%), Gaps = 1/305 (0%) Query: 1 MQTTNTVLMIRPTRFSFNQDTAANNRFQRPAAAAEDVQLKALQEFDGYVAALREHGVEVM 60 MQTTN +LMIRP F FN+ TA NN+FQ A+ +VQ +AL+EFD +V LR++ V+V Sbjct: 1 MQTTNHILMIRPVDFKFNEQTAGNNKFQ-VASTETNVQTEALKEFDAFVDLLRKNNVDVT 59 Query: 61 VHNDSEAPHTPDSIFPNNWWSSHPDGTLVLYPMQGHNRRLERDKGVLDWLRDAYRIEQLL 120 V +D+ P TPDSIFPNNW S H DG++ LYPM NRRLER K +LD L++ + + + Sbjct: 60 VVDDTLQPETPDSIFPNNWVSFHEDGSVYLYPMFSENRRLERRKEILDGLKENFEVNHIS 119 Query: 121 DLSDLEQQEVFLEGTGSMVLDREQRICYAGYSTRTHAKALDQVVEHLGYELCAFNAVDRH 180 DLS E Q FLEGTGSMVLDR +I YA S RT + LD GYE AF AVD Sbjct: 120 DLSFYEHQHAFLEGTGSMVLDRTNKIAYACLSVRTDEEVLDNFCMLTGYEPVAFQAVDES 179 Query: 181 GVPIYHTNVMMSVGRQLAVVCLESVSDLDERNALRSRLECSGKQVLTLSFDQLESFAGNM 240 PIYHTNVMM +G + AV+CL+S+ D +E+ + L+ SGK+++ ++ +Q+ FAGNM Sbjct: 180 NFPIYHTNVMMCIGDRFAVICLDSIKDPEEKLNVTISLKGSGKEIIEINLEQMNKFAGNM 239 Query: 241 LEVHNAAGEPLLVMSRTAWRSLHADQRRMVEAYAKPLPVNIDTIERIGGGSARCMLAEVY 300 L++ NA E LLVMS A+ SL A+Q +E Y++ + + TIE+ GGGSARCMLAE++ Sbjct: 240 LQLTNADDESLLVMSEQAYLSLTAEQIVALEQYSRIIYAPLYTIEKNGGGSARCMLAEIH 299 Query: 301 LPKRV 305 LP ++ Sbjct: 300 LPSKL 304 Lambda K H 0.320 0.133 0.397 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: 239 Number of extensions: 8 Number of successful extensions: 2 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: 311 Length of database: 304 Length adjustment: 27 Effective length of query: 284 Effective length of database: 277 Effective search space: 78668 Effective search space used: 78668 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 (21.8 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