Align Guanidinobutyrase; GBase; EC 3.5.3.7; D-arginase; EC 3.5.3.10 (uncharacterized)
to candidate Echvi_3131 Echvi_3131 Arginase/agmatinase/formimionoglutamate hydrolase, arginase family
Query= curated2:Q8KZT5 (353 letters) >FitnessBrowser__Cola:Echvi_3131 Length = 356 Score = 94.7 bits (234), Expect = 3e-24 Identities = 94/323 (29%), Positives = 142/323 (43%), Gaps = 55/323 (17%) Query: 41 ADVTVVGVPFDSGVSYRPGARFGANHVREASRLLRPYNP----AWDVSPF-----ENIQV 91 A V +V VP++ VSY PG G + +AS + + AW + EN+ Sbjct: 33 ASVVIVPVPWEVTVSYAPGTANGPQAILDASSQVDLFQDDITDAWTMGIHMLPIPENVYS 92 Query: 92 AD------AGD----------------MAVNPFNINEAIET----IQQNALDLTANGSKL 125 + AG+ P I++A ++ + + A D G + Sbjct: 93 NNTKYRILAGNYIDWLERGSPKEERERFGAVPALIDKACQSMNDWVYETAKDQLNQGKLV 152 Query: 126 VTLGGDHTIALPLLRAAAERAGEPIAMLHFDAHLDTWDTYFGAEYTHGTPFRRAVEEGIL 185 +GGDH+ L ++A +ER +L DAH D D Y G Y+H + + I Sbjct: 153 ALVGGDHSTPLGHIKALSERYSS-FGILQIDAHADLRDQYEGFNYSHASISHNFLN--IP 209 Query: 186 DTEAISHVGTRGPLYGKKD-LDDDHRFGFGIVTSADVY-----YQGVLETVAKIRDRIGN 239 E + VG R + D +D D R I T D + Y+GV T I D++ Sbjct: 210 QVEKLVQVGVRDYCEEESDRIDGDDR----ITTFFDHHIKEQLYEGV--TWRTICDQVIA 263 Query: 240 ---RPLYISVDIDVLDPAHAPGTGTPEAGGITSRELLEIIRGF--RGMNLVGADVVEVAP 294 R +YI++DID LDP P TGTP GG +LL +++ G ++G D+VEVAP Sbjct: 264 SLPREIYITIDIDGLDPKLCPHTGTPVPGGFDLNQLLYLMKLIVKSGRKIIGFDLVEVAP 323 Query: 295 AYDHAEITGVAGSHVAYELVTLM 317 D +E G G+ + Y + LM Sbjct: 324 GEDDSEWDGNVGARLLYRMSNLM 346 Lambda K H 0.318 0.137 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: 339 Number of extensions: 22 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 353 Length of database: 356 Length adjustment: 29 Effective length of query: 324 Effective length of database: 327 Effective search space: 105948 Effective search space used: 105948 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 (21.7 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