Align Formiminoglutamase (EC 3.5.3.8) (characterized)
to candidate 5210946 Shew_3372 arginase/agmatinase/formiminoglutamase (RefSeq)
Query= reanno::SB2B:6939103 (345 letters) >FitnessBrowser__PV4:5210946 Length = 347 Score = 419 bits (1076), Expect = e-122 Identities = 220/340 (64%), Positives = 251/340 (73%), Gaps = 1/340 (0%) Query: 1 MQHLIIFSAKDMTPILGKRPGETRLGNHFLLPEGPT-LVAILESAKAQGARFVLLGVGED 59 MQ LI F+A+ + KR GET++G EG T L L SAKA G RFV+LG+GED Sbjct: 1 MQTLIPFTAERCQGFVAKREGETKIGQTIHCYEGKTPLGEQLASAKADGVRFVILGIGED 60 Query: 60 AGPRANLGRGGATNAFEAMLKYLVNLQSNRFYRGDDCLLLGQLDFGDLLPGEDADVDALR 119 GPRANLGRGGA + FEA + N QSN+F G CL+LGQ+ DL E + ALR Sbjct: 61 IGPRANLGRGGAVDGFEAAMAQFCNFQSNQFLDGGHCLVLGQIATDDLQLPEGSSAQALR 120 Query: 120 AAVAAMDERVIEVASAIMEAGLEPIVIGGGHNNAFGLLMSVKNAFGRPAAAVNLDPHSDF 179 V +DERVIE+ IM AGLEPIVIGGGHNNA+GLLM+ K A G+ AAVNLDPHSDF Sbjct: 121 ENVDKLDERVIEIVGEIMAAGLEPIVIGGGHNNAYGLLMATKQATGKMVAAVNLDPHSDF 180 Query: 180 RLREGRHSGNGFSYAAASGALDFYHVLGLHELKNSEANLEQLAAFGGSWHTLQQIWVRGE 239 R REGRHSGNGFSYAAASGAL YHVLGLHELKNS+ LEQL AFGG WHTLQ IWVR E Sbjct: 181 RPREGRHSGNGFSYAAASGALGHYHVLGLHELKNSQQTLEQLTAFGGKWHTLQAIWVRRE 240 Query: 240 LSLDDALKHIGKTLRATGLPVALELDLDAIANMPSSAMTAAGVPLLDAARYISHIARHCD 299 SL+ ALK I + L A+ LPVALELDLDAI NMPSSA TAAG+PLLDA Y++ +A Sbjct: 241 TSLEQALKAIVEDLNASDLPVALELDLDAITNMPSSASTAAGIPLLDALYYVNQVASKTP 300 Query: 300 CAYLHLAEAAPSCHDSGEDAGLRETGQSLTELVYAYIRGR 339 AYLHLAEAAPSCH +G +AG RETGQS+ EL+YAYI+GR Sbjct: 301 AAYLHLAEAAPSCHVAGVEAGRRETGQSIGELIYAYIQGR 340 Lambda K H 0.320 0.137 0.405 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: 390 Number of extensions: 9 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: 345 Length of database: 347 Length adjustment: 29 Effective length of query: 316 Effective length of database: 318 Effective search space: 100488 Effective search space used: 100488 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: 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