Align Carbon-nitrogen hydrolase family protein; EC 3.5.-.- (characterized, see rationale)
to candidate GFF2120 HP15_2074 carbon-nitrogen hydrolase family protein
Query= uniprot:Q5NHL7_FRATT (286 letters) >FitnessBrowser__Marino:GFF2120 Length = 307 Score = 216 bits (550), Expect = 5e-61 Identities = 123/298 (41%), Positives = 178/298 (59%), Gaps = 15/298 (5%) Query: 2 ANIKVAVVQLSFNDNEAENLAKLESKIIQAAKNGAKIILTPELPSYLYFCKKQNSKYFDL 61 + I VAV+Q + + ++A +LA E + +A +GA +++ EL + LYFC+ + + F+L Sbjct: 8 SQINVAVIQQACSSDKAASLATTEKLVREAVASGANLVILQELHATLYFCQTEETSVFEL 67 Query: 62 AKTIDESPIVKLYKLLAHKYNIVLPASFFERDGNACYNSIAMI-DADGSIMGVYRKAHIP 120 A+ I P K LA + IVL S FER N Y++ A++ + DGS+ G+YRK HIP Sbjct: 68 AEPIP-GPTSKRLSDLARELGIVLVGSIFERRMNGVYHNTAVVFEKDGSLAGLYRKMHIP 126 Query: 121 DGIGYQEKYYFSPGSA-------GFKVWDTKYAKVGVGICWDQWFPEAARVMALKGAEIL 173 D G+ EK+YF+PG A GF DT ++GV +CWDQW+PEAAR+MAL GAEIL Sbjct: 127 DDPGFYEKFYFTPGDAQFNDGRSGFTPIDTSVGRLGVLVCWDQWYPEAARLMALAGAEIL 186 Query: 174 LYPTAIGSE-PHLPDYDSK--DHWQRVMQGHAAANMLPVLASNRYATE---ANDDITATY 227 +YPTAIG + PD ++ D W V +GHA AN LPV+A NR TE + + Sbjct: 187 IYPTAIGWDVTDDPDEQARQLDAWVTVQRGHAVANNLPVVAPNRVGTEPDPSGHSDGIRF 246 Query: 228 YGSSFITDHTGDKIAEADRSGDDILYATFDFAELQQQRFYWGLFRDRRPELYDEIVRK 285 +G+SFI G+ +A D S + IL T D + + R W RDRR + Y +I+++ Sbjct: 247 WGNSFICGPQGELLARGDDSSECILAVTLDRSRSESVRRIWPYLRDRRIDAYGDILKR 304 Lambda K H 0.320 0.136 0.413 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: 246 Number of extensions: 17 Number of successful extensions: 5 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: 286 Length of database: 307 Length adjustment: 26 Effective length of query: 260 Effective length of database: 281 Effective search space: 73060 Effective search space used: 73060 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