Align Putative 4-guanidinobutyryl amide hydrolase (characterized, see rationale)
to candidate 6936284 Sama_0473 carbon-nitrogen family hydrolase (RefSeq)
Query= uniprot:A0A291T3M3 (267 letters) >FitnessBrowser__SB2B:6936284 Length = 280 Score = 84.0 bits (206), Expect = 3e-21 Identities = 84/280 (30%), Positives = 126/280 (45%), Gaps = 23/280 (8%) Query: 1 MKISGLQTAGTPGDVDANLHELDAACRRA-RAEGAELLVTTE---LFITGYDIGDTVRDL 56 M++S LQ + DV+ANL +++ R R G LV L G++ Sbjct: 1 MQVSLLQCQSSR-DVEANLAFIESQLERLPRVPGEPQLVVLPECCLLFGGHESEQLAWSG 59 Query: 57 ARTDLLTPARQMAASHGIALVLGAPEYDSG--AYYNSAFFIDPAGTVLGRHRKNHLF--- 111 L +AA G+ LV G SG Y+ + D AG VLG + K HLF Sbjct: 60 EDEPLKHALAALAARFGVFLVAGTIPARSGDGRVYSRCYVFDDAGNVLGHYEKIHLFDVD 119 Query: 112 -GELDRRY-----FTPGDRTAPVIDYGGVRIAMLICYDVEFPENVRAAALAGADLVAVPT 165 + + Y F PG+ V+D ++ + ICYDV FP+ RA LAGA+++A+P Sbjct: 120 VADGTKTYRESDTFCPGENLV-VVDTPFGKLGLAICYDVRFPDMFRALRLAGAEIIALPA 178 Query: 166 AQMR-PYEFIAEHLLRVRAWENQIYIAYVNHDG--DEGSQRYVGRSSIVSPSATVLDSVE 222 A R E E LL+ RA E+Q ++ G + GS+ G+S ++ P L + Sbjct: 179 AFTRVTGEAHWEILLKARAIESQCFVLGAAQWGAHNTGSRETWGQSMLIDPWGRTLAELV 238 Query: 223 HGNRLLFATVDPYTVREARKANPYLADLR---PDLFTPSA 259 G + A +D + R A P ++ R P+L A Sbjct: 239 QGTGWVQARLDRDELTRVRAAMPVVSHNRFAAPELLPTKA 278 Lambda K H 0.320 0.137 0.407 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: 141 Number of extensions: 6 Number of successful extensions: 3 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: 267 Length of database: 280 Length adjustment: 25 Effective length of query: 242 Effective length of database: 255 Effective search space: 61710 Effective search space used: 61710 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: 47 (22.7 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