Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate Synpcc7942_2132 Synpcc7942_2132 phosphoglucosamine mutase
Query= BRENDA::Q6I7B6 (450 letters) >FitnessBrowser__SynE:Synpcc7942_2132 Length = 472 Score = 158 bits (399), Expect = 4e-43 Identities = 135/446 (30%), Positives = 215/446 (48%), Gaps = 46/446 (10%) Query: 3 LFGTAGIRGTLWEKVTPELAMKVGMAVGTY------KSGKALVGRDGRTSSVMLKNAMIS 56 LFGT GIRG + E +T LA +VG G G +VG+D R SS ML A+ S Sbjct: 26 LFGTDGIRGRVGEHLTAPLAQQVGFWTGQVLRQAGGDRGPVVVGQDSRNSSNMLAMALSS 85 Query: 57 GLLSTGMEVLDADLIPTPALAWGT-RKLADAGVMITASHNPPTDNGVKVFNGDGTEFYVE 115 GL + G+EVL L PTP +A+ T A GVMI+ASHNPP DNG+KVF DG++ Sbjct: 86 GLAAAGVEVLHLGLCPTPGVAYLTHHSEAIGGVMISASHNPPGDNGIKVFGADGSKL--- 142 Query: 116 QERGLEEIIFSG------NFRKARWDEIKPVRNVEVIPDYINAVLDFVGHETN---LKVL 166 +R L+ I +G + W + ++ Y A+ +G N LK++ Sbjct: 143 -DRQLQAAIEAGLRGQQTSLPATTWGQ--HYYQPQLADHYQAAIAQSLGQRANLQGLKIV 199 Query: 167 YDGANGAGSLVAPYLLREMGAKVLSVNAHVDGHFPGRKPEPRYENIAYLGKLVRELGVDL 226 D A GA +L+AP L RE+GA+V++++ DG+ ++A L V E G D+ Sbjct: 200 LDLAWGAAALLAPRLFRELGAEVIALHDLPDGN--QINVNCGSTHLARLQAAVLEQGADM 257 Query: 227 AIAQDGDADRIAVFDEKGNYVDEDTVIALFAKLYVEEH--GGGTVVVSIDTGSRIDAVVE 284 A DGDADR+ D +G VD D ++ L+ + ++ G +V ++ + + Sbjct: 258 GFAFDGDADRVLAVDGRGRSVDGDHILFLWGRELEQQQQLPGQAIVTTVMANLGFERAWQ 317 Query: 285 RAGGRVVRIPLGQPH---DGIKRYKAIFAAEPWKLVHPKFGPWIDPFVTMGLLIKLIDEN 341 GG VR +G + + R + + ++ + D +T + L+ + Sbjct: 318 AVGGEFVRTAVGDQYVQAEMQARGAMLGGEQSGHILCRHYALTGDGTLTAAHVAALVQAS 377 Query: 342 G-PLSELVKEIPTYYLKKANVLCPDEYKAEVVRRA-AEEVERKLSSEIKEVLT--ISGFR 397 G L++LV + Y +++R E+ +R+ + + LT I+ Sbjct: 378 GVSLADLVDQSFRPY-------------PQLLRNVRVEDRDRRCNWQNCAALTQAIAAAE 424 Query: 398 IALNDGSWILIRPSGTEPKIRVVAEA 423 + D +L+R SGTEP +R++ EA Sbjct: 425 TDMGDRGRVLVRASGTEPLLRIMVEA 450 Lambda K H 0.318 0.138 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: 474 Number of extensions: 21 Number of successful extensions: 6 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: 450 Length of database: 472 Length adjustment: 33 Effective length of query: 417 Effective length of database: 439 Effective search space: 183063 Effective search space used: 183063 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 (21.6 bits) S2: 51 (24.3 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