Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate NP_661183.1 CT0279 phosphoglucomutase/phosphomannomutase
Query= metacyc::MONOMER-13382 (455 letters) >NCBI__GCF_000006985.1:NP_661183.1 Length = 460 Score = 197 bits (502), Expect = 5e-55 Identities = 149/453 (32%), Positives = 219/453 (48%), Gaps = 18/453 (3%) Query: 5 FGTFGVRGIANEKITPEFAMKIGMAFGTLLKREGRKKPLVVVGRDTRVSGEMLKEALISG 64 FGT G R I ++ T + +A G K V VG DTR + Sbjct: 5 FGTDGWRAIIAKEYTYDNLKLAALASGKYFLSHPDKSNGVCVGYDTRFMSKEFARYTAEV 64 Query: 65 LLSVGCDV-IDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMGLKKE 123 L S+G V + TPAV T+ GG +ITASHNPP YNG K+ G E Sbjct: 65 LSSMGLKVFLSSSFVSTPAVSLYTREHKLAGGVMITASHNPPIYNGFKVKASYGGPAHPE 124 Query: 124 REAIVEELFFKEDFDRAKWYEIGEVRREDIIKPYIEAIKSKVDVEAIKKRKPFVVVDTSN 183 +E+ D + DI YI ++SK+D++ I++ + + Sbjct: 125 VIDEIEKNLSGIDPSTLVKPAENLITMTDIKSEYIAYLESKLDLKLIRESGLKIAHNAMY 184 Query: 184 GAGSLTLPYLLRE--LGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKALGADFGVA 241 GAG + LL E + C +VN DG NPEP + +F+E K + D + Sbjct: 185 GAGQDIVTRLLDESMVNCYHCSVNPGFDGI----NPEPIPPYITDFVEFFKEVETDVAII 240 Query: 242 QDGDADRAVFIDENGRFIQGDKTFALVADAVLKEKGG-GLLVTTVATSNLLDDIAKKHGA 300 DGDADR +DE G F+ K FA+V ++++KG G + T A ++++D I +KH Sbjct: 241 NDGDADRIGMLDEKGEFVDSHKLFAIVLKYLVEQKGQRGEVAKTFALTDIIDRICQKHDL 300 Query: 301 KVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVEIFAKSGKKF 360 K+ VG V+R + N+ IGGEE+GG+ + RDG T ++EI A+ K Sbjct: 301 KMHLLPVGFKYVSRLMTTNDILIGGEESGGIGITSFLPERDGVYTGLLMLEIMARRQKTL 360 Query: 361 SELIDEL-PKY----YQIKTKRHVEGDRHAIVNKVA--EMARERGYTV---DTTDGAKII 410 + L++EL +Y Y R E + AI+ + ++ GY V + DG K Sbjct: 361 TGLVEELYDEYGFFSYNRLDLRVAESKKAAIIEAASGGKLKSIAGYPVTSFNDLDGFKYH 420 Query: 411 FEDGWVLVRASGTEPIIRIFSEAKSKEKAQEYL 443 FE GW+L+RASGTEP++RI+ EA S EK ++ L Sbjct: 421 FEGGWLLIRASGTEPVLRIYCEADSTEKVEKVL 453 Lambda K H 0.317 0.138 0.391 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: 490 Number of extensions: 28 Number of successful extensions: 6 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: 455 Length of database: 460 Length adjustment: 33 Effective length of query: 422 Effective length of database: 427 Effective search space: 180194 Effective search space used: 180194 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 24 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