Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate WP_011765122.1 AZO_RS07025 phosphoglucosamine mutase
Query= BRENDA::Q6I7B6 (450 letters) >NCBI__GCF_000061505.1:WP_011765122.1 Length = 451 Score = 150 bits (380), Expect = 6e-41 Identities = 143/464 (30%), Positives = 212/464 (45%), Gaps = 63/464 (13%) Query: 2 RLFGTAGIRGTLWE-KVTPELAMKVGMAVGTYKSGKA----------LVGRDGRTSSVML 50 + FGT G+RG + E +TPE M++G A G + L+G+D R S ML Sbjct: 4 KYFGTDGVRGRVGELPITPEFVMRLGYAAGVTLVAREHLPAGERPAILIGKDTRVSGYML 63 Query: 51 KNAMISGLLSTGMEVLDADLIPTPALAWGTRKL-ADAGVMITASHNPPTDNGVKVFNGDG 109 + A+ +G + G++VL A IPTPA+A+ TR L AGV+I+ASHNP DNG+K F+ G Sbjct: 64 EAALQAGFAAAGVDVLLAGPIPTPAVAYLTRALRLQAGVVISASHNPFYDNGIKFFSAGG 123 Query: 110 TEFYVEQERGLEEIIFS--GNFRKARWDEIKPV-----RNVEVIPDYINAVLDFVGHETN 162 + E +EE I G AR + + R +E LD G Sbjct: 124 AKLPDAVEAEIEERIGQPMGCAESARLGRARRIGDAAGRYIEFCKSSFPNELDLRG---- 179 Query: 163 LKVLYDGANGAGSLVAPYLLREMGAKVLSVNAHVDG-HFPGRKPEPRYENIAYLGKLVRE 221 L++ D A+GA +AP + E+GA+V+SV +G + R EN L + V Sbjct: 180 LRIALDCAHGAAYHIAPNVFHELGAEVISVGVDPNGLNINDGVGATRPEN---LRQAVLS 236 Query: 222 LGVDLAIAQDGDADRIAVFDEKGNYVDEDTVIALFAKLYVEEHGGGTVVVSIDTGSRIDA 281 G DL IA DGD DR+ + D +G D D ++ + A E VV ++ + + Sbjct: 237 HGADLGIALDGDGDRLIMVDRQGEIYDGDKLLYVIASARAAEGRLDGVVGTLMSNLGFEH 296 Query: 282 VVERAGGRVVRIPLGQPHDGIKRYKAIFAAE-PWKLVHPKFGPWI--------DPFVT-M 331 +ER G R +G RY E WK+ G I D ++ + Sbjct: 297 ALERRGVAFARAKVGD------RYVLEMLHERGWKIGGENSGHIICLDCHTTGDGIISAL 350 Query: 332 GLLIKLIDENGPLSELVKEIPTYYLKKANVLCPD--EYKAEV-VRRAAEEVERKLSSEIK 388 +L L LSE K++ Y + NV P ++KA+ + + A + ER Sbjct: 351 QVLAALKHREMSLSEACKDLVFYPQRLINVRLPAGFDWKADARIAQTAADAER------- 403 Query: 389 EVLTISGFRIALNDGSWILIRPSGTEPKIRVVAEAPTEKRRDEL 432 L D +L+RPSGTEP +RV+ E E+ + L Sbjct: 404 ----------TLGDTGRVLLRPSGTEPLLRVMVEGRDEQLVESL 437 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: 445 Number of extensions: 31 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: 450 Length of database: 451 Length adjustment: 33 Effective length of query: 417 Effective length of database: 418 Effective search space: 174306 Effective search space used: 174306 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