Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate WP_092482777.1 BM299_RS07120 phosphoglucomutase/phosphomannomutase family protein
Query= BRENDA::A0A0H3NJ17 (546 letters) >NCBI__GCF_900115975.1:WP_092482777.1 Length = 496 Score = 186 bits (471), Expect = 2e-51 Identities = 158/528 (29%), Positives = 250/528 (47%), Gaps = 66/528 (12%) Query: 40 VKFGTSGHRGSAGRHSFNEPHILAIAQAIAE-----ERAKNGITGPCYVGKDTHALSEPA 94 +KFGT G RG F ++ ++QA+A+ A GI VG D LS+ Sbjct: 4 IKFGTDGWRGIIA-DDFTFENVRVVSQAVADYINDRNMAHRGIV----VGYDNRFLSDRF 58 Query: 95 FISVLEVLAANGVDVIVQENNGFTPTPAVSNAILVHNKKGGPLADGIVITPSHNPPEDGG 154 +V +V+ NG+ V + + G PTP + A+ VH+ G +++T SHNPPE G Sbjct: 59 ADTVADVMIQNGIKVYL--SGGPLPTPVTAFAVKVHDAAGA-----VMLTASHNPPEYNG 111 Query: 155 IKYNPPNGGPADTNVTKVVEDRANALL-AGGLQGVKR-ISLDAAMASGHVKA-------- 204 K+ P GPA ++T+ +E+ L GG++ + + +++ A GH A Sbjct: 112 FKFIPDYAGPALPHITRAIEENVMRLQDVGGVRVLNQEAAVELAFKPGHTGAPAPAAHAT 171 Query: 205 ---------VDLVQPFVEGLADIVDMAAIQKAGLTLGVDPLGGSGIEYWKRIAEHYKLNL 255 +D + E L +VDM AI +A + + VD + GSG+ Y + + + + Sbjct: 172 KPHIAERIIIDPRPEYFEHLEQLVDMEAIGRANMEVMVDAMHGSGMGYLDVLLKKARARV 231 Query: 256 TLVNDQVDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDKFDLAFANDPDYDRHGIVTP 315 D F G++ A ++ L A D D DR GI+ Sbjct: 232 KECRCSRDPLF-------GGSMPEPTGKSLAGVCRWIQEEEGRLGLALDGDADRFGIIDA 284 Query: 316 AGL-MNPNHYLAVAINYLFQHRPLWGKDVAVGKTLVSSAMIDRVVNDLGRKLVEVPVGFK 374 G+ + PN +L + ++L + L G V +T+ +S M+DR+ G+ + E PVGFK Sbjct: 285 GGVYITPNQFLPLLYHHLITVKGLVGP---VTRTVATSHMLDRIARKHGQAVYETPVGFK 341 Query: 375 WFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMCLLAAEITAVTGKNPQEHYN 434 + L + GGEES G S +KDGI+ LLAAE+ AV GK+ + Sbjct: 342 YIGQNLMEKDCVLGGEESGGLSI-----KGHIPEKDGILAGLLAAEMVAVHGKSLADLAE 396 Query: 435 ELAARFGAPSYN-RLQASATSAQKAALSKLSPEMVSASTLAGDPITARLTAAPGNGASIG 493 E+A ++G Y+ RL T QK + + E+ A LAG P+ R+ + Sbjct: 397 EVARQYGGKLYSERLDVRTTPKQKQQVLEKLQELRPAE-LAGVPVAERV--------DLD 447 Query: 494 GLKVMTDNG-WFAARPSGTEDAYKIYCESFLGEEHR-KQIEKEAVEIV 539 GLK++ G W RPSGTE ++IY E+ G+ R +QI ++ +E+V Sbjct: 448 GLKLVLAGGEWVLVRPSGTEPLFRIYVET--GQPERIEQIRRDLMEMV 493 Lambda K H 0.316 0.134 0.395 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: 715 Number of extensions: 41 Number of successful extensions: 7 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: 546 Length of database: 496 Length adjustment: 35 Effective length of query: 511 Effective length of database: 461 Effective search space: 235571 Effective search space used: 235571 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: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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