Align Mannitol-1-phosphate 5-dehydrogenase; EC 1.1.1.17 (characterized)
to candidate BWI76_RS01720 BWI76_RS01720 L-sorbose 1-phosphate reductase
Query= SwissProt::Q5E1G4 (423 letters) >FitnessBrowser__Koxy:BWI76_RS01720 Length = 409 Score = 317 bits (811), Expect = 6e-91 Identities = 165/414 (39%), Positives = 260/414 (62%), Gaps = 17/414 (4%) Query: 3 QTTAAVICGEKDIQLRTFELPSISADELLVKNISNSVCLSTYKAALLGSKHKRVPENIDE 62 QTTA + G++D++L TFELP++ DE+L + +++S+CLS++K A G HK+VP+++ Sbjct: 2 QTTALRLYGKRDLRLETFELPAMQDDEILARVVTDSLCLSSWKEANQGEDHKKVPDDVAT 61 Query: 63 VPVITGHEYAGVIVEVGENLKDQFKAGDSFVLQPAMGLPTGYSA-GYSYETFGGNATYSI 121 P+I GHE+ G I+ VG+ + +F+AG +V+Q + LP GYS+ GG AT+ + Sbjct: 62 NPIIIGHEFCGEIIAVGKKWQHKFRAGQRYVIQANLQLPDRPDCPGYSFPWIGGEATHVV 121 Query: 122 IPKIAIDLGCVLPYDGSYYADASLAEPMSCIIGAFHASYHTTQFVYEHEMGIKEGGTLAL 181 IP ++ C+L ++G + + SL EP+SC+IGAF+A+YH + Y H MGI+ G + Sbjct: 122 IPNEVMEQDCLLSWEGDTWFEGSLVEPLSCVIGAFNANYHLQEGSYNHVMGIRPQGRTLI 181 Query: 182 LACAGPMGIGAIDYAINGPVKPRRIVVTDIDEDRLSRAESLIPVSAAKAQGIELIYVNTI 241 L GPMG+ AIDYA++GP+ P +VVTD ++ +LS A P ++ Q + ++ + Sbjct: 182 LGGTGPMGLLAIDYALHGPINPALLVVTDTNKPKLSYARQHYP---SEPQTL----IHYL 234 Query: 242 EMEDPVTY-LKSLNDDQGYDDVMVYAAVAQVLEQADALLGNDGCLNFFAGPTDKEFKVPF 300 + D L +L+ G+DD+ V+ Q++ A +LL DGCLNFFAGP DK+F P Sbjct: 235 DGRDASRETLMALSGGHGFDDIFVFVPNEQLITLASSLLAADGCLNFFAGPQDKQFSAPI 294 Query: 301 NFYNVHYESTHIVGTSGGSTGDMVESLELSAQGDINPSFMITHVGGLQAAPHTILNQLDI 360 NFY+VHY TH VGTSGG+T DM ++ L + + ++TH+ GL AA T L+ + Sbjct: 295 NFYDVHYAFTHYVGTSGGNTDDMRAAVALMQAKKVQAAKVVTHILGLNAAGETTLDLPAV 354 Query: 361 PGGKKLIYPHIDLPLTAIDNFASLAEQDPFFSELDAILAKNNYVWNQHAEKALL 414 GGKKL+Y ++PLT + +DP +L AI+ +++ +W++ AE+ LL Sbjct: 355 GGGKKLVYTGKNIPLTPLGEI-----RDP---QLAAIMERHHGIWSKEAEEYLL 400 Lambda K H 0.317 0.136 0.396 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: 485 Number of extensions: 25 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: 423 Length of database: 409 Length adjustment: 31 Effective length of query: 392 Effective length of database: 378 Effective search space: 148176 Effective search space used: 148176 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: 50 (23.9 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