Align Mannitol-1-phosphate 5-dehydrogenase; EC 1.1.1.17 (characterized)
to candidate 1936889 b4465 predicted dehydrogenase (NCBI)
Query= SwissProt::Q5E1G4 (423 letters) >FitnessBrowser__Keio:1936889 Length = 425 Score = 575 bits (1481), Expect = e-168 Identities = 275/419 (65%), Positives = 336/419 (80%) Query: 3 QTTAAVICGEKDIQLRTFELPSISADELLVKNISNSVCLSTYKAALLGSKHKRVPENIDE 62 +T A I G++D++LR FELP I+ +ELLV IS+SVCLST+KAALLGS+HKRVP++++ Sbjct: 2 KTKVAAIYGKRDVRLRVFELPEITDNELLVSVISDSVCLSTWKAALLGSEHKRVPDDLEN 61 Query: 63 VPVITGHEYAGVIVEVGENLKDQFKAGDSFVLQPAMGLPTGYSAGYSYETFGGNATYSII 122 PVITGHE AGVIVEVG+NL ++K G FVLQPAMGLP+GYSAGYSYE FGGNATY II Sbjct: 62 HPVITGHECAGVIVEVGKNLTGKYKKGQRFVLQPAMGLPSGYSAGYSYEYFGGNATYMII 121 Query: 123 PKIAIDLGCVLPYDGSYYADASLAEPMSCIIGAFHASYHTTQFVYEHEMGIKEGGTLALL 182 P+IAI+LGCVLPY GSY+A ASLAEPM CIIGA+HA+YHTTQ+VYEH MG+K GG +ALL Sbjct: 122 PEIAINLGCVLPYHGSYFAAASLAEPMCCIIGAYHANYHTTQYVYEHRMGVKPGGNIALL 181 Query: 183 ACAGPMGIGAIDYAINGPVKPRRIVVTDIDEDRLSRAESLIPVSAAKAQGIELIYVNTIE 242 ACAGPMGIGAIDYAING ++P R+VV DID+ RL++ + L+PV A ++GIEL+YVNT Sbjct: 182 ACAGPMGIGAIDYAINGGIQPSRVVVVDIDDKRLAQVQKLLPVELAASKGIELVYVNTKG 241 Query: 243 MEDPVTYLKSLNDDQGYDDVMVYAAVAQVLEQADALLGNDGCLNFFAGPTDKEFKVPFNF 302 M DPV L++L D G+DD+ VYAAV V+E AD LL DGCLNFFAGPTDK FKVPFNF Sbjct: 242 MSDPVQMLRALTGDAGFDDIFVYAAVPAVVEMADELLAEDGCLNFFAGPTDKNFKVPFNF 301 Query: 303 YNVHYESTHIVGTSGGSTGDMVESLELSAQGDINPSFMITHVGGLQAAPHTILNQLDIPG 362 YNVHY STH+VGTSGGST DM E++ LSA G + PSFM+TH+GGL A P T+LN DIPG Sbjct: 302 YNVHYNSTHVVGTSGGSTDDMKEAIALSATGQLQPSFMVTHIGGLDAVPETVLNLPDIPG 361 Query: 363 GKKLIYPHIDLPLTAIDNFASLAEQDPFFSELDAILAKNNYVWNQHAEKALLEFYDVSL 421 GKKLIY + +PLTAI +FA + DP F EL ++ + + +WN+ AEK LL + V + Sbjct: 362 GKKLIYNGVTMPLTAIADFAEKGKTDPLFKELARLVEETHGIWNEQAEKYLLAQFGVDI 420 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: 610 Number of extensions: 12 Number of successful extensions: 1 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: 425 Length adjustment: 32 Effective length of query: 391 Effective length of database: 393 Effective search space: 153663 Effective search space used: 153663 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