Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate 349906 BT0378 capsular polysaccharide biosynthesis protein capD (NCBI ptt file)
Query= SwissProt::Q9ZDJ5 (341 letters) >FitnessBrowser__Btheta:349906 Length = 641 Score = 146 bits (368), Expect = 2e-39 Identities = 111/326 (34%), Positives = 161/326 (49%), Gaps = 31/326 (9%) Query: 2 FVDKTLMITGGTGSFGNAVLSRFLKSNIINDIKEIRIFSRDEKKQEDMRIAL--NNSKLK 59 F K +++TG GS G+ + + + NI K++ +F E ++R+ N L Sbjct: 294 FCGKVVLVTGAAGSIGSELCRQLAQMNI----KKLIMFDSAESPLHNVRLEFEKNYPDLD 349 Query: 60 FY--IGDVRNYQSIDDAM--HGVDYVFHAAALKQVPTCEFYPMEAINTNVLGAENVLSAA 115 F IGDVR + + + +FHAAA K VP E P EA+ NV+G+ V A Sbjct: 350 FVPVIGDVRVKERLRMVFETYQPQIIFHAAAYKHVPLMEENPCEAVLVNVVGSRQVADMA 409 Query: 116 INNKVTKVIVLSTDKAVYPINAMGLSKALME----KLAIAKARMRSPGETILCVTRYGNV 171 + K+I++STDKAV P N MG SK L E L A + G T TR+GNV Sbjct: 410 VEYGAEKMIMVSTDKAVNPTNVMGCSKRLAEIYVQSLGCAIREGKVKGHTKFITTRFGNV 469 Query: 172 MASRGSVIPLFIHQIKQGKELTITEPSMTRFLMSLVDSVDLVLYAFEHGRQGDIFV-QKS 230 + S GSVIP F QI+ G +T+T P + RF M++ ++ LV+ A G +IFV + Sbjct: 470 LGSNGSVIPRFKEQIENGGPVTVTHPDIIRFFMTIPEACRLVMEAATMGEGNEIFVFEMG 529 Query: 231 PASTIEVLAKALQEIFGSKNA----IRFIGTRHGEKHYESLVSSEDMAKADDLGGYYRIP 286 A I LA + E+ G + I F G R GEK YE ++S ++ IP Sbjct: 530 KAVKIVDLATRMIELAGYRPGEDIEIEFTGLRPGEKLYEEVLSDKENT----------IP 579 Query: 287 MDGRDLNYAKYFVTGEKKVALLDDYT 312 + + + AK V + +LD YT Sbjct: 580 TENKKIMIAK--VRHYEYTDILDTYT 603 Lambda K H 0.319 0.135 0.373 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: 438 Number of extensions: 22 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: 341 Length of database: 641 Length adjustment: 33 Effective length of query: 308 Effective length of database: 608 Effective search space: 187264 Effective search space used: 187264 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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