Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate WP_013554916.1 NITSA_RS10015 polysaccharide biosynthesis protein
Query= SwissProt::Q9ZDJ5 (341 letters) >NCBI__GCF_000186245.1:WP_013554916.1 Length = 597 Score = 139 bits (351), Expect = 1e-37 Identities = 109/328 (33%), Positives = 164/328 (50%), Gaps = 29/328 (8%) Query: 5 KTLMITGGTGSFGNAVLSRFL----KSNIINDIKEIRIFSRDEKKQEDMRIALNNSKLKF 60 K ++ITG GS G+ + + L K I+ + E ++ E+ ++D + S L Sbjct: 280 KRILITGAGGSIGSEICRQCLAYGAKRLILVENSEYNLYRISEELEKDRIVPRLVSVL-- 337 Query: 61 YIGDVRNYQSIDDAMHGVDYVFHAAALKQVPTCEFYPMEAINTNVLGAENVLSAAINNKV 120 D + + A H D V HAAA K VP CE P AI N+LGA NV+ +I V Sbjct: 338 ---DRERLEEVFKAEHP-DVVIHAAAFKHVPLCELNPDTAIENNILGAMNVIDLSIRYGV 393 Query: 121 TKVIVLSTDKAVYPINAMGLSKALMEKLAIAKARMRSPGETILCVTRYGNVMASRGSVIP 180 KV+ +S+DKAV P N MG +K ++E A R T + R+GNV+ S GSV+P Sbjct: 394 EKVVNISSDKAVRPTNVMGATKRIIELYAQNVPNDR----TEIVSVRFGNVLGSSGSVVP 449 Query: 181 LFIHQIKQGKELTITEPSMTRFLMSLVDSVDLVLYAFEHGRQGDIFV--QKSPASTIEVL 238 F QI+ G +T+T P MTR+ M + ++ LVL A + G++F+ P ++ L Sbjct: 450 KFKAQIEAGGPVTVTHPEMTRYFMLIPEACQLVLQAAAMAQGGELFILDMGEPVKIVD-L 508 Query: 239 AKALQEIFGSKNAIRFI--GTRHGEKHYESLVSSEDMAKADDLGGYYRIPMDGRDLNYAK 296 A+ + ++G + + + G R GEK YE L+ ++ K Y I + GR NY Sbjct: 509 ARKMIRLYGKEGEVDIVYTGLRPGEKLYEELLINDAECKT----RYESIYVAGRS-NYPI 563 Query: 297 YFVTGEKKVALLDDYTSHNTKRLNLKEV 324 EK A + KR+ LKE+ Sbjct: 564 -----EKLRADIRHLLEAKDKRVLLKEI 586 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: 400 Number of extensions: 16 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: 597 Length adjustment: 33 Effective length of query: 308 Effective length of database: 564 Effective search space: 173712 Effective search space used: 173712 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 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