Align UDP-glucose-hexose-1-phosphate uridylyltransferase (EC 2.7.7.12) (characterized)
to candidate BWI76_RS08620 BWI76_RS08620 galactose-1-phosphate uridylyltransferase
Query= BRENDA::P09148 (348 letters) >FitnessBrowser__Koxy:BWI76_RS08620 Length = 348 Score = 685 bits (1768), Expect = 0.0 Identities = 321/348 (92%), Positives = 331/348 (95%) Query: 1 MTQFNPVDHPHRRYNPLTGQWILVSPHRAKRPWQGAQETPAKQVLPAHDPDCFLCAGNVR 60 M+ FNPVDHPHRRYNPLTGQWILVSPHRAKRPWQGAQETPAKQ LPAHDPDCFLC GN R Sbjct: 1 MSVFNPVDHPHRRYNPLTGQWILVSPHRAKRPWQGAQETPAKQSLPAHDPDCFLCPGNTR 60 Query: 61 VTGDKNPDYTGTYVFTNDFAALMSDTPDAPESHDPLMRCQSARGTSRVICFSPDHSKTLP 120 VTGDKNP+YTGT+VFTNDFAALM+DTPDAPES DPLMRCQSARGTSRVICFSPDHSKTLP Sbjct: 61 VTGDKNPNYTGTFVFTNDFAALMTDTPDAPESDDPLMRCQSARGTSRVICFSPDHSKTLP 120 Query: 121 ELSVAALTEIVKTWQEQTAELGKTYPWVQVFENKGAAMGCSNPHPHGQIWANSFLPNEAE 180 ELSV AL +VKTWQEQTA+LGKTYPWVQVFENKGAAMGCSNPHPHGQ+WANSFLPNEAE Sbjct: 121 ELSVEALEGVVKTWQEQTADLGKTYPWVQVFENKGAAMGCSNPHPHGQVWANSFLPNEAE 180 Query: 181 REDRLQKEYFAEQKSPMLVDYVQRELADGSRTVVETEHWLAVVPYWAAWPFETLLLPKAH 240 REDRLQK YF E +PMLVDY QRELADGSRTVVETEHWLAVVPYWAAWPFETLLLPKAH Sbjct: 181 REDRLQKAYFTEHGAPMLVDYAQRELADGSRTVVETEHWLAVVPYWAAWPFETLLLPKAH 240 Query: 241 VLRITDLTDAQRSDLALALKKLTSRYDNLFQCSFPYSMGWHGAPFNGEENQHWQLHAHFY 300 V R+TDLTD QRSDLALALKKLTSRYDNLFQCSFPYSMGWHGAPFN EEN HWQLHAHFY Sbjct: 241 VQRLTDLTDDQRSDLALALKKLTSRYDNLFQCSFPYSMGWHGAPFNDEENNHWQLHAHFY 300 Query: 301 PPLLRSATVRKFMVGYEMLAETQRDLTAEQAAERLRAVSDIHFRESGV 348 PPLLRSATVRKFMVGYEMLAETQRDLTAEQAAERLRAVSD+HFRESGV Sbjct: 301 PPLLRSATVRKFMVGYEMLAETQRDLTAEQAAERLRAVSDVHFRESGV 348 Lambda K H 0.319 0.133 0.425 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: 649 Number of extensions: 19 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: 348 Length of database: 348 Length adjustment: 29 Effective length of query: 319 Effective length of database: 319 Effective search space: 101761 Effective search space used: 101761 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: 49 (23.5 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