Align Uncharacterized protein (characterized, see rationale)
to candidate HSERO_RS15795 HSERO_RS15795 6-phosphogluconolactonase
Query= uniprot:Q881W7 (359 letters) >FitnessBrowser__HerbieS:HSERO_RS15795 Length = 352 Score = 238 bits (608), Expect = 1e-67 Identities = 137/357 (38%), Positives = 207/357 (57%), Gaps = 22/357 (6%) Query: 3 AATFAYISSPADGLISQYRLDEQSGALSLVEQTKAGDQVNPMAISPDGKALFAALRSKPY 62 AAT AY+S I RL+ G+++L+++ G V P+AISPD K L+A+LR +PY Sbjct: 16 AATIAYVSHADSQDIYVLRLNND-GSVNLIDKVDTGSTVMPLAISPDRKYLYASLRREPY 74 Query: 63 QVLSFSIEPATGHLKPLSQAPLAESLAYLSTDRSGRFLFGASYGADLLSVQPIDAQHR-P 121 V S++I+PA+G LK LS+APLA+++A ++TDRSGR+L ASY + +SV I + Sbjct: 75 AVASYAIDPASGKLKALSKAPLADNMANIATDRSGRYLLAASYFGNKISVNAIGSDGAVQ 134 Query: 122 SDSIETYKTGMHAHSVRTDPSNRFVYAGNLGVDRVLQYRLEPKDGKLVPIGEGFVAVPDN 181 + + TG +AHSV+ DP+N FV+A NLG D +LQYR +P G + P VA Sbjct: 135 TPPLAVIPTGKNAHSVQVDPANAFVFASNLGSDVILQYRFDPASGAVTPNTPPSVASKAG 194 Query: 182 TGPRHLAFSSDGRFLYVVGEMSGTVTAFLINEKTGALKQVSQADGIPARLKLAPGQARDA 241 GPRH FS D RFLY E+ TV+ + + + G L + +P + Sbjct: 195 AGPRHFVFSPDQRFLYCANELDATVSTYAYDRQAGTLTLLGSDSALPEGFQ--------- 245 Query: 242 RNNDLKDDPTPRIWAADIRLAPDGKWLFISERTTSSVSVFKVDPAKGNVTFVENYPVEEK 301 + ++ AAD+ L PDG++L+ +ERT+++++ ++VD A G +T + N P E Sbjct: 246 --------SSEQLAAADLHLTPDGRFLYATERTSNTLTGYRVDRASGKLTRILNIPT-ET 296 Query: 302 QPRNIAVSPNGRWLLVSGEKSDKVGSYAI-GASGALKRVSEAPSGKGALWIEMLSQP 357 QPR + P GR+LL G+K+ + SYAI ASG L + G+ W+E++ P Sbjct: 297 QPRAFNIDPQGRYLLAVGQKAG-LTSYAIDAASGTLTPLFRYTLGRNPNWVEIIDLP 352 Lambda K H 0.314 0.132 0.383 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: 450 Number of extensions: 42 Number of successful extensions: 15 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: 359 Length of database: 352 Length adjustment: 29 Effective length of query: 330 Effective length of database: 323 Effective search space: 106590 Effective search space used: 106590 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: 42 (22.0 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