Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate Synpcc7942_0026 Synpcc7942_0026 hypothetical protein
Query= BRENDA::Q8TZM9 (278 letters) >FitnessBrowser__SynE:Synpcc7942_0026 Length = 325 Score = 133 bits (334), Expect = 6e-36 Identities = 91/292 (31%), Positives = 146/292 (50%), Gaps = 40/292 (13%) Query: 18 VTAIGMGTWGIGGRETPDYSRDKESIE---AIRYGLELGMNLIDTAEFYGAGHAEEIVGE 74 V+A+G+GTW G Y +D + + + G++ DTAE YG G +E I+G Sbjct: 16 VSALGIGTWAWGDSLYWTYGQDYDEAQLQTTFATAIAAGVSFFDTAEIYGLGESERILGR 75 Query: 75 AIKEFEREDIFIVSKVWPT--HFGYEEAKKAARASAKRLGTY-IDLYLLHWPVDDFKKIE 131 +++ + + I +K +P FG + +KA S +RL I+LY +HWP Sbjct: 76 CLQQGD-QPAQIATKYFPIPWRFGSKAVQKALDQSLERLQRQSIELYQVHWPPAFLLGQT 134 Query: 132 ETLHALEDLVDEGVIRYIGVSNFNLELLQRSQEVMRKYEI--VANQVKYSVKDRWPETTG 189 + L L G I+ IGVSN+N L+++ ++ + + NQV+YS+ +R ET G Sbjct: 135 KILKTLAAAYKRGQIQAIGVSNYNARQLRQAHALLAEQGVPLAVNQVQYSLLERRIETNG 194 Query: 190 LLDYMKREGIALMAYTPLEKGTLA---------------------RNECLAK-------- 220 L + G+ ++AY PL +G L R++ L K Sbjct: 195 SLAAARELGVTILAYCPLAQGLLTGKYRPDADSRPTGARKINPQFRSQALEKLQPLLDQL 254 Query: 221 --IGEKYGKTAAQVALNYLIWEENVVAIPKASNKEHLKENFGAMGWRLSEED 270 +G++Y +T QVALN+LI + NV+ IP A + ++N GA+GW+LS ED Sbjct: 255 AALGDRYDRTIPQVALNWLIAQGNVIPIPGAKSPAQAQDNAGALGWQLSPED 306 Lambda K H 0.317 0.136 0.400 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: 203 Number of extensions: 9 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 278 Length of database: 325 Length adjustment: 27 Effective length of query: 251 Effective length of database: 298 Effective search space: 74798 Effective search space used: 74798 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 (21.7 bits) S2: 48 (23.1 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