Align D-alanine dehydrogenase (EC 1.4.99.-) (characterized)
to candidate HSERO_RS01605 HSERO_RS01605 amino acid dehydrogenase
Query= reanno::azobra:AZOBR_RS08020 (436 letters) >FitnessBrowser__HerbieS:HSERO_RS01605 Length = 421 Score = 257 bits (657), Expect = 4e-73 Identities = 148/413 (35%), Positives = 218/413 (52%), Gaps = 6/413 (1%) Query: 1 MRVIVLGSGVIGVSTAYFLAKAGHEVTVVDRQPGPALETSYANAGEVSPGYSAPWAAPGL 60 M + V+G+GVIGV+TAY L + GH+V+++D + P TS N ++S Y AP A P + Sbjct: 1 MHICVMGAGVIGVTTAYRLLQDGHQVSLIDERDQPGAGTSQGNGAQLSYSYVAPLADPSV 60 Query: 61 MAKAVKWMLMKHSPLVIRPKMDPAMWSWCLKLLANANERSYEINKGRMVRLAEYSRDCLR 120 +K ++ K SPL I+P ++ A + W L N S +++LA YSRD L Sbjct: 61 WSKWAYYLFSKDSPLTIKPTLEAAQYRWLAGFLRYCNAGSVRQTTIDLLQLAFYSRDQLT 120 Query: 121 VLRDETGIRYDERAKGTLQVFRTQKQVDAAATDMAVLDRFKVPYSLLDVEGCAAVEPALR 180 + +D + G L +F + ++AAA + ++ +LD C +EPAL Sbjct: 121 QWNGRLKLSFDHQRSGKLVMFTDAQGLEAAAGQVRFQAQYGCQQEVLDAAQCIRIEPALG 180 Query: 181 LVKEKIVGGLLLPGDETGDCFRFTNAL-AAMATELGVEFRYNTGIRKLESDGRRVTGVVT 239 + VGG+ +E GDC F AL AAM + F I + G ++ V Sbjct: 181 RSQRDWVGGVYTRSEEAGDCPAFCRALVAAMQADPNFRFIGGARITAVRRQGSALSAVQA 240 Query: 240 DAGTLTADSYVVAMGSYSPTLVKPFGLDLPVYPVKGYSLTLPIVD---AAGAPESTVMDE 296 ++A +V+A+G+ S + L LP+YP+KGYS+T+P+ D A AP+ ++ D Sbjct: 241 GNEWISAQRFVLALGADSADFARQLDLRLPLYPLKGYSITVPLEDEASRAAAPQVSITDI 300 Query: 297 THKIAVTRLGDRIRVGGTAELTGFDLTLRPGRRGPLDHVVSDLFP--TGGDLSKAEFWTG 354 KI RLG R+RV G EL G D ++ P L + +LFP G+ ++ W G Sbjct: 301 ARKIVYARLGQRLRVAGRIELVGQDRSIPPRAIAELKQGMRELFPDCVLGEDARLSPWMG 360 Query: 355 LRPNTPDGTPIVGPTPVRNLFLNTGHGTLGWTMAAGSGRVVADVVGGRQTEID 407 RP TP G PIVG PV NL+LN G G LGWT+A GS ++AD + GR ID Sbjct: 361 FRPATPSGVPIVGACPVDNLYLNIGQGALGWTLACGSAALIADQIAGRPCSID 413 Lambda K H 0.319 0.136 0.408 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: 439 Number of extensions: 25 Number of successful extensions: 4 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: 436 Length of database: 421 Length adjustment: 32 Effective length of query: 404 Effective length of database: 389 Effective search space: 157156 Effective search space used: 157156 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 (21.7 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