Align Succinate-semialdehyde dehydrogenase; SsaDH; EC 1.2.1.16 (characterized)
to candidate SMa0260 SMa0260 GabD3 succinate-semialdehyde dehdyrogenase
Query= SwissProt::Q8GAI8 (450 letters) >FitnessBrowser__Smeli:SMa0260 Length = 487 Score = 487 bits (1253), Expect = e-142 Identities = 246/444 (55%), Positives = 320/444 (72%) Query: 1 MLATLASATSEDAVAALEAACAAQTSWARTAPRVRAEILRRAFDLVTARSEDFALLMTLE 60 +LA +A A+ EDA A++AA AA W T R R+EILRR + L+T +E+ A L+ LE Sbjct: 42 LLAEVADASIEDAQRAVDAADAAAAGWRATPARQRSEILRRWYQLMTQHAEELATLIALE 101 Query: 61 MGKPLAEARGEVAYGAEFLRWFSEETVRDYGRYLTTPEGKNKILVQHKPVGPCLLITPWN 120 GK LA+ARGEVAY AEF RW++EE R G + TP G + ILV H+P+G +LITPWN Sbjct: 102 NGKALADARGEVAYAAEFFRWYAEEATRIPGEFRHTPSGSHNILVDHEPIGIAVLITPWN 161 Query: 121 FPLAMATRKVAPAVAAGCTMVLKPAKLTPLTSQLFAQTMMEAGLPAGVLNVVSSSSASGI 180 FP AMATRK+ PA+AAGCT++LKPA TPLT+ A+ EAG+P GV+NV+++S+ GI Sbjct: 162 FPAAMATRKIGPALAAGCTVILKPASETPLTAYAMARLGEEAGVPPGVVNVLTTSNPGGI 221 Query: 181 SGPLLKDSRLRKVSFTGSTPVGKRLMSDASRHVLRTSMELGGNAPFVVFEDADLDKAVEG 240 + +L D R+RK+SFTGST VG+ L+++A++ V+ SMELGGNAPF+VF+DADL+ A++G Sbjct: 222 TNAMLADPRVRKLSFTGSTGVGRVLLAEAAKSVVSCSMELGGNAPFIVFDDADLEVALDG 281 Query: 241 AMAAKMRNMGEACTAANRFLVQESVAQEFTRKFAAAMGALSTGRGTDPASQVGPLINNGA 300 AM AKMRN GEACTAANRF VQ + F A M +L G G DP +Q GP+I A Sbjct: 282 AMIAKMRNAGEACTAANRFYVQAGIHDAFVAGLTARMKSLKLGPGYDPETQCGPMITQNA 341 Query: 301 RDDIHALVTAAVDAGAVAVTGGAPVDGPGYFYQPTVLADVPNNAAILGQEIFGPVAPVTT 360 I LV+ A+ AGA A TGG P+ GYFY PTVL +VP NA+I +EIFGPVAPV Sbjct: 342 VRKIDRLVSEALAAGARATTGGKPLTENGYFYPPTVLENVPVNASIAREEIFGPVAPVYK 401 Query: 361 FTTEQDAIKLANASEYGLAAYLYSRDFNRLLRVAEQIEFGMVGFNAGIISNAAAPFGGVK 420 F ++ +AI+LAN +EYGLAAY+YSRD R ++V ++IE GM+G N G++S+ AAPFGGVK Sbjct: 402 FESDDEAIRLANNTEYGLAAYIYSRDLKRAMKVGKRIETGMLGINRGLMSDPAAPFGGVK 461 Query: 421 QSGLGREGGSEGIAEYTTTQYIGI 444 QSGLGREGG GI E+ +Y + Sbjct: 462 QSGLGREGGVTGILEFMEPKYFAV 485 Lambda K H 0.317 0.131 0.376 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: 528 Number of extensions: 15 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: 450 Length of database: 487 Length adjustment: 33 Effective length of query: 417 Effective length of database: 454 Effective search space: 189318 Effective search space used: 189318 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: 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