Align Succinate-semialdehyde dehydrogenase; SsaDH; EC 1.2.1.16 (characterized)
to candidate WP_085635633.1 MGEO_RS04980 NAD-dependent succinate-semialdehyde dehydrogenase
Query= SwissProt::Q8GAI8 (450 letters) >NCBI__GCF_002115805.1:WP_085635633.1 Length = 476 Score = 474 bits (1219), Expect = e-138 Identities = 234/442 (52%), Positives = 306/442 (69%) Query: 1 MLATLASATSEDAVAALEAACAAQTSWARTAPRVRAEILRRAFDLVTARSEDFALLMTLE 60 +LA++ASA DA AAL+AA AA WA PR R+E+LR+A++L+T R EDFA L+TLE Sbjct: 31 VLASVASAEIADADAALDAAEAAMAEWAARTPRERSEVLRKAWELMTVRLEDFAKLITLE 90 Query: 61 MGKPLAEARGEVAYGAEFLRWFSEETVRDYGRYLTTPEGKNKILVQHKPVGPCLLITPWN 120 GK +A GE Y AEF RWF+EE VR G P +I+VQHKP G +L+TPWN Sbjct: 91 NGKARTDAMGEATYAAEFFRWFAEEAVRADGLITHAPASGARIMVQHKPAGLAVLVTPWN 150 Query: 121 FPLAMATRKVAPAVAAGCTMVLKPAKLTPLTSQLFAQTMMEAGLPAGVLNVVSSSSASGI 180 +P AM TRK+APA+AAGC +++KPA TPLT + EAG+P G++NV+ S + Sbjct: 151 YPAAMGTRKIAPALAAGCAVIIKPASETPLTMLALMPLLEEAGVPPGLVNVLPSKRTGAL 210 Query: 181 SGPLLKDSRLRKVSFTGSTPVGKRLMSDASRHVLRTSMELGGNAPFVVFEDADLDKAVEG 240 +L D R+R VSFTGST VG++L+ A+ VL+ +MELGGNAP VVFEDAD+D A+EG Sbjct: 211 VDHMLHDPRVRVVSFTGSTGVGRKLLHSAADQVLKPAMELGGNAPVVVFEDADMDTAIEG 270 Query: 241 AMAAKMRNMGEACTAANRFLVQESVAQEFTRKFAAAMGALSTGRGTDPASQVGPLINNGA 300 M AKMRN+GEACTAANR V E++A+ FT++ M AL G G DP VGPL+N Sbjct: 271 TMLAKMRNLGEACTAANRIYVHEAIAETFTKRLTEKMSALKVGDGIDPTVDVGPLVNAET 330 Query: 301 RDDIHALVTAAVDAGAVAVTGGAPVDGPGYFYQPTVLADVPNNAAILGQEIFGPVAPVTT 360 RD + V AV GA+ GG +GPG++Y PTVL++VP A + EIFGPVA + T Sbjct: 331 RDKVAEFVADAVAKGAIIECGGTTPEGPGFYYPPTVLSNVPETADCVHDEIFGPVAAIQT 390 Query: 361 FTTEQDAIKLANASEYGLAAYLYSRDFNRLLRVAEQIEFGMVGFNAGIISNAAAPFGGVK 420 F +++ I+ AN +EYGL AY++S D R L+V E++++GMVG N G++S+ AAPFGG K Sbjct: 391 FRDQEEVIRRANDTEYGLVAYVFSGDMKRALQVCERLDYGMVGLNRGLVSDPAAPFGGTK 450 Query: 421 QSGLGREGGSEGIAEYTTTQYI 442 QSGLGREGG EG+ E+ TQYI Sbjct: 451 QSGLGREGGHEGMLEFMETQYI 472 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: 17 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: 476 Length adjustment: 33 Effective length of query: 417 Effective length of database: 443 Effective search space: 184731 Effective search space used: 184731 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 24 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