Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate WP_085635633.1 MGEO_RS04980 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::Q88RC0 (480 letters) >NCBI__GCF_002115805.1:WP_085635633.1 Length = 476 Score = 416 bits (1069), Expect = e-121 Identities = 207/469 (44%), Positives = 302/469 (64%), Gaps = 3/469 (0%) Query: 14 YINGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTAKERS 73 YING W+ + + V NPAT EV+ +V A+ A++AA+ A+ W A T +ERS Sbjct: 7 YINGTWVSGASKERFDVLNPATEEVLASVASAEIADADAALDAAEAAMAEWAARTPRERS 66 Query: 74 AKLRRWFELMIENQDDLARLMTTEQGKPLAEAKGEIAYAASFIEWFAEEAKRIYGDTIPG 133 LR+ +ELM +D A+L+T E GK +A GE YAA F WFAEEA R G Sbjct: 67 EVLRKAWELMTVRLEDFAKLITLENGKARTDAMGEATYAAEFFRWFAEEAVRADGLITHA 126 Query: 134 HQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPYSALALV 193 R++V +P G+ +TPWN+PAAM TRK PALAAGC +++KPAS+TP + LAL+ Sbjct: 127 PASGARIMVQHKPAGLAVLVTPWNYPAAMGTRKIAPALAAGCAVIIKPASETPLTMLALM 186 Query: 194 ELAHRAGIPAGVLSVVTGS-AGEVGGELTGNSLVRKLSFTGSTEIGRQLMEECAKDIKKV 252 L AG+P G+++V+ G + + + VR +SFTGST +GR+L+ A + K Sbjct: 187 PLLEEAGVPPGLVNVLPSKRTGALVDHMLHDPRVRVVSFTGSTGVGRKLLHSAADQVLKP 246 Query: 253 SLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYDAFAEKLAAA 312 ++ELGGNAP +VF+DAD+D A+EG +++K RN G+ C ANRIYV + + + F ++L Sbjct: 247 AMELGGNAPVVVFEDADMDTAIEGTMLAKMRNLGEACTAANRIYVHEAIAETFTKRLTEK 306 Query: 313 VAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGKLIEGN--FFEPTI 370 ++ LK+G+G++ GPL++ + KV E + DAV+KGA + GG EG ++ PT+ Sbjct: 307 MSALKVGDGIDPTVDVGPLVNAETRDKVAEFVADAVAKGAIIECGGTTPEGPGFYYPPTV 366 Query: 371 LVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDMSRVFRVAEA 430 L +VP+TA +E FGP+A + F+D+ EVI +NDTE+GL +Y ++ DM R +V E Sbjct: 367 LSNVPETADCVHDEIFGPVAAIQTFRDQEEVIRRANDTEYGLVAYVFSGDMKRALQVCER 426 Query: 431 LEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCIS 479 L+YGMVG+N GL+S+ APFGG K SGLGREG G+ +++E +Y+ S Sbjct: 427 LDYGMVGLNRGLVSDPAAPFGGTKQSGLGREGGHEGMLEFMETQYISAS 475 Lambda K H 0.317 0.134 0.384 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: 588 Number of extensions: 20 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: 480 Length of database: 476 Length adjustment: 34 Effective length of query: 446 Effective length of database: 442 Effective search space: 197132 Effective search space used: 197132 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 (21.6 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