Align Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial; P5C dehydrogenase; Aldehyde dehydrogenase family 4 member A1; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate RR42_RS13660 RR42_RS13660 aldehyde dehydrogenase
Query= SwissProt::Q8CHT0 (562 letters) >FitnessBrowser__Cup4G11:RR42_RS13660 Length = 490 Score = 148 bits (373), Expect = 6e-40 Identities = 126/430 (29%), Positives = 191/430 (44%), Gaps = 37/430 (8%) Query: 115 WDLKPMADRAQVFLKAADMLSGPRRAEVLAKTM-VGQGKTVIQAEIDAAAELIDFFRFNA 173 W + +RA V + AD++ RAE LA+ + GK + + A F+F A Sbjct: 60 WAQRKPHERAAVLHRVADLIRA--RAEPLAQRQRLDNGKPISETRA-LVASAAGTFQFFA 116 Query: 174 KFAVELEGEQPISVPPSTNHTVYRGLEGFVAAISPFNFTAIGGNLAGAPALM-GNVVLWK 232 LE + +V+ + G VAAI+P+N APAL GN V+ K Sbjct: 117 AACETLEEALTPARGDFLTMSVHEAM-GVVAAITPWNSPIASEAQKLAPALAAGNAVVIK 175 Query: 233 PSDTAMLASYAVYRILREAGLPPNIIQFVPADGPTFGDTVTSSEHLCGINFTGSVPTFKH 292 P++ L + + I EAG+P +I +P G GD +T + ++FTG T +H Sbjct: 176 PAEITPLMALELAAICEEAGVPKGLISVLPGKGSVIGDAITKHPLVRRVSFTGGTTTGRH 235 Query: 293 LWRQVAQNLDRFRTFPRLAGECGGKNFHFVHSSADVDSVVSGTLRSAFEYGGQKCSACSR 352 + A + ++ E GGK+ V AD+D V+G L F G+ C A SR Sbjct: 236 IAHIAADKM------MPVSLELGGKSPTMVFDDADLDHAVNGVLYGIFSSSGESCIAGSR 289 Query: 353 LYVPKSLWPQIKGRLLEEHSRIKVGDPAEDFGTFFSAVIDAKAFARIKKWLEHARSSPSL 412 L+V +SL+ RL E +R++VGDPA++ + D + + S +L Sbjct: 290 LFVARSLYEPFMDRLAEGAARLRVGDPADERTQMGPLISD--------RHRDSIESYVAL 341 Query: 413 SILAGGQCNE----------SVGYYVEPCIIESKDPQEPIMKEEIFGPVLTVYVYPDDKY 462 + GGQ GY+ P IIE D + +EEIFGPVL + D+ Sbjct: 342 GVSEGGQLRTGGIRPAVAGCENGYFYTPTIIEGLDNSARVCQEEIFGPVLVAMAFDDE-- 399 Query: 463 RETLQLVDSTTSYGLTGAVFAQDKAIVQEATRMLRNAAGNFYINDKSTGSVVGQQPFGGA 522 + L + + Y L V+ +D R ++ AGN +IN S+ PFGG Sbjct: 400 -DDLIAQANDSVYALAAGVWTRDYKRAWRFARAVQ--AGNVWINTYKQFSI--STPFGGW 454 Query: 523 RASGTNDKPG 532 R SG + G Sbjct: 455 RDSGLGREKG 464 Lambda K H 0.319 0.135 0.411 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: 619 Number of extensions: 26 Number of successful extensions: 3 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: 562 Length of database: 490 Length adjustment: 35 Effective length of query: 527 Effective length of database: 455 Effective search space: 239785 Effective search space used: 239785 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 (21.8 bits) S2: 52 (24.6 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