Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized)
to candidate WP_073948994.1 RH94_RS20650 aldehyde dehydrogenase family protein
Query= curated2:Q9K5Z5 (515 letters) >NCBI__GCF_001906585.1:WP_073948994.1 Length = 462 Score = 240 bits (613), Expect = 7e-68 Identities = 169/465 (36%), Positives = 226/465 (48%), Gaps = 27/465 (5%) Query: 50 DKIVSVNPAMKEQVIGVVSKASREIVDDAFKSAETAFHTWKNVNPEERANILIRAAAIIR 109 D I VNPA EQVI V + E VD A ++A A W P ERA L ++ Sbjct: 20 DAIEVVNPA-DEQVIATVPAGTAEDVDAAVRAARAALPGWAATPPAERAARLTALRDVLV 78 Query: 110 RRKHEFSAWLVKEAGKPWKEADADTAEA-IDFLEYYARQMITLKDGKPVNSREGEHNRYF 168 RK E + + E G P + A A I YA T + V + H Sbjct: 79 ARKDEIAETVTAELGSPLAFSQAVHAGVPIAVAGSYADLAATYAFEEKVGNSTVHHE--- 135 Query: 169 YTPIGVCVTISPWNFALAIMAGTTVAPIVTGNTVLLKPASTTPVVAAKFVEVLEEAGLPK 228 P+GV I+PWN+ L + + G T++LKPA TP+ A F E EAG+P Sbjct: 136 --PVGVVGAITPWNYPLHQIVAKAAPALAAGCTIVLKPAEDTPLTAQLFAEAAHEAGIPA 193 Query: 229 GVVNFVPGSGTDIGDYLIDHPKTSLITFTGSRDVGVRLYERAAVVHPGQQHLKRVIVEMG 288 GV+N V G G G L +HP L++FTGS VG R+ A +KRV +E+G Sbjct: 194 GVLNLVTGLGPVAGQALAEHPDVDLVSFTGSTAVGRRIGATAGAA------VKRVALELG 247 Query: 289 GKDTVVVDKDADLDLAAQSIVTSAFGFSGQKCSAGSRAVIHQDVYDVVLEKAVALTKQLS 348 GK V+ ADL A V + SGQ CSA +R ++H+D YD +E +A T Sbjct: 248 GKSANVILPSADLARAVNVGVANVMSNSGQTCSAWTRMLVHRDQYDEAVE--LAATAAAK 305 Query: 349 VGEPTAPDVYMGPVVDQGAFSKIMSYIEVGKEEG-RLMVGG-EGDDSKGFFIQPTIFADV 406 G+ +GPVV+ +++ YIE G EG RL+ GG E KG+F+ PT+FADV Sbjct: 306 YGD------RIGPVVNAKQRARVRGYIEKGIAEGARLVAGGPEAPCEKGYFVSPTVFADV 359 Query: 407 DPHARIMQEEIFGPVVAFSKARDFDHALEIANNTEYGLTGAVITTNRHHIEKAKRDFHVG 466 P + QEEIFGPV++ + D D AL IAN T YGL GAV + R G Sbjct: 360 TPDMTVAQEEIFGPVLSILRYDDEDDALRIANGTVYGLAGAVWAADETEAVAFARRMDTG 419 Query: 467 NLYFNRNCTGAIVGYHPFGGFKMSGTDSKAGGPDYLALHMQAKTV 511 + N G PFGG+K SG + G L ++Q K++ Sbjct: 420 QVDIN---GGRFNPLAPFGGYKQSGVGRELGAHG-LTEYLQTKSL 460 Lambda K H 0.318 0.135 0.394 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: 541 Number of extensions: 22 Number of successful extensions: 6 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: 515 Length of database: 462 Length adjustment: 34 Effective length of query: 481 Effective length of database: 428 Effective search space: 205868 Effective search space used: 205868 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: 52 (24.6 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