Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate WP_043917574.1 jaqu_RS03630 betaine-aldehyde dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_495 (480 letters) >NCBI__GCF_000877395.1:WP_043917574.1 Length = 485 Score = 324 bits (830), Expect = 5e-93 Identities = 185/470 (39%), Positives = 274/470 (58%), Gaps = 6/470 (1%) Query: 14 FIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALPAWRALTAKERA 73 F+DGAWV+ +G + V PATG+++ V A RA+ +A A W A ER Sbjct: 12 FVDGAWVEDQDGPALDVVYPATGKVVARVHGATDAVLDRALASAAGAQTEWAATDPAERG 71 Query: 74 TKLRRWYELIIENQDDLARLMTLEQGKPLAEAK-GEIVYAASFIEWFAEEAKRIYGDVIP 132 LRR +LI DL+ L TL+ GKPL E + A +E+F A I G+ + Sbjct: 72 RILRRAADLIRARNRDLSELETLDTGKPLQETLVADAASGADALEYFGALAADIRGETM- 130 Query: 133 GHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFSAFAL 192 I++P+GV A I WN+P + KA PALAAG MV KP+ TP A + Sbjct: 131 -RFGADWAYTIRRPLGVCAGIGAWNYPTQIACWKAAPALAAGNAMVFKPSEATPLGALRI 189 Query: 193 AELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLMSECAKDIKKV 252 AE+ AG+PAG+F+VV G G +G+ LT++ V K+S TGS GR++ A +K V Sbjct: 190 AEILHEAGLPAGLFNVVQGD-GRVGATLTTDRRVAKVSLTGSVPTGREVAGAAAGAMKHV 248 Query: 253 SLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVYDAFAEKLKVA 312 ++ELGG +P ++F+DADL AV GAI + ++GQ C R+++Q G+ DAF +L Sbjct: 249 TMELGGKSPLLIFEDADLGDAVSGAINGNFYSSGQVCSNGTRVFVQRGLRDAFVSRLTER 308 Query: 313 VAKLKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVLAGGKPM--EGNFFEPTI 370 +A + IG+ L+ T GP+ E + V +HI A ++GATV AGG + EG + EPTI Sbjct: 309 LAGVVIGDPLDEATNYGPMTTEAQMRIVLDHIGRARAEGATVGAGGTRIDREGYWIEPTI 368 Query: 371 LTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARDLGRVFRVAEA 430 LT++ ++ A +EE FGP+ + F+DE + IA +N T FGLA+ + RDL R RVA A Sbjct: 369 LTDLTDDMACVREEIFGPVLSVLTFEDEDEAIARANATGFGLAAGIFTRDLTRAHRVAAA 428 Query: 431 LEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLGI 480 ++ G + +N ++ PFGG K SG+GRE ++ ++ Y E++ + +G+ Sbjct: 429 MQAGTIWINQYNLTPAGMPFGGSKMSGIGRENARAALDHYTEVQTIYVGM 478 Lambda K H 0.317 0.135 0.390 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: 589 Number of extensions: 23 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: 485 Length adjustment: 34 Effective length of query: 446 Effective length of database: 451 Effective search space: 201146 Effective search space used: 201146 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