Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate HSERO_RS19695 HSERO_RS19695 aldehyde dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_495 (480 letters) >FitnessBrowser__HerbieS:HSERO_RS19695 Length = 480 Score = 373 bits (958), Expect = e-108 Identities = 191/467 (40%), Positives = 287/467 (61%), Gaps = 2/467 (0%) Query: 12 QAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALPAWRALTAKE 71 Q +IDG + + + +V +PATG++LG +P A+ AI+AA +A WR ++ E Sbjct: 6 QLYIDGRFHGVEGRRYQEVRDPATGDVLGRLPWAERADIEEAIQAAHRAFQQWRQVSPLE 65 Query: 72 RATKLRRWYELIIENQDDLARLMTLEQGKPLAEAKGEIVYAASFIEWFAEEAKRIYGDVI 131 R+ LRR L E +A +T++ GKPLA+A EI+ AA ++W AEE +R+YG V+ Sbjct: 66 RSDILRRAAALARERAQAMAPAITMDNGKPLADAVAEIINAAEHLDWHAEEGRRLYGRVV 125 Query: 132 PGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFSAFA 191 P+ R +V+++P+GV AAI+PWNFP +K A+AAGCT+VLK S++P + Sbjct: 126 GARHPEVRQLVVREPVGVCAAISPWNFPFGQAMKKVAAAMAAGCTVVLKGPSESPAAIVL 185 Query: 192 LAELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLMSECAKDIKK 251 +A+L AG+PAGVF++VSG + +I L +P+VR +SFTGS +G +L ++ A +K+ Sbjct: 186 MAQLFHDAGVPAGVFNIVSGVSSEISQHLIESPLVRNISFTGSVPVGSKLAAQAALHMKR 245 Query: 252 VSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVYDAFAEKLKV 311 +S+ELGG+AP +VFDDA+++ A K RN GQ CV +R Y+Q G+Y F Sbjct: 246 MSMELGGHAPVLVFDDAEVEPAARLLARLKTRNAGQVCVSPSRFYVQKGIYARFVTAFAE 305 Query: 312 AVAKLKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVLAGGKPM--EGNFFEPT 369 A+ ++K+G G E G GPLI + VQ I DAL++G+ ++ GG + G+F+ PT Sbjct: 306 ALLQIKVGPGHEPGVQMGPLIHGRRFEAVQGLIDDALAQGSELVTGGARLGQRGHFYAPT 365 Query: 370 ILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARDLGRVFRVAE 429 ++T VP +A V +EE FGP+A + F + IAM+N GLASY + + L RV+ Sbjct: 366 LITGVPPSARVMQEEPFGPIAAVTPFSQAEEAIAMANALPLGLASYVFTQSLDTAHRVSR 425 Query: 430 ALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYL 476 L+ GMV +N +++ PFGGI SG G EG G E +L K + Sbjct: 426 DLQAGMVNINHSGMAHPELPFGGIGESGFGSEGGVEGFESFLVTKMI 472 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: 562 Number of extensions: 25 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: 480 Length of database: 480 Length adjustment: 34 Effective length of query: 446 Effective length of database: 446 Effective search space: 198916 Effective search space used: 198916 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 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