Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate CA265_RS14635 CA265_RS14635 aldehyde dehydrogenase
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__Pedo557:CA265_RS14635 Length = 501 Score = 319 bits (817), Expect = 2e-91 Identities = 185/483 (38%), Positives = 277/483 (57%), Gaps = 16/483 (3%) Query: 23 FINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAK 82 +I G++ A + F+ + P+ K A D++ A+ AA F+ WS +S + Sbjct: 17 YIGGKFVAPVKGAYFDNISPIDGKVFTKAAHSTKEDLELAVDAAHEAFKT--WSKTSSTE 74 Query: 83 RKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEV 142 R +LNK+A ME + E LA +ET+D GK +R +L D+P R++A I G + Sbjct: 75 RSIILNKIAQRMEDNLEYLAAVETIDNGKAVRETLAADLPLGVDHFRYFAGVIRAEEGSL 134 Query: 143 ATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIR 202 + + +++IV EP+GV+A I+PWNFPLL+ WKL PALAAGN V+LKP+E +P+S + Sbjct: 135 SELDQNTVSLIVHEPIGVVAQIIPWNFPLLMGIWKLAPALAAGNCVVLKPAESTPVSIMV 194 Query: 203 LAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMK 262 L L + LP GV+NVV GFG E G+AL + + AFTGST TG+ +++ A + N+ Sbjct: 195 LMELIGDL-LPPGVVNVVNGFGSELGRALVTNPKVSKAAFTGSTPTGRLVMQYATE-NII 252 Query: 263 RVWLEAGGKSANIVF----ADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEF 318 V LE GGKS NI F A+ A A NQG++C +RLL++E I ++F Sbjct: 253 PVTLELGGKSPNIFFSSVMAEDDAFLDKAVEGAVMFALNQGEICTCPSRLLIQEDIYEKF 312 Query: 319 LALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDG-------R 371 +A + ++ + + G PLD MG + + ++I+ G+ +G +L G Sbjct: 313 IAKVIERTKAIKIGSPLDRTVMMGAQASKIQFEKIAAYIKLGKEEGAEVLTGGEINELPG 372 Query: 372 NAGLAAAIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWT 431 G I PTIF + + +EEIFGPVL VT F + E+A+++AND+ YGLGA VWT Sbjct: 373 ELGGGYYIKPTIFKGHN-KMRIFQEEIFGPVLAVTTFKTVEEAIEIANDTLYGLGAGVWT 431 Query: 432 RDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWI 491 RD +++ R ++AG V+VN Y+ PFGGYKQSG GR+ L + + K + I Sbjct: 432 RDAHELYQVPRAIQAGRVWVNQYHAYPAGAPFGGYKQSGVGRENHKMMLGHYRQTKNMLI 491 Query: 492 SLE 494 S + Sbjct: 492 SYD 494 Lambda K H 0.317 0.133 0.389 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: 521 Number of extensions: 18 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: 495 Length of database: 501 Length adjustment: 34 Effective length of query: 461 Effective length of database: 467 Effective search space: 215287 Effective search space used: 215287 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 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