Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate WP_011842150.1 RSPH17029_RS16005 aldehyde dehydrogenase
Query= BRENDA::P23883 (495 letters) >NCBI__GCF_000015985.1:WP_011842150.1 Length = 495 Score = 470 bits (1210), Expect = e-137 Identities = 235/488 (48%), Positives = 326/488 (66%), Gaps = 4/488 (0%) Query: 9 WQDKALSLAIENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARG 68 W +A ++A+ NR FI+G+Y + ETF + P PL +A + D+D A+ +AR Sbjct: 7 WHARAKAVALPNRPFIDGQYVDSLSGETFACIYPGDGRPLTDVASCNAADVDVAVRSARR 66 Query: 69 VFERGDWSLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAI 128 FE G WS +PA R+ +L + ++L+ A+ EELALLETL+ GKPI ++ D+ AA I Sbjct: 67 AFEAGVWSRMAPADRRRILLRFSELILANREELALLETLNVGKPIANAYNGDVVSAAACI 126 Query: 129 RWYAEAIDKVYGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSV 188 WYAEAIDKVYGEVA T+ +++REP+G++AA+VPWN+P+ + WKLGPALA GNSV Sbjct: 127 AWYAEAIDKVYGEVAATAHDMTTLVMREPLGIVAAVVPWNYPMSMAAWKLGPALATGNSV 186 Query: 189 ILKPSEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRT 248 ILKP+E+SP +A++ LA EAG+P GVLNVV G GH AG+AL H D+D + FTGST Sbjct: 187 ILKPAEQSPFTALKFGELAIEAGMPPGVLNVVPGLGHIAGKALGLHMDVDCVGFTGSTEV 246 Query: 249 GKQLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRL 308 GK ++ +G SN+KR+ LE GGKS +V ADC DL AA+ AAGIF N GQVC AG+RL Sbjct: 247 GKYFMQYSGQSNIKRIGLELGGKSPQVVLADCDDLDAAAAGIAAGIFANTGQVCNAGSRL 306 Query: 309 LLEESIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLL 368 +++E I D+ L + QA+ + PG PLD AT MG+++ D V +I G + G + Sbjct: 307 IVDEKIHDQLLEKIAAQAKVFAPGDPLDTATRMGSMVSEEQMDRVLGYIDAGRADGARPV 366 Query: 369 DG----RNAGLAAAIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYG 424 G + I PTIF V + +++EEIFGPVL ++A+ +AND+ YG Sbjct: 367 IGGGRVKTETGGFYIEPTIFEGVRNDMKIAQEEIFGPVLSAIPVKGFDEAMAVANDTVYG 426 Query: 425 LGAAVWTRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFT 484 L AVWT + AHR ++ L+AG V+VN ++ G + VPFGG+KQSG GRDKSLHA++K+T Sbjct: 427 LAGAVWTGSVKNAHRAAKSLRAGVVWVNCFDRGSLAVPFGGFKQSGFGRDKSLHAMDKYT 486 Query: 485 ELKTIWIS 492 +LK +W + Sbjct: 487 DLKAVWFA 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: 684 Number of extensions: 25 Number of successful extensions: 2 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: 495 Length adjustment: 34 Effective length of query: 461 Effective length of database: 461 Effective search space: 212521 Effective search space used: 212521 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 Apr 10 2024. 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