Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate GFF657 Psest_0671 NAD-dependent aldehyde dehydrogenases
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__psRCH2:GFF657 Length = 506 Score = 325 bits (833), Expect = 2e-93 Identities = 191/484 (39%), Positives = 274/484 (56%), Gaps = 18/484 (3%) Query: 23 FINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAK 82 FINGE+ + F + PV P+A+ R + DI++A+ AA + W +S Sbjct: 22 FINGEFVEPVNGQYFTNLSPVNGQPIAEFPRSDAADIEKALDAAHAAADA--WGKTSVQA 79 Query: 83 RKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEV 142 R +L ++AD +E + E LA+ ET D GK +R +L DIP AA R++A I G Sbjct: 80 RSLILLQIADRIEQNLEMLAVTETWDNGKAVRETLNADIPLAADHFRYFAGCIRAQEGTS 139 Query: 143 ATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIR 202 A H A EP+GV+ I+PWNFP+L+ WKL PALAAGN V+LKP+E++PL Sbjct: 140 AEIDEHTAAYHFHEPLGVVGQIIPWNFPILMAAWKLAPALAAGNCVVLKPAEQTPLGITV 199 Query: 203 LAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMK 262 L + + LP GVLNVV G+G EAG+AL+ I IAFTGST G ++K A ++ + Sbjct: 200 LMEVIGDL-LPPGVLNVVQGYGREAGEALASSKRIAKIAFTGSTPVGSHIMKRAAEAIIP 258 Query: 263 RVWLEAGGKSANIVFADCPD-----LQQAASATAAGIFYNQGQVCIAGTRLLLEESIADE 317 +E GGKS NI F D +++AA G F+NQG+VC +R L++ESI Sbjct: 259 ST-VELGGKSPNIYFEDIMQAEPTFIEKAAEGLVLG-FFNQGEVCTCPSRALVQESIYAP 316 Query: 318 FLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRNA---- 373 F+ + ++ + G PLD T +G D + S++ + +G +L G A Sbjct: 317 FMEAVMKKVAQIKRGDPLDTETMVGAQASQQQFDKIMSYLEIAKGEGAEVLTGGAAEKLE 376 Query: 374 -GLAAA--IGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVW 430 LA I PT+ + + +EEIFGPV+ VT F E +AL +AND++YGLGA VW Sbjct: 377 GSLATGYYIQPTLLKGTN-QMRVFQEEIFGPVIGVTTFKDEAEALAIANDTEYGLGAGVW 435 Query: 431 TRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIW 490 TRD++RA+RM R +KAG V+ N Y+ FGGYK+SG GR+ L+ + + K + Sbjct: 436 TRDINRAYRMGRAIKAGRVWTNCYHLYPAHAAFGGYKRSGVGRETHKMILDSYQQTKNLL 495 Query: 491 ISLE 494 IS + Sbjct: 496 ISYD 499 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: 526 Number of extensions: 20 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: 495 Length of database: 506 Length adjustment: 34 Effective length of query: 461 Effective length of database: 472 Effective search space: 217592 Effective search space used: 217592 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