Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate BPHYT_RS05370 BPHYT_RS05370 aldehyde dehydrogenase
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__BFirm:BPHYT_RS05370 Length = 479 Score = 355 bits (910), Expect = e-102 Identities = 208/481 (43%), Positives = 289/481 (60%), Gaps = 15/481 (3%) Query: 19 ENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLS 78 E R FI GE++AA+ ET +DP P ++ARG + DID A+ AAR FE G W + Sbjct: 3 EARHFIGGEWSAASGGETIAVLDPSDGQPFTQLARGTAADIDAAVHAARRAFE-GPWGQA 61 Query: 79 SPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKV 138 S A+R +L +L+ L+ A EELA LE DTGKP++ + R D AR +YA A DK+ Sbjct: 62 SAAERGRILYRLSMLVAARQEELAQLEARDTGKPLKQA-RADSAALARYFEFYAGAADKL 120 Query: 139 YGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPL 198 +GE + + +REP GV IVPWN+P+ + +G ALA GN+ ++KP+E + L Sbjct: 121 HGETLPYQTGYTVLTIREPHGVTGHIVPWNYPMQIFGRSVGAALATGNACVVKPAEDACL 180 Query: 199 SAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGD 258 S +R+A LA EAGLP G LN+VTGFGHEAG AL+RH ID I+FTGS TGK + + A + Sbjct: 181 SVLRVAELAAEAGLPAGALNIVTGFGHEAGAALARHPGIDHISFTGSPDTGKLVTQMAAE 240 Query: 259 SNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEF 318 +++ V LE GGKS IVFAD DL A + I N GQ C AG+R+L++ +I + Sbjct: 241 NHVP-VTLELGGKSPQIVFADA-DLDAALPVLVSAIVQNAGQTCSAGSRVLIDRAIYEPL 298 Query: 319 LALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGE-------SKGQLLLDGR 371 L L + G P G LI V F+ + + + G+++ + Sbjct: 299 LDRLSSAFHALRVG-PSQADLDCGPLISAKQQRRVWDFLSDAQHDGIAMAAHGEVIPEAP 357 Query: 372 NAGLAAAIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWT 431 +G A PT+ DV + L+R+E+FGPVL F+ E++AL LAN + +GL A +WT Sbjct: 358 ESGFYQA--PTLLRDVPASHRLARDEVFGPVLAAMSFSDEDEALTLANGTPFGLVAGIWT 415 Query: 432 RDLSRAHRMSRRLKAGSVFVNNYN-DGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIW 490 RD +R R++RRL++G VF+NNY G + +PFGG K SG+GR+K AL FT LKTI Sbjct: 416 RDGARQMRLARRLRSGQVFINNYGAGGGVELPFGGVKHSGHGREKGFEALYGFTALKTIA 475 Query: 491 I 491 I Sbjct: 476 I 476 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: 604 Number of extensions: 33 Number of successful extensions: 7 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: 479 Length adjustment: 34 Effective length of query: 461 Effective length of database: 445 Effective search space: 205145 Effective search space used: 205145 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