Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate RR42_RS25010 RR42_RS25010 betaine-aldehyde dehydrogenase
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__Cup4G11:RR42_RS25010 Length = 485 Score = 374 bits (960), Expect = e-108 Identities = 202/475 (42%), Positives = 287/475 (60%), Gaps = 5/475 (1%) Query: 21 RLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSP 80 RL I G + AA +TFE ++P T+ L +A S DID A++AAR F+ W SP Sbjct: 14 RLLIGGRWVEAASGKTFEVINPSTEELLCHVAEANSADIDAAVAAARHAFDNSSWVGMSP 73 Query: 81 AKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYG 140 R L ++AD ++ HA+ELA +ETLD G P+ S AA R+Y K+ G Sbjct: 74 HARTRALLRIADQIDRHADELAAIETLDNGMPLWFSTAVATT-AADIFRYYGGWCTKILG 132 Query: 141 EVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSA 200 + + +REP+GV I+PWN P+L+ KL AL GN++ILKP+E + L++ Sbjct: 133 STIPSDASGFVYTLREPLGVCGQIIPWNVPILMASIKLANALCCGNTLILKPAELACLTS 192 Query: 201 IRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSN 260 +RLA L +E LP GV+N++ GFG AG AL+ H D+D IAFTGST GKQ+++ A SN Sbjct: 193 LRLAELIQETDLPPGVINMLPGFGATAGAALALHPDVDKIAFTGSTAIGKQIVQ-ASTSN 251 Query: 261 MKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLA 320 +K+V LE GGKS N++FAD DL +A A N GQVC AGTRL + ES+ DE Sbjct: 252 LKKVTLELGGKSPNVIFADA-DLDKAVQAAVKTFCGNSGQVCSAGTRLFVHESVHDEVSE 310 Query: 321 LLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRN--AGLAAA 378 + + A + G PL P T +G LI D V S+I G++ G L G + +G Sbjct: 311 RVTRLAATYTVGDPLAPDTKLGPLISAKQRDRVLSYIEAGQAGGASLQLGGSQWSGRGYF 370 Query: 379 IGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDLSRAH 438 + P +F V +++EEIFGPVL + F E+ A+ ND+ YGL AAVWTRD++RAH Sbjct: 371 VAPAVFDGVTNGMRIAQEEIFGPVLSIIPFRDEDDAVFKGNDTTYGLSAAVWTRDVARAH 430 Query: 439 RMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWISL 493 +++R LKAG V++N Y + D +PFGGYKQSG GR+ +++ +T++K + + + Sbjct: 431 KVARALKAGRVWINTYGEADPAMPFGGYKQSGWGREFGQESIDAYTQVKAVMLRM 485 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: 593 Number of extensions: 25 Number of successful extensions: 5 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: 485 Length adjustment: 34 Effective length of query: 461 Effective length of database: 451 Effective search space: 207911 Effective search space used: 207911 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