Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate PP_5278 PP_5278 4-guanidinobutyraldehyde dehydrogenase
Query= reanno::SB2B:6938906 (486 letters) >FitnessBrowser__Putida:PP_5278 Length = 497 Score = 190 bits (482), Expect = 1e-52 Identities = 157/471 (33%), Positives = 232/471 (49%), Gaps = 22/471 (4%) Query: 4 FINGQWL-AGEGKEMQSKNPANGEVIWQGKAAVPAQVQAAVMAARDAQFE---WFMLGFE 59 FING++ A G+ + +P +G + + + A AV AR A F W L Sbjct: 23 FINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENAR-ATFNSGVWSQLAPA 81 Query: 60 GRQAIVEAYRNELEANKAELAEVIAQETGKPRWETAT----EAAAMIGKIGLSVSAYHKR 115 R+A + + + L N ELA + + GKP ++++ AA I ++ + Sbjct: 82 KRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDE 141 Query: 116 TGTEVNEGAAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSELTPK 175 ++ ++ +P GVV P+NFP + + PAL GN+VV KPSE +P Sbjct: 142 VAPTPHDQLG---LVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPL 198 Query: 176 VAELMLKLWEKAGLPAGVINLVQGEVET-GKALASHPQLDGLFFTGSSRTGHLLHQQYAG 234 A + +L +AG+PAGV+N++ G T GKALA H +D L FTGS++ L YAG Sbjct: 199 TAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQL-MVYAG 257 Query: 235 HPG-KILALEMGGNNPLIV-KGVSDTRAAIHDIIQSAFISSGQRCTCARRLYVEKGAEGD 292 K + LE GG +P IV D +AA + + G+ CT RL VE+ + D Sbjct: 258 ESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIK-D 316 Query: 293 KLLAGLVEAVKAIKVGPWNADPQPFMGSMISETAAKGMLDAQRNLLNLGAKSLV--EMTH 350 K L +VEA+K K G DPQ +G+++ +L GAK L + T Sbjct: 317 KFLPMVVEALKGWKPGN-PLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTL 375 Query: 351 LQAGTGLVSPGLID-VTEVIELPDEEYFGPLLQVVRYTSFDEAIRLANDTRYGLSAGILA 409 + G V P + D VT + + EE FGP+L V+ + + +EA+ +ANDT YGL+AGI Sbjct: 376 EETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWT 435 Query: 410 DDKADYEYFLARIRAGIVNWNKQITGASGAAPFGGVGASGNHRASAFYAAD 460 D + +RAG V W Q G APFGG SGN R + +A + Sbjct: 436 SDISKAHKTARAVRAGSV-WVNQYDGGDMTAPFGGFKQSGNGRDKSLHALE 485 Lambda K H 0.317 0.133 0.393 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: 588 Number of extensions: 28 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: 486 Length of database: 497 Length adjustment: 34 Effective length of query: 452 Effective length of database: 463 Effective search space: 209276 Effective search space used: 209276 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 (21.6 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