Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate WP_092344789.1 BLU87_RS03510 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P23883 (495 letters) >NCBI__GCF_900107645.1:WP_092344789.1 Length = 452 Score = 224 bits (572), Expect = 4e-63 Identities = 139/454 (30%), Positives = 223/454 (49%), Gaps = 6/454 (1%) Query: 38 ETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAKRKAVLNKLADLMEAH 97 E+++P T L + + A G ++ +W +S A+RK++L K A ++ Sbjct: 4 ESLNPATGEVLETFDEWSDEQVATTIEAVHGAYQ--NWRTTSFAERKSLLLKAAVILRQR 61 Query: 98 AEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEVATTSSHELAMIVREP 157 +E A + L+ GKP+ R +I A +YAE +++ S + + P Sbjct: 62 KDEFATMMALEMGKPVVEG-RAEIEKCALVCNYYAENAEQMLAPEPIASDASRSYVAFRP 120 Query: 158 VGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIRLAGLAKEAGLPDGVL 217 G++ A++PWNFP PAL AGN +LK + P A+ + + EAG P V Sbjct: 121 QGIVLAVMPWNFPFWQVFRFAAPALMAGNVGVLKHASNVPRCALAIEQVFVEAGYPADVF 180 Query: 218 NVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMKRVWLEAGGKSANIVF 277 + + Q + H + A TGS G+++ + +G + +K+ +E GG IV Sbjct: 181 RTLMIGSGKVAQVIE-HPYVVATTLTGSDIAGRKVAEKSG-AMLKKSVMELGGSDPFIVL 238 Query: 278 ADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLALLKQQAQNWQPGHPLDP 337 D DL AAS N GQ CIA R ++E+ I + FL K + G P D Sbjct: 239 NDA-DLDLAASVAVTARCINSGQSCIAAKRFIVEDGIYETFLEKFKANMAALKMGDPCDE 297 Query: 338 ATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRNAGLAAAIGPTIFVDVDPNASLSREE 397 T +G +H + +KG ++ G G AA PTI V EE Sbjct: 298 TTQVGPQAREDLMRELHRQVEGSVAKGAKVILGGMPGEAAFYPPTILTQVSKGMPAYNEE 357 Query: 398 IFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDLSRAHRMSRRLKAGSVFVNNYNDG 457 FGPV +V R E+AL +AND+++GLG +VWTRD+ + +++ +++G+VFVN+ Sbjct: 358 FFGPVAIVIRVKDAEEALFVANDTEFGLGGSVWTRDIIKGEKIAGEIRSGAVFVNSMTKS 417 Query: 458 DMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWI 491 D +PFGG SG GR+ S + +++F ++T+WI Sbjct: 418 DPRLPFGGVGISGFGRELSHYGIKEFVNIQTVWI 451 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: 473 Number of extensions: 24 Number of successful extensions: 4 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: 452 Length adjustment: 33 Effective length of query: 462 Effective length of database: 419 Effective search space: 193578 Effective search space used: 193578 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: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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