Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_090447367.1 BLS63_RS19060 aldehyde dehydrogenase
Query= reanno::WCS417:GFF5420 (497 letters) >NCBI__GCF_900100495.1:WP_090447367.1 Length = 497 Score = 854 bits (2206), Expect = 0.0 Identities = 420/497 (84%), Positives = 460/497 (92%) Query: 1 MTTLTRADWEQRAKDLKIEGRAYINGEYTAAVSGDTFECISPVDGRLLATVASCDAADAQ 60 MT+LTRADWEQRAK L IEGRA+I+GEY AA SG TFECISPVDGRLLA VASCD ADA+ Sbjct: 1 MTSLTRADWEQRAKTLTIEGRAFIHGEYRAAKSGATFECISPVDGRLLAQVASCDLADAE 60 Query: 61 RAVENARATFNSGVWSRLAPAKRKSAMLRFAALLKANAEELALLETLDMGKPISDSLNID 120 AV +AR TF+SG WSRLAP RK M+RFAAL++ + EELALLETLDMGKPI D+L ID Sbjct: 61 IAVADARTTFDSGAWSRLAPVARKEVMIRFAALIEQHGEELALLETLDMGKPIGDALAID 120 Query: 121 VPGAANALSWSGEAIDKIYDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGP 180 V AA A+ WSGEAIDKIYDEVAATPH++LGLVTREP+GVV AIVPWNFPL+M+CWKLGP Sbjct: 121 VSSAARAIRWSGEAIDKIYDEVAATPHNELGLVTREPIGVVAAIVPWNFPLLMSCWKLGP 180 Query: 181 ALSTGNSVILKPSEKSPLTAIRIAALAVEAGIPKGVFNVLPGYGHTVGNALALHMDVDTL 240 AL+TGNSVILKPSEKSPLT IR+A LA+EAGIP GVFNVLPGYGHTVG ALALHMDVDTL Sbjct: 181 ALATGNSVILKPSEKSPLTGIRLAQLAIEAGIPAGVFNVLPGYGHTVGKALALHMDVDTL 240 Query: 241 VFTGSTKIAKQLLIRSGESNMKRVWLEAGGKSPNIVFADAPDLQAAAESAAGAIAFNQGE 300 VFTGSTKIAKQL++ +GESNMKRVWLEAGGKSPNIVFADAPDLQAAAE+AAGAIAFNQGE Sbjct: 241 VFTGSTKIAKQLMVYAGESNMKRVWLEAGGKSPNIVFADAPDLQAAAEAAAGAIAFNQGE 300 Query: 301 VCTAGSRLLVERSIKDKFLPLVIEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAG 360 VCTAGSRLLVE SIK++F+P+V+EA+K WKPGNPLDPATNVGALVDT QMN VL+YI+AG Sbjct: 301 VCTAGSRLLVENSIKERFVPMVVEAIKAWKPGNPLDPATNVGALVDTTQMNNVLAYIQAG 360 Query: 361 HADGAKLVAGGKRTLEETGGTYVEPTIFDGVTNAMKIAKEEIFGPVLSVITFDSAEEAVA 420 H DGAKLVAGGKR LEETGGTYVEPT+FDGV+NAM+IA+EEIFGPVLSVI FDSAEEAVA Sbjct: 361 HDDGAKLVAGGKRVLEETGGTYVEPTVFDGVSNAMRIAREEIFGPVLSVIGFDSAEEAVA 420 Query: 421 IANDTIYGLAAAVWTADISKAHLTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKS 480 IAND+ YGLAAAVWT+++SKAHLTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKS Sbjct: 421 IANDSPYGLAAAVWTSNLSKAHLTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKS 480 Query: 481 LHAFDKYTELKATWIKL 497 LHAFDKYTELKATWIKL Sbjct: 481 LHAFDKYTELKATWIKL 497 Lambda K H 0.316 0.132 0.386 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: 858 Number of extensions: 22 Number of successful extensions: 2 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: 497 Length of database: 497 Length adjustment: 34 Effective length of query: 463 Effective length of database: 463 Effective search space: 214369 Effective search space used: 214369 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 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