Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_011842150.1 RSPH17029_RS16005 aldehyde dehydrogenase
Query= reanno::WCS417:GFF5420 (497 letters) >NCBI__GCF_000015985.1:WP_011842150.1 Length = 495 Score = 590 bits (1520), Expect = e-173 Identities = 288/491 (58%), Positives = 359/491 (73%) Query: 4 LTRADWEQRAKDLKIEGRAYINGEYTAAVSGDTFECISPVDGRLLATVASCDAADAQRAV 63 L DW RAK + + R +I+G+Y ++SG+TF CI P DGR L VASC+AAD AV Sbjct: 2 LQEIDWHARAKAVALPNRPFIDGQYVDSLSGETFACIYPGDGRPLTDVASCNAADVDVAV 61 Query: 64 ENARATFNSGVWSRLAPAKRKSAMLRFAALLKANAEELALLETLDMGKPISDSLNIDVPG 123 +AR F +GVWSR+APA R+ +LRF+ L+ AN EELALLETL++GKPI+++ N DV Sbjct: 62 RSARRAFEAGVWSRMAPADRRRILLRFSELILANREELALLETLNVGKPIANAYNGDVVS 121 Query: 124 AANALSWSGEAIDKIYDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGPALS 183 AA ++W EAIDK+Y EVAAT HD LV REP+G+V A+VPWN+P+ MA WKLGPAL+ Sbjct: 122 AAACIAWYAEAIDKVYGEVAATAHDMTTLVMREPLGIVAAVVPWNYPMSMAAWKLGPALA 181 Query: 184 TGNSVILKPSEKSPLTAIRIAALAVEAGIPKGVFNVLPGYGHTVGNALALHMDVDTLVFT 243 TGNSVILKP+E+SP TA++ LA+EAG+P GV NV+PG GH G AL LHMDVD + FT Sbjct: 182 TGNSVILKPAEQSPFTALKFGELAIEAGMPPGVLNVVPGLGHIAGKALGLHMDVDCVGFT 241 Query: 244 GSTKIAKQLLIRSGESNMKRVWLEAGGKSPNIVFADAPDLQAAAESAAGAIAFNQGEVCT 303 GST++ K + SG+SN+KR+ LE GGKSP +V AD DL AAA A I N G+VC Sbjct: 242 GSTEVGKYFMQYSGQSNIKRIGLELGGKSPQVVLADCDDLDAAAAGIAAGIFANTGQVCN 301 Query: 304 AGSRLLVERSIKDKFLPLVIEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAGHAD 363 AGSRL+V+ I D+ L + K + PG+PLD AT +G++V +QM+ VL YI+AG AD Sbjct: 302 AGSRLIVDEKIHDQLLEKIAAQAKVFAPGDPLDTATRMGSMVSEEQMDRVLGYIDAGRAD 361 Query: 364 GAKLVAGGKRTLEETGGTYVEPTIFDGVTNAMKIAKEEIFGPVLSVITFDSAEEAVAIAN 423 GA+ V GG R ETGG Y+EPTIF+GV N MKIA+EEIFGPVLS I +EA+A+AN Sbjct: 362 GARPVIGGGRVKTETGGFYIEPTIFEGVRNDMKIAQEEIFGPVLSAIPVKGFDEAMAVAN 421 Query: 424 DTIYGLAAAVWTADISKAHLTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHA 483 DT+YGLA AVWT + AH AK+LRAG VWVN +D G + PFGGFKQSG GRDKSLHA Sbjct: 422 DTVYGLAGAVWTGSVKNAHRAAKSLRAGVVWVNCFDRGSLAVPFGGFKQSGFGRDKSLHA 481 Query: 484 FDKYTELKATW 494 DKYT+LKA W Sbjct: 482 MDKYTDLKAVW 492 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: 726 Number of extensions: 23 Number of successful extensions: 1 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: 495 Length adjustment: 34 Effective length of query: 463 Effective length of database: 461 Effective search space: 213443 Effective search space used: 213443 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 Apr 10 2024. 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