Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate 6938547 Sama_2650 methylmalonate-semialdehyde dehydrogenase (RefSeq)
Query= reanno::WCS417:GFF5420 (497 letters) >FitnessBrowser__SB2B:6938547 Length = 496 Score = 220 bits (560), Expect = 1e-61 Identities = 153/466 (32%), Positives = 231/466 (49%), Gaps = 33/466 (7%) Query: 23 YINGEYTAAVSGDTFECISPVDGRLLATVASCDAADAQRAVENARATFNSGVWSRLAPAK 82 ++NG++TA S T P G A V+ + A+ A+A F S WS++ P Sbjct: 7 FVNGQHTAP-SARTQTVFEPATGEARAQVSLASTQEVGEAIAVAKAAFES--WSQMTPLN 63 Query: 83 RKSAMLRFAALLKANAEELALLETLDMGKPISDSLNIDVPGAANALSWSGEAIDKIYDEV 142 R + +F AL++AN +ELA L T + GK + D+ + G ++ + Sbjct: 64 RARILFKFKALVEANMDELAQLITREHGKVLDDAKGELIRGL------------EVVEFA 111 Query: 143 AATPH-------DQLGL-----VTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVIL 190 PH Q+G +P+GVV I P+NFP+M+ W A++ GN+ I+ Sbjct: 112 CGIPHLLKGEHTAQVGTGVDAWAVNQPLGVVAGIAPFNFPVMVPMWMFPIAIACGNTFIM 171 Query: 191 KPSEKSPLTAIRIAALAVEAGIPKGVFNVLPGYGHTVGNALALHMDVDTLVFTGSTKIAK 250 KPSEK P + +RIA L EAG+P GVFNV+ G V + L H D+ + F GST IA Sbjct: 172 KPSEKDPSSVMRIAELLKEAGLPDGVFNVVNGDKEAV-DTLLTHKDIQAVSFVGSTPIA- 229 Query: 251 QLLIRSGESNMKRVWLEAGGKSPNIVFADAPDLQAAAESAAGAIAFNQGEVCTAGSRLLV 310 + + + ++ KRV G K+ ++ DA DL A + GA + GE C A S +L Sbjct: 230 EYIYATASAHGKRVQALGGAKNHMLLMPDA-DLDQAVNALMGAAYGSAGERCMAISVVLA 288 Query: 311 ERSIKDKFLPLVIEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAGHADGAKLVAG 370 D + ++ + K GN L P +G L+ Q ++ V SY+EAG +GA L+ Sbjct: 289 VGDAGDALVEKLLPKIAALKVGNGLIPDMEMGPLISAQHLDKVSSYVEAGVREGASLLVD 348 Query: 371 GKRTL--EETGGTYVEPTIFDGVTNAMKIAKEEIFGPVLSVITFDSAEEAVAIANDTIYG 428 G+ ++ G ++ +FD VT M I KEEIFGPVLS++ A+ + ND +G Sbjct: 349 GRELSMEDKANGYFLGACLFDHVTPQMSIYKEEIFGPVLSIVRVPDYNSALQLINDHEFG 408 Query: 429 LAAAVWTADISKAHLTAKALRAGSVWVNQYDGGDMT-APFGGFKQS 473 A++T A ++ G V VN M FGG+K+S Sbjct: 409 NGTAIFTQSGEAARHFCHHVQVGMVGVNVPIPVPMAFHSFGGWKRS 454 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: 551 Number of extensions: 34 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: 497 Length of database: 496 Length adjustment: 34 Effective length of query: 463 Effective length of database: 462 Effective search space: 213906 Effective search space used: 213906 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 09 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