Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_004308006.1 C665_RS10280 aldehyde dehydrogenase
Query= BRENDA::P77674 (474 letters) >NCBI__GCF_000310185.1:WP_004308006.1 Length = 500 Score = 324 bits (831), Expect = 4e-93 Identities = 183/481 (38%), Positives = 270/481 (56%), Gaps = 16/481 (3%) Query: 4 KLLINGELVSGEGEKQ-PVYNPATGDVLLEIAEASAEQVDAAVRAADAAF--AEWGQTTP 60 ++ I GE V G V +PA+G V + A +D AV AA AF +W + P Sbjct: 22 RMAIGGEWVEALGGGMLEVVDPASGQVFDRVPAGEATDIDRAVAAARRAFEQGDWPRMRP 81 Query: 61 KVRAECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNG 120 R LL+LA+++E + Q AE+E+ + GKP+ A ++ +VD R+ AG A + G Sbjct: 82 VDRERLLLRLAELVEAHAQELAEIEALDNGKPVTMARAVDVALVVDFLRYMAGWATKIEG 141 Query: 121 --------LAAGEYLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLK 172 L G+T RR+P+GVV +I PWN+PL+M AWK PALA+G +VLK Sbjct: 142 STMEVSVPLVRDREFFGYT---RREPVGVVGAIIPWNFPLLMVAWKAGPALASGCTMVLK 198 Query: 173 PSEITPLTALKLAELAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEH 231 P+E TPL+AL+ AEL + +PAGV N++ G G + G L H V V+ TGS G+ Sbjct: 199 PAEETPLSALRFAELVQQAGYPAGVFNVVTGHGHSAGAALAAHKGVDKVAFTGSTEIGKL 258 Query: 232 IISHTASSIKRTHMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKG 291 + ++ R +ELGGK+PVIV DDAD G ++N GQ C A R+Y K Sbjct: 259 VGKAALDNMTRVSLELGGKSPVIVLDDADPAVAAAGAAQAIFFNQGQVCCAGSRLYVHKS 318 Query: 292 IYDTLVEKLGAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGE 351 ++ +VE L A +K GA + ST++GPL S +RV + G + + GG Sbjct: 319 RFERVVEGLSGIAADMKLGAGIEPSTQIGPLVSAVQQQRVLGYIRSGFEEG-ARALAGGA 377 Query: 352 KRKGNGYYYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVW 411 +G GY+ PT+L D +V++E+FGPVV P+D+ ++V AND+ YGL +S+W Sbjct: 378 AGEGEGYFVKPTVLVDTRDDMRVVREEIFGPVVVAMPYDDLDEVARRANDTPYGLGASIW 437 Query: 412 TKDVGRAHRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVM 471 + D+ R HR+ +++ G WVN H +L + MP GG K SG G++M L+ YT + V+ Sbjct: 438 SNDLSRVHRLVPKIKAGTVWVNCHNILDASMPFGGYKQSGIGREMGRAVLDLYTEGKSVI 497 Query: 472 V 472 + Sbjct: 498 M 498 Lambda K H 0.317 0.134 0.397 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: 593 Number of extensions: 25 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: 474 Length of database: 500 Length adjustment: 34 Effective length of query: 440 Effective length of database: 466 Effective search space: 205040 Effective search space used: 205040 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: 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