Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_013449840.1 SULKU_RS12970 phenylacetaldehyde dehydrogenase
Query= BRENDA::G5DDC2 (506 letters) >NCBI__GCF_000183725.1:WP_013449840.1 Length = 481 Score = 269 bits (687), Expect = 2e-76 Identities = 169/482 (35%), Positives = 253/482 (52%), Gaps = 24/482 (4%) Query: 14 FVDGEWRPPAQGRRLPVVNPTTEAHIGEIPAGTAEDVDAAVAAARAALKRNRGRDWARAP 73 F++G+ +P G+ + VNP T ++ +AED++ A++ A AA K WA+ Sbjct: 7 FINGQNKPSHPGKVIDDVNPATGEVFAKVHLASAEDIEEAISTAYAASKL-----WAKTT 61 Query: 74 GAVRAKYLRAIAAKVIERKQELAKLEALDCGKPYDEAAWDMDDVAGCFEYFADQAEALDK 133 + L A R E+ + + G Y +A +++ VA A +A + Sbjct: 62 PREKEAVLLKAADIFESRTDEIRTILMRESGSVYAKAMFEIGLVADILRVAAGEARRVFG 121 Query: 134 R---QNSPVSLPMETFKCHLRREPIGVVGLITPWNYPLLMATWKVAPALAAGCAAVLKPS 190 + N P L T R P+GV+ I+P+N P++++T K A A+AAG A VLKPS Sbjct: 122 QTFTSNDPGVLSYST------RRPLGVIAGISPFNAPMILSTKKFAMAIAAGNAFVLKPS 175 Query: 191 ELASVTCLELADICKEVGLPPGVLNIVTGLGPDAGAPLSAHPDVDKVAFTGSFETGKKIM 250 + L +I KE GLP GVLNI+ D G P + + TGS GK + Sbjct: 176 SHTPICGLIFGEIFKEAGLPDGVLNIIPCSSGDLGETFQTDPRIAMITLTGSTRVGKLVA 235 Query: 251 AAAAPMVKPVTLELGGKSPIVVFDDVDIDKAVEWTLFGCFWTNGQICSATSRLLVHTKIA 310 A+AA +K T+ELGGKSP +V D D+D AV+ F F GQIC A SR++V I Sbjct: 236 ASAAMHLKKCTVELGGKSPTIVLGDADVDYAVDTATFSIFLHQGQICMAGSRIIVEENIY 295 Query: 311 KEFNEKMVAWAKNIKVSDPLEEGCRLGPVVSEGQYEKIKKFILNAKSEGATILTGGVRPA 370 EF EK A K +KV +P + +GP++ E Q I I +A ++GAT+L+G Sbjct: 296 DEFCEKFAAKVKTLKVGNPEDPSTIIGPLIEEAQCRFIDGLIDDAVAKGATLLSG----- 350 Query: 371 HLEKGFFIEPTIITDITTSMEIWREEVFGPVLCVKEFSTEDEAIELANDTQYGLAGAVIS 430 +G F +PT+++++T M I+ EE FGP + + D IELAN++ YGL+ ++I+ Sbjct: 351 REHEGCFYKPTVVSNVTEEMVIFHEEAFGPAAAIIKARDLDHVIELANNSNYGLSSSIIT 410 Query: 431 GDRERCQRLSEEIDAGIIWVNCSQPCF---CQAPWGGNKRSGFGRELGEGGIDNYLSVKQ 487 + RLSEEI++G++ +N P P+GG K SG GRE G I+ +K Sbjct: 411 DNLSAALRLSEEIESGMVHIN--GPTIQDEAHIPFGGVKESGMGREGGHFAIEEMTELKW 468 Query: 488 VT 489 VT Sbjct: 469 VT 470 Lambda K H 0.318 0.135 0.421 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: 600 Number of extensions: 24 Number of successful extensions: 3 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: 506 Length of database: 481 Length adjustment: 34 Effective length of query: 472 Effective length of database: 447 Effective search space: 210984 Effective search space used: 210984 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