Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate Ac3H11_1480 Aldehyde dehydrogenase B (EC 1.2.1.22)
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1480 Length = 486 Score = 312 bits (799), Expect = 2e-89 Identities = 178/472 (37%), Positives = 264/472 (55%), Gaps = 4/472 (0%) Query: 1 MQHKLLINGELVSGE-GEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTT 59 ++ + I+G+ V + G V NPA G ++ I A A Q A+ AAD AF W T Sbjct: 12 LKARCYIDGQWVDADNGATLAVNNPANGALIGTIPNAGAAQTQTAIAAADRAFGPWKDRT 71 Query: 60 PKVRAECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLN 119 + RA L + +++ ++ + A + + GKPL A EI +FA AR + Sbjct: 72 AEDRARILRRWFELMLQHQEDLALIMTSEQGKPLAEA-RGEIAYAASYIEWFAEEARRIY 130 Query: 120 GLAAGEYLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPL 179 G ++ R+P+GV A+I PWN+P M K+APALAAG +++KP+ TPL Sbjct: 131 GEVIPSPWLDKRIVVTREPVGVCAAITPWNFPAAMITRKVAPALAAGCTIIVKPATQTPL 190 Query: 180 TALKLAELAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTAS 238 +AL +AELA PAGV +++ G + +G LT P VR ++ TGS G + + A Sbjct: 191 SALAMAELAARAGVPAGVFSVITGDARPIGAELTASPVVRKLTFTGSTEIGRVLAAQCAP 250 Query: 239 SIKRTHMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVE 298 ++K+ +ELGG AP IVF+DAD++A V G Y N GQ C A R+ Q G+YD E Sbjct: 251 TLKKMSLELGGNAPFIVFEDADLDAAVAGAMASKYRNTGQTCVCANRLLVQDGVYDAFAE 310 Query: 299 KLGAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGY 358 KL VA LK G +E E GPL A L +V V +AKA G +V+TGG + G Sbjct: 311 KLARTVAALKVGHGLEEGVEQGPLIDEASLTKVEALVADAKARG-ARVVTGGRRHALGGT 369 Query: 359 YYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRA 418 +Y PT+LA D + ++E+FGPV + F E + + AND+++GLA+ +++DVGR Sbjct: 370 FYEPTILADITPDMRMAREEIFGPVAPLFRFHTEAEAIQMANDTEFGLAAYFYSRDVGRV 429 Query: 419 HRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHV 470 RVS LQYG +N + + P GG K SG G++ S++G+E+Y +++ Sbjct: 430 WRVSGALQYGMVGINAGVISTAVAPFGGVKQSGMGREGSVHGIEEYVDTKYL 481 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: 546 Number of extensions: 25 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: 474 Length of database: 486 Length adjustment: 34 Effective length of query: 440 Effective length of database: 452 Effective search space: 198880 Effective search space used: 198880 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: 51 (24.3 bits)
This GapMind analysis is from Sep 17 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