Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_034273599.1 AMYHA_RS20335 aldehyde dehydrogenase family protein
Query= BRENDA::P77674 (474 letters) >NCBI__GCF_000504245.1:WP_034273599.1 Length = 496 Score = 337 bits (863), Expect = 7e-97 Identities = 190/480 (39%), Positives = 281/480 (58%), Gaps = 19/480 (3%) Query: 4 KLLINGELV--SGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAE--WGQTT 59 +L I+G V +G + V NPA L + EA + VDAAV AA AF + W TT Sbjct: 3 ELFIDGRWVDTTGTAPARVVLNPANAAELATVCEADEKDVDAAVAAARRAFDDSPWRATT 62 Query: 60 PKVRAECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLN 119 + R E L ++A +++ + + A ES + GK + D + + VFR++A A Sbjct: 63 ARERGELLREIARLLQRDKEHLARTESLDTGKTMAEGRVD-VDDVTSVFRYYANLA---- 117 Query: 120 GLAAGEYLE-GHTSMIRR---DPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSE 175 AG ++ G S+I R +P+GV + IAPWNYPL+ +WKLAPALAAGN VV+KPSE Sbjct: 118 DNEAGRVVDTGDASVISRVVHEPVGVCSLIAPWNYPLLQMSWKLAPALAAGNTVVMKPSE 177 Query: 176 ITPLTALKLAELAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIIS 234 +TPLT ++L L ++ PAGV+N++ G G VG P+ HP V +VS TG + TG+ I++ Sbjct: 178 VTPLTTIELMRLVEEAGVPAGVVNLVLGGGANVGAPMVSHPDVDLVSFTGGLETGKKIMA 237 Query: 235 HTASSIKRTHMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYD 294 A +KR +ELGGK P +VF DAD + V+ + ++GQ C+A R+ + I+D Sbjct: 238 MAAEGVKRVALELGGKNPNVVFADADFDTAVDYALMAAFAHSGQVCSAGSRLIVESDIHD 297 Query: 295 TLVEKLGAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGG---- 350 V +L ++ G D +TE GPLSS H ++V + +EEAK G +++ GG Sbjct: 298 EFVAELARRADAIRLGDGLDPATECGPLSSAEHRDKVERHIEEAKTEG-ARLVVGGHRPT 356 Query: 351 EKRKGNGYYYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSV 410 E +GY+ PT+ A ++ IVQ EVFGPVV+V FD E++ + AND++YGLA +V Sbjct: 357 EPELADGYFLRPTVFADCDREMRIVQDEVFGPVVTVERFDTEDEAIRLANDTEYGLAGAV 416 Query: 411 WTKDVGRAHRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHV 470 WT D RA RV+ L++G W+N + + GG SG G+++ GLE+Y +H+ Sbjct: 417 WTSDASRAQRVAGALRHGTVWINDFHPYLPQAEWGGFGKSGIGRELGPSGLEEYRETKHI 476 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: 541 Number of extensions: 23 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: 496 Length adjustment: 34 Effective length of query: 440 Effective length of database: 462 Effective search space: 203280 Effective search space used: 203280 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