Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate 6938545 Sama_2648 aldehyde dehydrogenase (RefSeq)
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__SB2B:6938545 Length = 498 Score = 281 bits (720), Expect = 3e-80 Identities = 176/485 (36%), Positives = 264/485 (54%), Gaps = 34/485 (7%) Query: 4 KLLINGELVSGEGEKQ-PVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAE--WGQTTP 60 + ING G++ +P G +L ++A D AV A A F W +P Sbjct: 22 RAFINGHYCDAVGKETFDCISPVDGRLLTQVASCQQADADIAVANARAVFESGVWSLQSP 81 Query: 61 KVRAECLLKLADVIEENGQVFAELESRNCGKPL-HSAFNDEIPAIVDVFRFFAGAARCLN 119 R + +++ A+++E + A LE+ + GKP+ HS VDV AGAAR + Sbjct: 82 VKRKKVMIRFAELLEAHADELALLETLDMGKPIAHSK-------AVDV----AGAARAIR 130 Query: 120 GLAAGEYLE-----------GHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNC 168 +GE ++ MI R+P+GVVA+I PWN+P++MA WKL PALA GN Sbjct: 131 W--SGEAIDKIYDELAPTPHNEIGMITREPVGVVAAIVPWNFPMLMACWKLGPALATGNS 188 Query: 169 VVLKPSEITPLTALKLAELAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIA 227 VVLKPSE +PLTA+++A+LAK+ P GV+N+L G G TVG L H V + TGS Sbjct: 189 VVLKPSEKSPLTAIRMAQLAKEAGLPDGVLNVLPGFGHTVGQALALHMDVDTLVFTGSTK 248 Query: 228 TGEHIISHTA-SSIKRTHMELGGKAPVIVFDDA-DIEAVVEGVRTFGYYNAGQDCTAACR 285 + ++ + S++KR +E GGK+P IVF+DA D++A E + +N G+ CTA R Sbjct: 249 IAKQLMVYAGQSNMKRVWLEAGGKSPNIVFNDAPDLKAAAEAAASAIAFNQGEVCTAGSR 308 Query: 286 IYAQKGIYDTLVEKLGAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIK 345 + + G+ D L++ + + + G P D +T G + L+ V ++ G K Sbjct: 309 LLVESGVKDELIKLIVKEMEAWQPGHPLDPATTCGAVVDKQQLDTVLGYIKAGHDEG-AK 367 Query: 346 VITGGEK--RKGNGYYYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQ 403 ++ GG + + G Y APT+ G I ++E+FGPV+SV FD ++ V AND+ Sbjct: 368 LMCGGSQVLAETGGVYVAPTVFDGVTNQMKIAREEIFGPVMSVITFDGMDEAVAIANDTI 427 Query: 404 YGLASSVWTKDVGRAHRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLED 463 YGLA+ VWT D+ +AH+ + L+ G W+N + P GG K SG G+D SL+ E Sbjct: 428 YGLAAGVWTSDISKAHKTAKALRSGMVWINHYDGGDMTAPFGGYKQSGNGRDKSLHAFEK 487 Query: 464 YTVVR 468 YT V+ Sbjct: 488 YTEVK 492 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: 582 Number of extensions: 29 Number of successful extensions: 6 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: 498 Length adjustment: 34 Effective length of query: 440 Effective length of database: 464 Effective search space: 204160 Effective search space used: 204160 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 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