Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_011385953.1 AMB_RS18195 DUF1487 domain-containing protein
Query= BRENDA::P77674 (474 letters) >NCBI__GCF_000009985.1:WP_011385953.1 Length = 496 Score = 286 bits (731), Expect = 1e-81 Identities = 175/472 (37%), Positives = 258/472 (54%), Gaps = 14/472 (2%) Query: 4 KLLINGELV-SGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKV 62 K LI G+LV +G GE V NPATG+++ A + E VD AV +A AA +W + + + Sbjct: 19 KHLIGGKLVPAGCGEVFEVDNPATGEIIGTAAFGTKEDVDIAVISAKAAQKDWAKQSARA 78 Query: 63 RAECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLA 122 R + + + V+ + + L + GK L + E + D+F FF G L Sbjct: 79 RGKLVAECGRVLSAHVEELGRLVALETGKALRTESRVEAGVLADMFTFFGG----LGSEL 134 Query: 123 AGEYLEGHTSMIR---RDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPL 179 GE + + M+ R+P+GVV I PWN PL++ A K A AL AGN VV+K +E PL Sbjct: 135 KGETIPFNPDMLTVTVREPVGVVGCIIPWNVPLLLMAMKAAAALVAGNSVVVKSAEEAPL 194 Query: 180 TALKLAELAKDIFPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASS 239 T L++AE+ + P G+ N+L G G G PL HP V+ V+ TGS+ TG + A Sbjct: 195 TVLRVAEIMNTVLPPGLFNMLSGFGPECGAPLVEHPDVKKVTFTGSVETGRIVYKAAAEK 254 Query: 240 IKRTHMELGGKAPVIVFDDADIEAVVEG-VRTFGYYNAGQDCTAACRIYAQKGIYDTLVE 298 + +ELGGK+P+IV DAD++ V G + + GQ CTA+ R++ + I+D V Sbjct: 255 LIPVTLELGGKSPMIVCADADMDQAVAGALAGMRFTRQGQSCTASSRLFVHESIHDEFVA 314 Query: 299 KLGAAVATLKSGAPDDESTELGPLSSLAHLERVG---KAVEEAK-ATGHIKVITGGEKRK 354 K+ A V + G P DE T++G + S LERV K EE K AT H+ + + Sbjct: 315 KVKAKVDAMVMGDPLDEKTDIGTIVSDGQLERVRSYIKIGEETKGATKHVCSALPTDPKL 374 Query: 355 GNGYYYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKD 414 G + P + G D + Q+E+FGPV +V + + E V+ ANDS+YGLA+S+WT+D Sbjct: 375 AKGRFVQPVIFTGMKNSDRLCQEEIFGPVCAVIKWSDYEDVLAQANDSEYGLAASIWTRD 434 Query: 415 VGRAHRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYG-LEDYT 465 A + RL+ G VN + ++ + +GG K SG GK+ SL LE +T Sbjct: 435 FKLAMDATKRLEAGFVQVNQNLVVQPGLSYGGVKTSGIGKEASLESMLEHFT 486 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: 509 Number of extensions: 27 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: 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 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