Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate Pf1N1B4_4355 Gamma-glutamyl-aminobutyraldehyde dehydrogenase (EC 1.2.1.-)
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4355 Length = 496 Score = 784 bits (2025), Expect = 0.0 Identities = 380/495 (76%), Positives = 435/495 (87%) Query: 3 TLTRADWEQRAQQLKIEGRAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRA 62 T TR+DWEQR Q L +EGRAFI+G+Y A+SG+TFEC+SPVDGRFLA +AS D ADAN A Sbjct: 2 TNTRSDWEQRFQSLTLEGRAFIDGQYCPALSGDTFECISPVDGRFLANIASTDEADANAA 61 Query: 63 VENARATFNSGVWSQLAPAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIP 122 V+ AR TF SG+W++L PA+RK LIRFADL+ +N EELALLETLDMGKPI DS SIDIP Sbjct: 62 VQVARRTFESGIWAKLPPAERKRVLIRFADLILQNQEELALLETLDMGKPISDSMSIDIP 121 Query: 123 GAAQAIHWTAEAIDKVYDEVAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPAL 182 A AI W+AEAIDK+YDEVA TPHDQLGL+TREP GVV AIVPWNFPL+MA WK PAL Sbjct: 122 ATANAIRWSAEAIDKIYDEVAATPHDQLGLITREPAGVVAAIVPWNFPLIMASWKFAPAL 181 Query: 183 ATGNSVVLKPSEKSPLTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVF 242 A GNS +LKPSEKSPLTAIRIAQLA+EAGIP GV NVLPG+GHTVGKALALHMDVD L F Sbjct: 182 AAGNSFILKPSEKSPLTAIRIAQLALEAGIPKGVFNVLPGFGHTVGKALALHMDVDVLAF 241 Query: 243 TGSTKIAKQLMVYAGESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVC 302 TGST IAKQL++YAG+SNMKR+WLEAGGKSPN+VFADAPDL+AAA AA SAIAFNQGEVC Sbjct: 242 TGSTAIAKQLLIYAGQSNMKRVWLEAGGKSPNVVFADAPDLRAAARAAVSAIAFNQGEVC 301 Query: 303 TAGSRLLVERSIKDKFLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHK 362 TAGSRLLVERSI+++F+P++VEAL+ WKPG+ LDP+TTVGA+VD +Q++ VL YI+ G Sbjct: 302 TAGSRLLVERSIREQFIPLLVEALQAWKPGHALDPETTVGAVVDQRQLDNVLRYIQVGKD 361 Query: 363 DGAKLLAGGKRTLEETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIA 422 GA+L+AGG RTL +TGG YVEP IFDGVTNAM IA+EEIFGPVLS+I FDTAEEA+ IA Sbjct: 362 QGAQLIAGGNRTLADTGGLYVEPAIFDGVTNAMTIAREEIFGPVLSLITFDTAEEALQIA 421 Query: 423 NDTPYGLAAGIWTSDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLH 482 ND+ +GLAAG+WTS++SKAH AR +RAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLH Sbjct: 422 NDSIFGLAAGVWTSNLSKAHTFARGLRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLH 481 Query: 483 ALEKYTELKATWIKL 497 A +KYTELKATWIKL Sbjct: 482 AFDKYTELKATWIKL 496 Lambda K H 0.316 0.132 0.390 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: 762 Number of extensions: 20 Number of successful extensions: 2 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: 497 Length of database: 496 Length adjustment: 34 Effective length of query: 463 Effective length of database: 462 Effective search space: 213906 Effective search space used: 213906 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 (21.6 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