Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_011842384.1 RSPH17029_RS17490 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-11560 (497 letters) >NCBI__GCF_000015985.1:WP_011842384.1 Length = 791 Score = 302 bits (774), Expect = 3e-86 Identities = 183/469 (39%), Positives = 260/469 (55%), Gaps = 26/469 (5%) Query: 23 FINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAK 82 +I+G +T A + E +P G LA++ + A+ AV ARA F+ WSQL + Sbjct: 36 YIDGAFTGAETA-AIEVENPATGEILARIPAAGEAEIEAAVAAARAAFSG--WSQLPGFE 92 Query: 83 RKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIH----WTAEAIDKV 138 R L A L+K ++LETLD GK I ++ + D+P A + + W A V Sbjct: 93 RARYLYAIARGLQKRERFFSVLETLDNGKAIRETRTADVPLAIRHFYHHAGWAA-----V 147 Query: 139 YDEVAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPL 198 E P EP+GV G ++PWNFP+LM WK+ PALA GN+VVLKP++ +PL Sbjct: 148 LGEEFPG---------HEPLGVCGQVIPWNFPMLMLAWKIAPALAAGNTVVLKPADLTPL 198 Query: 199 TAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGE 258 TA+ A++ E G+P GV+N++ G G G L H V + FTGST + +++ Sbjct: 199 TAVAFAEMLDEIGLPRGVVNIVHG-GAETGALLVRHPGVAKVAFTGSTAVGREIRRATAG 257 Query: 259 SNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKF 318 S K + LE GGKSP +V ADA DL AA E + FNQGEVC AGSRLL++ I ++F Sbjct: 258 SG-KSLTLELGGKSPFVVCADA-DLDAAVEGVVEGVWFNQGEVCCAGSRLLLQEGIAERF 315 Query: 319 LPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEET 378 L + ++ + G+PLD T +GA+V +Q + I ++G +L Sbjct: 316 LAKLRARMEKIRVGDPLDKSTDMGAIVSARQKARIEELIAGAAREGYRLEQAACPL--PA 373 Query: 379 GGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDI 438 G +V P F A +AQ EIFGP+ F T +EAVA+AN+TPYGLAA +W+ +I Sbjct: 374 AGHFVAPGFFADTEPAATVAQVEIFGPIAVTTTFRTVDEAVALANNTPYGLAASVWSENI 433 Query: 439 SKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKY 487 + A + A +RAG VW+N + D A FGG K+SG GR+ + L Y Sbjct: 434 NAATELAARIRAGVVWINASNLFDAGASFGGMKESGFGREGAREGLGAY 482 Score = 79.0 bits (193), Expect = 6e-19 Identities = 66/231 (28%), Positives = 107/231 (46%), Gaps = 19/231 (8%) Query: 40 LSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAKRKAKLIRF-ADLLRKNV 98 L+PV GR D AVE A + W+ A A +A+++ F A+ + Sbjct: 547 LAPVSGR----------KDIRNAVE---AALKAKGWA--ANAHGRAQVLFFLAENIAARA 591 Query: 99 EELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEVAPTPHDQLGLVTREPV 158 E+LA L G ++ ++ + + + A DK + T L L +EP+ Sbjct: 592 EDLAA--ALVQGGAGRSEAAAEVRSLIERVFFYAGMADKDDGRIHATKPRHLTLSVKEPL 649 Query: 159 GVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIRIAQLAIEAGIPAGVLN 218 GVVG + P PLL + P +A GN VV PS L A + Q+ + +P GV+N Sbjct: 650 GVVGVLAPDEAPLLSLMSLILPLIAAGNRVVAVPSPAQALLAQPLTQIFDTSDLPGGVVN 709 Query: 219 VLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMKRIWLEAG 269 ++ G + + + LA H VD + + GS K A ++ + N+K++W G Sbjct: 710 LVTGDRNLLARTLAEHDAVDGIWYHGSAKGAAEVEALSA-GNLKQVWTNGG 759 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: 1021 Number of extensions: 47 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 497 Length of database: 791 Length adjustment: 38 Effective length of query: 459 Effective length of database: 753 Effective search space: 345627 Effective search space used: 345627 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: 54 (25.4 bits)
This GapMind analysis is from Apr 10 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