Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_011383248.1 AMB_RS04115 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase
Query= metacyc::MONOMER-11560 (497 letters) >NCBI__GCF_000009985.1:WP_011383248.1 Length = 485 Score = 336 bits (862), Expect = 1e-96 Identities = 196/474 (41%), Positives = 280/474 (59%), Gaps = 16/474 (3%) Query: 24 INGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAKR 83 ING ++ S T L+P + + ++A+ A+ +AV A+ F W+ L PA + Sbjct: 6 INGRQVESAS--TIANLNPANNEVICQIAAGGEAEVAQAVAAAKEAFPK--WAGL-PASQ 60 Query: 84 KAKLIR-FADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEV 142 +AKL+R DL+ ++V+E+A LE+LD G+ + + +P AA ++ A+ V E Sbjct: 61 RAKLLRKVGDLINQHVDEIAKLESLDTGQSYWRTKKMLVPRAADNFYFFADTCCHVDGET 120 Query: 143 APTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIR 202 PT +D L +PVGVVG I PWN P + A WK P LA GN+ VLK SE SPL+A R Sbjct: 121 YPT-NDHLNYTLYQPVGVVGLISPWNVPFMTATWKTAPCLAFGNTAVLKMSELSPLSADR 179 Query: 203 IAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMK 262 + QL +EAGIPAGV N++ GYG VG+AL H DV + FTGST +++ G +K Sbjct: 180 LGQLILEAGIPAGVFNIVHGYGSAVGEALVKHPDVRGVSFTGSTATGNRIIQSGG---LK 236 Query: 263 RIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLPMV 322 + +E GGKSPNI+F D D + A +AA A+ N GE CT G+R+LV+ + D+F+ + Sbjct: 237 KYSMELGGKSPNIIFDDC-DFERAVDAAIVAVYGNNGESCTNGTRILVQDGLYDRFVAAL 295 Query: 323 VEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEE----- 377 E + G+PLD T VG ++ V SYIE G +GA+++AGG T E Sbjct: 296 AERTRKVVVGDPLDEATNVGPMITRDHWKKVTSYIELGISEGARVVAGGLGTPEGLAPHL 355 Query: 378 TGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSD 437 G +V PT+ V N+ R+AQEEIFGPV VI F EA+ IAN T YGLA+ +WT + Sbjct: 356 KNGNFVRPTVLADVDNSWRVAQEEIFGPVACVIRFKDEAEALKIANATSYGLASYVWTEN 415 Query: 438 ISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELK 491 ++A + A + AG V+VN + D+ PFGG K SG GR+ ++ E + E+K Sbjct: 416 GARAIRMAEGIEAGLVFVNSQNVRDLRQPFGGIKGSGTGREGGHYSYEAFLEVK 469 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: 630 Number of extensions: 28 Number of successful extensions: 5 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: 485 Length adjustment: 34 Effective length of query: 463 Effective length of database: 451 Effective search space: 208813 Effective search space used: 208813 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