Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate WP_011424478.1 RHE_RS05810 betaine-aldehyde dehydrogenase
Query= BRENDA::Q83XU8 (485 letters) >NCBI__GCF_000092045.1:WP_011424478.1 Length = 487 Score = 335 bits (858), Expect = 3e-96 Identities = 191/459 (41%), Positives = 261/459 (56%), Gaps = 9/459 (1%) Query: 25 PLNNAVIAKVHEAGRAEVDAAVAAAQAALKGAWGRMSLAQRVEVLYAVADGINRRFDDFL 84 P VIA++H A A V+ A+AAA+ A + W MS R +L AD + R + Sbjct: 29 PATGEVIARLHAATPAIVEKAIAAAKRA-QPEWAAMSPMARGRILKRAADIMRERNRELS 87 Query: 85 AAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVGAINYAVRRPV 144 E DTGKP+ D GA F+ F V P P G Y R P+ Sbjct: 88 ELETLDTGKPIQETIVADPTSGADAFEFFGGVA---PAGLNGSHIPLGQD-FAYTKRVPL 143 Query: 145 GVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPPGVYN 204 GV I WN P + WK PAL GN +V KPSE TP A + E+++ AG+P G++N Sbjct: 144 GVCVGIGAWNYPQQIACWKGAPALISGNAMVFKPSENTPLGALKIAEILHEAGLPKGLFN 203 Query: 205 VVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADGARPVSLELGGKNAAIVFA 264 V+ G TG L +HPDV ++ TG TG + AAA + V++ELGGK+ IVF Sbjct: 204 VIQG--DRDTGPLLVNHPDVAKVSLTGSVPTGRRVAAAAAGSLKHVTMELGGKSPLIVFD 261 Query: 265 DCDLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLGRPEDLAT 324 D DLD A+ G + F + GQVC RV+V++ + F+ RLK E M +G P D AT Sbjct: 262 DADLDSAVGGAMLGNFYSTGQVCSNGTRVFVQKAVKAEFLKRLKARTEAMLIGDPLDEAT 321 Query: 325 GMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQPTIWTGLGDDSV 384 +GP++S REKV++Y +K GAT+V GGG+P G +VQPT++ + DD Sbjct: 322 QIGPMVSWAQREKVIAYIEKGKAEGATLVAGGGIPN--NVSGEGYYVQPTVFADVTDDMT 379 Query: 385 VAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVGIAWVN 444 +AREEIFGP V+ FD E+EVI RAN +++GL+ ++T +LSRAHRV +E G W+N Sbjct: 380 IAREEIFGPVMSVLDFDDEDEVITRANASEFGLSGGVFTADLSRAHRVVDRLEAGTLWIN 439 Query: 445 SWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNVCI 483 ++ L + FGGSKQSG GRE + +LE Y+ELK V + Sbjct: 440 TYNLCPVEIPFGGSKQSGFGRENSLAALEHYSELKTVYV 478 Lambda K H 0.318 0.135 0.406 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: 628 Number of extensions: 30 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: 485 Length of database: 487 Length adjustment: 34 Effective length of query: 451 Effective length of database: 453 Effective search space: 204303 Effective search space used: 204303 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