Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_011383257.1 AMB_RS04160 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::C6KEM4 (506 letters) >NCBI__GCF_000009985.1:WP_011383257.1 Length = 499 Score = 291 bits (746), Expect = 3e-83 Identities = 179/479 (37%), Positives = 268/479 (55%), Gaps = 16/479 (3%) Query: 13 FIGGAWREPCLGRRLPVVNPATEATIGDIPAGTAEDVEIAVAAARDAFSRDGGRQWSRAP 72 ++ G W GRR V++PAT I +P A + A+ AA A++ W + Sbjct: 28 YVDGVWVGADDGRRFDVLDPATGGLIASVPDLGATETRRAIDAAEAAWN-----PWRQRT 82 Query: 73 GAVRANFLRAIAAKIKDRKSELALLETLDSGKPLDEASGDMDDVAACFEYYADLAEALDG 132 RA + A I + LA L + + GKPL EA G++ A+ ++A+ +G Sbjct: 83 AKDRAAVMMAWHDLIMAHQDALARLLSAEQGKPLAEAMGEISYGASFISWFAE-----EG 137 Query: 133 KQRSPISLPM--ENFKSYVLKEPIGVVGLITPWNYPLLMATWKVAPALAAGCTTILKPSE 190 K+ +P + + V+K+PIGVV +TPWN+P+ M T K APALAAGC ++KP+E Sbjct: 138 KRAYGDLIPTTASDRRLLVMKQPIGVVAAVTPWNFPMAMITRKCAPALAAGCPVVVKPAE 197 Query: 191 LASVSCLELGAICMEIGLPPGVLNIITGLGPEA-GAPLSSHSHVDKVAFTGSTETGKRIM 249 +S L L + GLP G+ NI+T P A G ++ ++ V K++FTGST GK +M Sbjct: 198 DTPLSALALAELAHRAGLPKGLFNIVTTRQPAAVGGEMTGNAKVRKLSFTGSTRVGKLLM 257 Query: 250 TSAAQMVKPVSLELGGKSPLIVFDDIGDIDKAVEWTMFGIFANAGQVCSATSRLLLHEKI 309 A+ VK VSLELGG +P IVFDD D+D AV + + N+GQ C T+R L+ I Sbjct: 258 AQCAETVKKVSLELGGNAPFIVFDDC-DLDAAVAGALASKYRNSGQTCICTNRFLVQAGI 316 Query: 310 AKKFLDRLVAWAKNIKVSDPLEEGCRLGSVISEGQYEKIKKFISTARSEGATILYGGGRP 369 + F +L A + V L + G +I+ K+ ++ A S+GA +L GG RP Sbjct: 317 YEDFAVKLAEKAAAMAVGHALSGVVQQGPLINAAAVAKVAAHVADAVSKGARVLTGG-RP 375 Query: 370 QHLRRGFFLEPTIITDVSTSMQIWQEEVFGPVICVKEFRTDSEAVELANDTHYGLAGAVI 429 L GF+ +PT++ DV+ +M ++EE FGPV + F T++EA+ LAN + +GLAG Sbjct: 376 HALGGGFW-QPTVLADVTPAMLCFREETFGPVAPLLRFETEAEAIALANASEFGLAGYFY 434 Query: 430 SNDQERCERISKALHSGIIWINCSQPCFVQAPWGGNKRSGFGRELGEWGLDNYLTVKQV 488 S D R R+++AL G++ +N S AP+GG K SG GRE ++GLD+++ K V Sbjct: 435 SRDVARVFRVAEALECGMVGVNESLISNEVAPFGGIKESGLGREGSKYGLDDFMETKYV 493 Lambda K H 0.318 0.136 0.418 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: 654 Number of extensions: 41 Number of successful extensions: 6 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: 506 Length of database: 499 Length adjustment: 34 Effective length of query: 472 Effective length of database: 465 Effective search space: 219480 Effective search space used: 219480 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