Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate AZOBR_RS19635 AZOBR_RS19635 succinate-semialdehyde dehydrogenase
Query= BRENDA::C6KEM4 (506 letters) >FitnessBrowser__azobra:AZOBR_RS19635 Length = 485 Score = 318 bits (815), Expect = 3e-91 Identities = 189/483 (39%), Positives = 277/483 (57%), Gaps = 12/483 (2%) Query: 5 QTIPRRGLFIGGAWREPCLGRRLPVVNPATEATIGDIPAGTAEDVEIAVAAARDAFSRDG 64 Q++ R ++ G WR+ G+ V NPAT + + AE+ A+ AA A Sbjct: 6 QSLLRTQAYVNGVWRDAFSGKTFAVTNPATGEELAQVADVGAEETRQAINAADAALPA-- 63 Query: 65 GRQWSRAPGAVRANFLRAIAAKIKDRKSELALLETLDSGKPLDEASGDMDDVAACFEYYA 124 W RA LR I + +LA+L TL+ GKPL EA G++ A+ E++A Sbjct: 64 ---WRAKTAKERAAILRRWFELIMAAQEDLAVLMTLEQGKPLAEARGEVAYGASFIEWFA 120 Query: 125 DLAEALDGKQRSPISLPMENFKSYVLKEPIGVVGLITPWNYPLLMATWKVAPALAAGCTT 184 + + + G I N + VLKEPIGVV ITPWN+P M T KV PALAAGCT Sbjct: 121 EEGKRVYG---DVIPSFAGNKRIVVLKEPIGVVAAITPWNFPNAMITRKVGPALAAGCTI 177 Query: 185 ILKPSELASVSCLELGAICMEIGLPPGVLNIITGLGPEA-GAPLSSHSHVDKVAFTGSTE 243 ++KP+E +S L L + G+P GV NI+TG P A G L++ V K++FTGSTE Sbjct: 178 VVKPAEDTPLSALALAELAERAGVPAGVFNIVTGSDPVAIGGELTASPIVRKLSFTGSTE 237 Query: 244 TGKRIMTSAAQMVKPVSLELGGKSPLIVFDDIGDIDKAVEWTMFGIFANAGQVCSATSRL 303 GK +M +A VK VSLELGG +P IVFDD D+D+AV+ + + N+GQ C +RL Sbjct: 238 VGKILMRQSADTVKKVSLELGGNAPFIVFDD-ADLDEAVKGALASKYRNSGQTCVCANRL 296 Query: 304 LLHEKIAKKFLDRLVAWAKNIKVSDPLEEGCRLGSVISEGQYEKIKKFISTARSEGATIL 363 L+ + F +L K I+V + +E G G +I+ EK+++ + A ++GA + Sbjct: 297 LVQAGVYDAFAAKLAEAVKQIRVGNGMEAGVTQGPMINGQAVEKVEELMGDALAKGAKVA 356 Query: 364 YGGGRPQHLRRGFFLEPTIITDVSTSMQIWQEEVFGPVICVKEFRTDSEAVELANDTHYG 423 GG R H G F EPTI+T V+T M++ +EE+FGPV + +F T+++A+ +ANDT +G Sbjct: 357 LGGKR--HGLGGTFFEPTILTGVTTEMRVAREEIFGPVAPLFKFETEADAIRMANDTEFG 414 Query: 424 LAGAVISNDQERCERISKALHSGIIWINCSQPCFVQAPWGGNKRSGFGRELGEWGLDNYL 483 LA S D R R+++ L G++ IN AP+GG K+SG GRE ++G++++L Sbjct: 415 LAAYFYSRDIGRVWRVAEQLEYGMVGINEGILSTEVAPFGGIKQSGIGREGSKYGVEDFL 474 Query: 484 TVK 486 +K Sbjct: 475 EIK 477 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: 623 Number of extensions: 38 Number of successful extensions: 7 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: 485 Length adjustment: 34 Effective length of query: 472 Effective length of database: 451 Effective search space: 212872 Effective search space used: 212872 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