Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate WP_086509263.1 BZY95_RS07130 aldehyde dehydrogenase family protein
Query= curated2:Q87L22 (485 letters) >NCBI__GCF_002151265.1:WP_086509263.1 Length = 496 Score = 215 bits (548), Expect = 2e-60 Identities = 147/455 (32%), Positives = 224/455 (49%), Gaps = 23/455 (5%) Query: 3 HWIAGEWV-QGQGEEFVSLSPYNQE-VIWRGNGATAEQVDQAVAAARAAFVEWKKRPFAE 60 ++I G+WV G G F + +P +Q+ ++ + + +A+AAA AF W++ P ++ Sbjct: 21 NYIDGQWVASGSGATFENRNPADQDDLLGLFQASGVDDARRAIAAADRAFTAWRETPISQ 80 Query: 61 REAIVLAFAEKVKENSEKIAEVIAKETGKPIWETRTEAAAMAGKIAISIRAYHDRTGEA- 119 R I+ A+ + EN E+ A + +E GK + +R E A + TGE Sbjct: 81 RAKILNRAADYLMENVEQFARELTREEGKLLANSRDEVTRSAQTLRFYAVEGQTITGETF 140 Query: 120 TREAAGNQIVLRHRPLGVMAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSEQTPWTGEL 179 ++ A + + PLGV + P+NFP +P I PAL+ GNTVVFKPS P G Sbjct: 141 PQDDAKMTVYTQREPLGVATIITPWNFPISIPARKIAPALITGNTVVFKPSSDAPLIGYR 200 Query: 180 AMKLWEEAGLPKGVINLVQGAKET-GIALADAKGIDGILFTGSANTGHILHRQFAGQPGK 238 + AG+P GV N + GA G + + I FTGS G +HR A Sbjct: 201 LAEALHHAGVPAGVFNFITGAASAIGEEITANPVVKAISFTGSTAAGERIHR--AAAMAT 258 Query: 239 MLALEMGGNNPMVISDNYGDLDATVYTIIQSAFISAGQRCTCARRLYVPFGEKGDALITK 298 +E+GG NP+++ ++ D+D V ++ F GQ CT R+ + K + L T+ Sbjct: 259 RTQMELGGKNPLIVLED-ADIDTAVDLTVKGGFSLTGQACTGTSRVLIARSRKQEYL-TR 316 Query: 299 LVEATKNIRMDQPFAEPAPFMGPQISVAAAKFILDA---------QANLQSLGGESLIEA 349 LVE K +++ +E G QI A + LD + GGE L E Sbjct: 317 LVEQVKTLKIGNGMSE-----GIQIGPLATRQQLDTVLGYVETGRKEATHVYGGEHLTEG 371 Query: 350 KAGEAAFVSPGII-DVTNIAELPDEEYFGPLLQVVRYEGLDKAVELANDTRFGLSAGLVS 408 + +V+P I DVT + EE FGP++ V+ +G + A+ ANDT +GL+AGLV+ Sbjct: 372 DYAKGFYVTPAIFSDVTQEMRIAREEIFGPVVAVIEVDGYEDAIAKANDTPYGLAAGLVT 431 Query: 409 TDDQEWEYFVDHIRAGIVNRNRQLTGASGDAPFGG 443 + + F I+AG V NR TG +APFGG Sbjct: 432 KNFDYIQRFPLDIQAGTVKINRTTTGNLVNAPFGG 466 Lambda K H 0.316 0.134 0.397 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: 553 Number of extensions: 22 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: 496 Length adjustment: 34 Effective length of query: 451 Effective length of database: 462 Effective search space: 208362 Effective search space used: 208362 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 24 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