Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate RR42_RS27350 RR42_RS27350 aldehyde dehydrogenase
Query= curated2:Q87L22 (485 letters) >FitnessBrowser__Cup4G11:RR42_RS27350 Length = 486 Score = 221 bits (564), Expect = 3e-62 Identities = 149/451 (33%), Positives = 228/451 (50%), Gaps = 15/451 (3%) Query: 3 HWIAGEWVQG-QGEEFVSLSPYNQ-EVIWRGNGATAEQVDQAVAAARAAFVEWKKRPFAE 60 ++I GEW + G F +++P + +++ R +TA+ AVAAA AAF WKK P ++ Sbjct: 11 NYINGEWSKSASGRTFDNVNPADTADIVGRFQASTADDAQAAVAAAAAAFDAWKKTPISK 70 Query: 61 REAIVLAFAEKVKENSEKIAEVIAKETGKPIWETRTEAAAMAGKIAISIRAYHDRTGEAT 120 R I+ A+ ++ N+E+IAE + +E GK + ++ E A I +GE Sbjct: 71 RAKILNGAADYLEANAEQIAEELTREEGKALNLSKDEVLRSAQTIRFYAVEGQSFSGETY 130 Query: 121 REAAGNQIVLRHR-PLGVMAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSEQTPWTGEL 179 + + IV R PLGV+ V P+NFP +P I PAL+AGNTVVFKPS P +G Sbjct: 131 PQDDPDMIVYSQREPLGVVTVISPWNFPVSIPARKIAPALIAGNTVVFKPSSDAPLSGYR 190 Query: 180 AMKLWEEAGLPKGVINLVQG-AKETGIALADAKGIDGILFTGSANTGHILHRQFAGQPGK 238 + + EAG+PKGV+N + G A + G A+ +A + I FTGS G +HR + Sbjct: 191 LAQAFVEAGIPKGVLNFITGRAGDVGAAITEAPAVRAISFTGSTAAGQHIHRSVS--LST 248 Query: 239 MLALEMGGNNPMVISDNYGDLDATVYTIIQSAFISAGQRCTCARRLYVPFGEKGDALITK 298 +E+GG NP+++ ++ DLD V I+ +GQ CT R+ V K A K Sbjct: 249 RTQMELGGKNPLIVMED-ADLDRAVDLTIKGGLSLSGQACTGTSRVLVMASVKA-AYTEK 306 Query: 299 LVEATKNIRMDQPFAEPAPFMGP-----QISVAAAKFILDAQANLQSLGGESLIEAKAGE 353 L+ K +++ P +GP Q+ GG+ L + Sbjct: 307 LLAKVKTLKIGSGMT-PGMDVGPLATRKQLETVLGYVEAGKSEATHLCGGDRLGGEPYDK 365 Query: 354 AAFVSPGII-DVTNIAELPDEEYFGPLLQVVRYEGLDKAVELANDTRFGLSAGLVSTDDQ 412 +VSP + VT + EE FGP++ ++ A+ ANDT +GLSA +V+++ + Sbjct: 366 GFYVSPAVFTGVTQQMRIAREEIFGPVIAIIEVSSYADAIAKANDTEYGLSAAIVTSNPR 425 Query: 413 EWEYFVDHIRAGIVNRNRQLTGASGDAPFGG 443 F I++G V NR TG +APFGG Sbjct: 426 YAHDFAHDIQSGTVKINRTTTGNLINAPFGG 456 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: 567 Number of extensions: 27 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: 485 Length of database: 486 Length adjustment: 34 Effective length of query: 451 Effective length of database: 452 Effective search space: 203852 Effective search space used: 203852 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