Align Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_179243903.1 B9O00_RS00790 aldehyde dehydrogenase family protein
Query= reanno::Smeli:SM_b20891 (477 letters) >NCBI__GCF_900177295.1:WP_179243903.1 Length = 480 Score = 687 bits (1773), Expect = 0.0 Identities = 347/479 (72%), Positives = 395/479 (82%), Gaps = 3/479 (0%) Query: 1 MTLHQNLIAGEWVGGDGVA-NINPSNTDDVVGEYARASAEDAKAAIAAAKAAFPAWSRSG 59 MT+H NLIAGEWV + N NPS+ DVVG YA+ A A AI AA AAFPAWSRS Sbjct: 1 MTMHANLIAGEWVDAPNASENRNPSDLSDVVGLYAQGDAAQAGQAIDAAAAAFPAWSRST 60 Query: 60 ILERHAILKKTADEILARKDELGRLLSREEGKTLAEGIGETVRAGQIFEFFAGETLRLAG 119 +R IL EILARK+ELGRLLSREEGKTL EGIGETVRAGQIF+FFAGE LR+AG Sbjct: 61 PQQRFDILDAAGTEILARKEELGRLLSREEGKTLPEGIGETVRAGQIFKFFAGEALRIAG 120 Query: 120 EVVPSVRPGIGVEITREPAGVVGIITPWNFPIAIPAWKLAPALCYGNTIVFKPAELVPGC 179 + + S RPG+ E TREP GVVG+ITPWNFPIAIPAWKLAPAL +GN +V KPA+LVPGC Sbjct: 121 DRIDSTRPGVIAEATREPLGVVGLITPWNFPIAIPAWKLAPALAFGNCVVMKPADLVPGC 180 Query: 180 SWAIVDILHRAGLPKGVLNLVMGKGSVVGQAMLDSPDVQAITFTGSTATGKRVAVASVEH 239 +WA+ DIL RAGLPKGV NLVMG+GSVVG+A+L SP V AI+FTGS ATG+ VA +E Sbjct: 181 AWALADILQRAGLPKGVFNLVMGRGSVVGEAILASPKVAAISFTGSVATGRHVARRCIEG 240 Query: 240 N--RKYQLEMGGKNPFVVLDDADLSVAVEAAVNSAFFSTGQRCTASSRIIVTEGIHDRFV 297 +K+QLEMGGKNPFVVLDDADL VA +A+N AFFSTGQRCTASSR+IVTEGIHDRFV Sbjct: 241 EAMKKFQLEMGGKNPFVVLDDADLEVAANSALNGAFFSTGQRCTASSRLIVTEGIHDRFV 300 Query: 298 AAMGERIKGLVVDDALKPGTHIGPVVDQSQLNQDTDYIAIGKQEGAKLAFGGEVISRDTP 357 A+ ++K L VD+ALK GT IGPVVDQ QL+QD DYI +G+ EGAKLA+GGE ++R+T Sbjct: 301 EALTSKLKALKVDNALKEGTQIGPVVDQRQLDQDLDYIKVGQDEGAKLAWGGERLNRETE 360 Query: 358 GFYLQPALFTEATNEMRISREEIFGPVAAVIRVKDYDEALAVANDTPFGLSSGIATTSLK 417 GFYLQPALFTE N MRI+REEIFGPVA+VIRVKDYD ALAVANDT FGLS+GIAT+SLK Sbjct: 361 GFYLQPALFTETDNAMRINREEIFGPVASVIRVKDYDSALAVANDTQFGLSAGIATSSLK 420 Query: 418 HATHFKRNAEAGMVMVNLPTAGVDFHVPFGGRKASSYGPREQGKYAAEFYTNVKTAYTL 476 HA HFKRN++AGMVMVNLPTAGVD+HVPFGGRK SSYG REQG+YA EFYT VKTAY + Sbjct: 421 HAEHFKRNSQAGMVMVNLPTAGVDYHVPFGGRKNSSYGAREQGRYAVEFYTTVKTAYAM 479 Lambda K H 0.317 0.134 0.391 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: 739 Number of extensions: 21 Number of successful extensions: 3 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: 477 Length of database: 480 Length adjustment: 34 Effective length of query: 443 Effective length of database: 446 Effective search space: 197578 Effective search space used: 197578 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: 51 (24.3 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