Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate WP_012607209.1 AFE_RS08085 aldehyde dehydrogenase
Query= reanno::SB2B:6938906 (486 letters) >NCBI__GCF_000021485.1:WP_012607209.1 Length = 506 Score = 143 bits (360), Expect = 2e-38 Identities = 148/478 (30%), Positives = 220/478 (46%), Gaps = 56/478 (11%) Query: 4 FINGQWLAG-EGKEMQSKNPANGEVIWQGKAAVPAQVQAAVMAARDAQFEWFMLGFEGRQ 62 FI G+W+A +G+ P NG+ Q + ++ A+ AA +W R Sbjct: 22 FIGGKWVAPVKGQYFDVITPINGKSYTQAARSTAEDIELALDAAHAIADKWGKTSPAERA 81 Query: 63 AIVEAYRNELEANKAELAEVIAQETGKPRWETATEAAAMIGKIGLSVSAYHKRTG----- 117 I+ + +EAN LA + GKP ET I L+V + G Sbjct: 82 NILLKVADRIEANLELLAYAETVDNGKPIRETLN------ADIPLAVDHFRYFAGCVRAQ 135 Query: 118 ----TEVNEGAAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSELT 173 ++++E A H+P GVV P+NFP + + + PAL AGN VV KP+E T Sbjct: 136 EGGISDIDENTV--AYHFHEPLGVVGQIIPWNFPILMASWKLAPALGAGNVVVLKPAEST 193 Query: 174 P----KVAELMLKLWEKAGLPAGVINLVQG-EVETGKALASHPQLDGLFFTGSSRTGHLL 228 P +AEL+ L LP GV+N+V G E G LA+ ++ + FTGS+ TG ++ Sbjct: 194 PISILILAELIADL-----LPPGVLNIVNGYGREAGMPLATSKRIAKIAFTGSTTTGRVI 248 Query: 229 HQQYAGHPGKILALEMGGNNPLIV------KGVSDTRAAIHDIIQSAFISSGQRCTCARR 282 Q A + LE+GG +P I K S AI ++ AF + G+ CTC R Sbjct: 249 -AQAAANSLIPATLELGGKSPNIFFADVMDKDDSFLDKAIEGLVLFAF-NQGEVCTCPSR 306 Query: 283 LYVEKGAEGDKLLAGLVEAVKAIKVG-PWNADPQPFMGSMISETAAKGMLDAQRNLLNLG 341 +++ DK + ++ +KAIK G P + + +MI A+K L + L+LG Sbjct: 307 ALIQESIY-DKFMERCLDRIKAIKQGNPLDTN------TMIGAQASKEQLTKILSYLDLG 359 Query: 342 AK--SLVEMTHLQA-------GTGLVSPGLIDVTEVIELPDEEYFGPLLQVVRYTSFDEA 392 + + V + QA G V P L + + EE FGP+L V + EA Sbjct: 360 KQEGAQVLIGGSQAIVDGDLDGGYYVQPTLFKGHNKMRIFQEEIFGPVLAVTTFKDEAEA 419 Query: 393 IRLANDTRYGLSAGILADDKADYEYFLAR-IRAGIVNWNKQITGASGAAPFGGVGASG 449 + +ANDT YGL AG+ + + + Y + R I+AG V W A FGG SG Sbjct: 420 LSIANDTLYGLGAGVWSRN-GNVAYRMGRAIKAGRV-WINCYHAYPAHAAFGGYKESG 475 Lambda K H 0.317 0.133 0.393 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: 551 Number of extensions: 27 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: 486 Length of database: 506 Length adjustment: 34 Effective length of query: 452 Effective length of database: 472 Effective search space: 213344 Effective search space used: 213344 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 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