Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_084931611.1 HA51_RS01965 aldehyde dehydrogenase
Query= BRENDA::Q9RW56 (523 letters) >NCBI__GCF_002095475.1:WP_084931611.1 Length = 498 Score = 217 bits (553), Expect = 7e-61 Identities = 153/474 (32%), Positives = 230/474 (48%), Gaps = 29/474 (6%) Query: 55 IQSINPCDTSEVVGTTAKATIGDAENALQGAWKAFES--WKKWDMDARARILLKAAAILK 112 +++ NP T EV+ A D A+QGA AFES W + R +LLK A +L+ Sbjct: 38 LETTNPA-TGEVLAHIAACNGHDVNTAVQGARSAFESGSWSQLHPGERKAVLLKLADLLE 96 Query: 113 RRRLEACALMSIEVGKNYAEA-DVEVAEAIDFLEYYARSAMKY----AGFGSSETTWFEG 167 + + S++ GK +E V+V E I + ++A + K A GS Sbjct: 97 NEVTQLAVMESLDSGKPVSECLAVDVPETIHVIRWHAEAIDKLYDQTAPAGSGAMAMIVR 156 Query: 168 EENGLMSIPLGVGVSISPWNFPCAIFVGMAAAPIVAGNCVVVKPAEDAGLIAGFMVDILR 227 E P+GV + PWNFP + + AG V+VKPAE L A + ++ Sbjct: 157 E-------PIGVVGCVLPWNFPLLMLAWKIGPALAAGCSVIVKPAEQTSLTALRVAELAH 209 Query: 228 EAGLPAGVLQFLPGVGKEVGEYLTTHAKTRFITFTGSRAVGLHINEVAAKVQPGQKWIKR 287 EAG+PAGVL + G GK+VGE + HA ++FTGS A G +A+ +K+ Sbjct: 210 EAGIPAGVLNIVTGTGKDVGEPIGLHADIDMVSFTGSTATGRRFLHYSAESN-----LKK 264 Query: 288 VIMELGGKDGLIV-DETADIENAITAATQGAFGFNGQKCSAMSRLIVVDSVYDEVVNGFV 346 +++E GGK+ +V D+ D+ + GAF G+ CSA SRL+V ++V D+++ Sbjct: 265 IVLECGGKNPAVVFDDADDLASVAANVLSGAFWNMGENCSATSRLLVHENVKDKLLALIA 324 Query: 347 ERAKALKMGTGEENAN-VTAVVNQMSFNKIKGYLELAPSEGKVLLGGEATGEANGKQGYY 405 E+ +MG + N + ++ F K+ YL+ A EG ++ G T +G Y Sbjct: 325 EQIGDWRMGNPLDPENRLGTMITAEHFCKVSDYLKTARKEGLRIIQGGFT-----DRGIY 379 Query: 406 IQPTIVGDVDRNSRLAQEEIFGPVVAVLRAKDWQDALDIANSTEYGLTGGVCSNSRERLE 465 +QPTIV V S L +EEIFGPV+ V K +A+ +AN T+YGL V + R Sbjct: 380 VQPTIVDGVTPKSALFREEIFGPVLCVTTFKTEAEAIALANDTDYGLAASVYTGKLSRAI 439 Query: 466 QARAEFEVGNLYFNRKITGAIVGVQPFGGYNMSGTDSKAGGPDYLSNFMQLKTV 519 + G + N G PFGGY SG + L + +LKT+ Sbjct: 440 RVSRAIRAGTVTVN--CFGEGDATTPFGGYKQSGFGGRDKSVYALDQYTELKTI 491 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: 587 Number of extensions: 30 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: 523 Length of database: 498 Length adjustment: 34 Effective length of query: 489 Effective length of database: 464 Effective search space: 226896 Effective search space used: 226896 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