Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_011842390.1 RSPH17029_RS17535 aspartate aminotransferase family protein
Query= curated2:Q9YBY6 (388 letters) >NCBI__GCF_000015985.1:WP_011842390.1 Length = 442 Score = 154 bits (390), Expect = 4e-42 Identities = 127/411 (30%), Positives = 192/411 (46%), Gaps = 55/411 (13%) Query: 20 KGSMQYVWDDSGRKYLDCHAGHGAAFLGHSNPAIVEAVVRQARELVAASSSFSTPSLEEA 79 +G Y+ D GR+YLD G + LGHSN A+ A+ Q L A + F T E Sbjct: 19 EGEGCYILDAEGRRYLDGSGGAAVSCLGHSNAAVRAALHDQLDRLAFAHTGFFTSEPAER 78 Query: 80 LTE-FSRIAPPWAEEIVFLNTGTEAVEAALKAA---WLATGKRG---IVALKNSFHGRTL 132 L + + AP E + ++ G+EAVEAALK A ++ G+ G ++A + S+HG TL Sbjct: 79 LADRLAAAAPEGIERVYLVSGGSEAVEAALKLARQYFMEVGQPGRHRVIARRQSYHGNTL 138 Query: 133 ASLSVTWNP-RYRRGVPVL-DTRFLSPSTD---------------------PGEVEKLVP 169 +L+ N R + P+L +T +SP + E+++L P Sbjct: 139 GALAAGGNEWRRAQFAPLLVETSHVSPCYEYRGRAEDESLEAYGLRVADELEAEIQRLGP 198 Query: 170 EDTAAIIVEPIQGE-GGLTKIYAELAKALREAADRVGALLIFDEIQTGFGRTGRVWAHES 228 E A + EP+ G G K +RE DR G LLI DE+ G GRTG ++A Sbjct: 199 ETVMAFVAEPVVGATAGAVPAVPGYLKRIREICDRHGVLLILDEVMCGMGRTGHLFACAE 258 Query: 229 LGVEPDIMTAGKSI-AGGLPASAVLSREGVLATLASG----RHGSTHAANPLSMAAVAAA 283 GV PD++T K + AG P A+L + + +A+G +HG T+ + ++ AA A Sbjct: 259 DGVAPDMITIAKGLGAGYQPIGALLVQGRLYDAIAAGSGFFQHGHTYMGHAMAAAAANAV 318 Query: 284 SRFLREEGVPDKARAAGALLEGLLRDRIEGLRLVRGVRGEGLMLGVEL--------RLDP 335 + + R GA LEGLL++R+ V +RG GL G+EL DP Sbjct: 319 LDEIEGRDLLQAVRRQGARLEGLLQERLGQHPHVGDIRGRGLFRGIELVADRETKEPFDP 378 Query: 336 GPVLRCLQESER----VLALRSGATV-------VRLLPPYSISREDAEMVV 375 L ++E ++ G T+ + L PP+ IS + E +V Sbjct: 379 ARKLHARIKAEAFAGGLICYPMGGTLDGVRGDHILLAPPFIISNAELEELV 429 Lambda K H 0.319 0.136 0.398 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: 421 Number of extensions: 26 Number of successful extensions: 4 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: 388 Length of database: 442 Length adjustment: 31 Effective length of query: 357 Effective length of database: 411 Effective search space: 146727 Effective search space used: 146727 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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