Align 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate 200453 SO1275 succinate-semialdehyde dehydrogenase (NCBI ptt file)
Query= metacyc::MONOMER-13361 (500 letters) >FitnessBrowser__MR1:200453 Length = 482 Score = 278 bits (712), Expect = 2e-79 Identities = 161/480 (33%), Positives = 261/480 (54%), Gaps = 13/480 (2%) Query: 23 YIDGNF--VTSASSFANINPVNGKLISDVFEADAKQVNEAVVAAQNALKGPWGKLSVQDR 80 YI+G + S + A NP G +I+ V + A+ AA+ AL W L+ ++R Sbjct: 14 YINGQWCDANSKETVAITNPATGAVIACVPVMGQAETQAAIAAAEAALPA-WRALTAKER 72 Query: 81 AALIHKIADGIQARFEEFVAAEVADTGRPVHQARTLDIPRAIANFRTFADLAKTSHTDLF 140 A + + + + ++ ++ G+P+ +A+ ++ A + FA+ AK + D Sbjct: 73 GAKLRRWFELLNENSDDLALLMTSEQGKPLTEAKG-EVTYAASFIEWFAEEAKRIYGDTI 131 Query: 141 EMSTSDGSGALNYTVRKPLGVIGVISPWNLPLLLFTWKVAPALACGNTVVAKPSEESPSS 200 D + +++P+GV I+PWN P + T K APALA G T+V KP+ ++P + Sbjct: 132 PGHQGDKRIMV---IKQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMVVKPAPQTPFT 188 Query: 201 ATLLAEVMHDAGVPPGVFNLIHGFGKDSAGEFLTQHPGISALTFTGESKTGSTIMKAVAD 260 A LA + AG+P GVF++I G E T +P + L+FTG + G +M A Sbjct: 189 ALALAVLAERAGIPAGVFSVITGDAIAIGNEMCT-NPIVRKLSFTGSTNVGIKLMAQCAP 247 Query: 261 GVKEVSFELGGKNAAVVFADADLDAAIEGVLRSSFTNSGQVCLCSERVYVHRSIFDEFVS 320 +K++S ELGG +VF DA++DAA+EG + + + N+GQ C+C+ R+YV ++DEF Sbjct: 248 TLKKLSLELGGNAPFIVFDDANIDAAVEGAMIAKYRNAGQTCVCANRIYVQAGVYDEFAE 307 Query: 321 GLKVEAERLVVGYPDQDGVNMGPLISHGHRDKVLSYYRLAVDEGATVVTGGGVPKFNDER 380 L + +L VG GV GPLI+ +KV S+ A+ +GATV+ GG V + Sbjct: 308 KLSMAVAKLKVGEGIIAGVTTGPLINAAAVEKVQSHLEDAIKKGATVLAGGKVHELG--- 364 Query: 381 DQGAYVQPTIWTGLSDKARCVTEEIFGPVCHISPFDDEDEVINRVNDSNYGLACAIWTTN 440 G + +PT+ T R EE FGP+ + F+D D+VI + ND+ +GLA + + Sbjct: 365 --GNFFEPTVLTNADKSMRVAREETFGPLAPLFKFNDVDDVIKQANDTEFGLAAYFYGRD 422 Query: 441 LSRAHRVSRQIHVGLVWVNTWYLRDLRTPFGGVKLSGLGREGGRFSMDFYSDIANICIKI 500 +S +V+ + G+V VNT + PFGG+K SGLGREG ++ ++ Y +I IC+ + Sbjct: 423 ISLVWKVAESLEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKYGIEEYLEIKYICMSV 482 Lambda K H 0.318 0.135 0.405 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: 517 Number of extensions: 22 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: 500 Length of database: 482 Length adjustment: 34 Effective length of query: 466 Effective length of database: 448 Effective search space: 208768 Effective search space used: 208768 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 (21.7 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