Align 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate 6938534 Sama_2637 succinate-semialdehyde dehydrogenase (NAD(P)(+)) (RefSeq)
Query= metacyc::MONOMER-13361 (500 letters) >FitnessBrowser__SB2B:6938534 Length = 480 Score = 280 bits (715), Expect = 1e-79 Identities = 161/480 (33%), Positives = 263/480 (54%), Gaps = 15/480 (3%) Query: 23 YIDGNF--VTSASSFANINPVNGKLISDVFEADAKQVNEAVVAAQNALKGPWGKLSVQDR 80 YI+G + S + NP + I+ V + EA+ AA+ AL W L+ ++R Sbjct: 14 YINGEWRDALSGETVTIANPATNEAIASVPVMGRDETREAIAAAEAALPA-WRALTAKER 72 Query: 81 AALIHKIADGIQARFEEFVAAEVADTGRPVHQARTLDIPRAIANFRTFADLAKTSHTDLF 140 A + + + + ++ + G+P+ +A+ ++ A + FA+ AK + D Sbjct: 73 GAKLRRWYELMLENADDLALMMTTEQGKPLAEAKG-EVVYAASFIEWFAEEAKRLYGDTI 131 Query: 141 EMSTSDGSGALNYTVRKPLGVIGVISPWNLPLLLFTWKVAPALACGNTVVAKPSEESPSS 200 D + +++ +GV I+PWN P + T K PALA G T++ KP+ ++P + Sbjct: 132 PGHQGDKRIMV---IKQGVGVTAAITPWNFPAAMITRKAGPALAAGCTMIVKPAPQTPFT 188 Query: 201 ATLLAEVMHDAGVPPGVFNLIHGFGKDSAGEFLTQHPGISALTFTGESKTGSTIMKAVAD 260 A LAE+ +AG+PPGVF+++ G + G L ++P + L+FTG + G +M+ A Sbjct: 189 ALALAELAAEAGIPPGVFSVVTGDAV-AIGNELCENPVVRKLSFTGSTGVGIKLMQQCAP 247 Query: 261 GVKEVSFELGGKNAAVVFADADLDAAIEGVLRSSFTNSGQVCLCSERVYVHRSIFDEFVS 320 +K+VS ELGG +VF DADLDAA+EG + S + N+GQ C+C+ R+YV ++D F Sbjct: 248 TLKKVSLELGGNAPFIVFNDADLDAAVEGAMISKYRNAGQTCVCANRLYVQDGVYDAFAQ 307 Query: 321 GLKVEAERLVVGYPDQDGVNMGPLISHGHRDKVLSYYRLAVDEGATVVTGGGVPKFNDER 380 L +L VG + GV GPLI+ +KV S+ + A+D+GAT+V GG + Sbjct: 308 KLAAAVAKLKVGNGAEPGVTTGPLINAAALEKVQSHLQDALDKGATLVAGG-------KP 360 Query: 381 DQGAYVQPTIWTGLSDKARCVTEEIFGPVCHISPFDDEDEVINRVNDSNYGLACAIWTTN 440 G +++P I T + + EE FGP+ + F D D+VI + ND+ +GLA + + Sbjct: 361 LGGNFMEPAIVTNVDASMKVAREETFGPLAPLFRFSDVDDVIRQANDTEFGLAAYFYGRD 420 Query: 441 LSRAHRVSRQIHVGLVWVNTWYLRDLRTPFGGVKLSGLGREGGRFSMDFYSDIANICIKI 500 +S +V+ + G+V VNT + PFGG+K SGLGREG ++ +D Y +I IC+ + Sbjct: 421 ISLIWKVAEALEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKYGIDEYVEIKYICLSV 480 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: 536 Number of extensions: 20 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: 480 Length adjustment: 34 Effective length of query: 466 Effective length of database: 446 Effective search space: 207836 Effective search space used: 207836 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 Sep 17 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