Align 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate WP_011385953.1 AMB_RS18195 DUF1487 domain-containing protein
Query= metacyc::MONOMER-13361 (500 letters) >NCBI__GCF_000009985.1:WP_011385953.1 Length = 496 Score = 282 bits (722), Expect = 2e-80 Identities = 162/451 (35%), Positives = 251/451 (55%), Gaps = 10/451 (2%) Query: 39 NPVNGKLISDVFEADAKQVNEAVVAAQNALKGPWGKLSVQDRAALIHKIADGIQARFEEF 98 NP G++I + V+ AV++A+ A K W K S + R L+ + + A EE Sbjct: 39 NPATGEIIGTAAFGTKEDVDIAVISAKAAQKD-WAKQSARARGKLVAECGRVLSAHVEEL 97 Query: 99 VAAEVADTGRPVHQARTLDIPRAIANFRTFADLAKTSHTDLFEMSTSDGSGALNYTVRKP 158 +TG+ + ++ F F L + + L TVR+P Sbjct: 98 GRLVALETGKALRTESRVEAGVLADMFTFFGGLGSELKGETIPFNPD----MLTVTVREP 153 Query: 159 LGVIGVISPWNLPLLLFTWKVAPALACGNTVVAKPSEESPSSATLLAEVMHDAGVPPGVF 218 +GV+G I PWN+PLLL K A AL GN+VV K +EE+P + +AE+M+ +PPG+F Sbjct: 154 VGVVGCIIPWNVPLLLMAMKAAAALVAGNSVVVKSAEEAPLTVLRVAEIMNTV-LPPGLF 212 Query: 219 NLIHGFGKDSAGEFLTQHPGISALTFTGESKTGSTIMKAVADGVKEVSFELGGKNAAVVF 278 N++ GFG + G L +HP + +TFTG +TG + KA A+ + V+ ELGGK+ +V Sbjct: 213 NMLSGFGPE-CGAPLVEHPDVKKVTFTGSVETGRIVYKAAAEKLIPVTLELGGKSPMIVC 271 Query: 279 ADADLDAAIEGVLRSS-FTNSGQVCLCSERVYVHRSIFDEFVSGLKVEAERLVVGYPDQD 337 ADAD+D A+ G L FT GQ C S R++VH SI DEFV+ +K + + +V+G P + Sbjct: 272 ADADMDQAVAGALAGMRFTRQGQSCTASSRLFVHESIHDEFVAKVKAKVDAMVMGDPLDE 331 Query: 338 GVNMGPLISHGHRDKVLSYYRLAVD-EGATVVTGGGVPKFNDERDQGAYVQPTIWTGLSD 396 ++G ++S G ++V SY ++ + +GAT +P + + +G +VQP I+TG+ + Sbjct: 332 KTDIGTIVSDGQLERVRSYIKIGEETKGATKHVCSALPT-DPKLAKGRFVQPVIFTGMKN 390 Query: 397 KARCVTEEIFGPVCHISPFDDEDEVINRVNDSNYGLACAIWTTNLSRAHRVSRQIHVGLV 456 R EEIFGPVC + + D ++V+ + NDS YGLA +IWT + A ++++ G V Sbjct: 391 SDRLCQEEIFGPVCAVIKWSDYEDVLAQANDSEYGLAASIWTRDFKLAMDATKRLEAGFV 450 Query: 457 WVNTWYLRDLRTPFGGVKLSGLGREGGRFSM 487 VN + +GGVK SG+G+E SM Sbjct: 451 QVNQNLVVQPGLSYGGVKTSGIGKEASLESM 481 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: 528 Number of extensions: 25 Number of successful extensions: 7 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: 496 Length adjustment: 34 Effective length of query: 466 Effective length of database: 462 Effective search space: 215292 Effective search space used: 215292 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