Align 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate 5210745 Shew_3173 succinic semialdehyde dehydrogenase (RefSeq)
Query= metacyc::MONOMER-13361 (500 letters) >FitnessBrowser__PV4:5210745 Length = 485 Score = 294 bits (753), Expect = 4e-84 Identities = 168/480 (35%), Positives = 257/480 (53%), Gaps = 10/480 (2%) Query: 19 QLLNYIDGNFVTSASSFANINPVNGKLISDVFEADAKQVNEAVVAAQNALKGPWGKLSVQ 78 +L +YIDG + F +NP + ++I+ V +A EA++AA+ AL W K S Sbjct: 11 KLSSYIDGRWTVGEQRFDVVNPASQEVIAQVVDASLDDTQEAILAAKRALP-EWSKRSAN 69 Query: 79 DRAALIHKIADGIQARFEEFVAAEVADTGRPVHQARTLDIPRAIANFRTFADLAKTSHTD 138 +RAAL+ K + + E+ + G+P+ +A+ +I A FA+ K + D Sbjct: 70 ERAALMRKWFNLMMEHQEDLGRLLTLEQGKPLAEAKG-EIAYGAAFIDWFAEEGKRVYGD 128 Query: 139 LFEMSTSDGSGALNYTVRKPLGVIGVISPWNLPLLLFTWKVAPALACGNTVVAKPSEESP 198 +D + +++P+GV+ I+PWN P + K A ALA G T VA+PS +P Sbjct: 129 TIPAPANDKRILV---IKQPVGVVASITPWNFPNAMIARKAAAALAAGCTFVARPSPLTP 185 Query: 199 SSATLLAEVMHDAGVPPGVFNLIHGFGKDSAGEFLTQHPGISALTFTGESKTGSTIMKAV 258 SA +AE+ AG+P GVFN++ G G+ LTQHP ++ TFTG + G ++ Sbjct: 186 LSALAMAELAERAGIPAGVFNIVVGEDAVGMGKVLTQHPDVAKFTFTGSTAVGKILLAQC 245 Query: 259 ADGVKEVSFELGGKNAAVVFADADLDAAIEGVLRSSFTNSGQVCLCSERVYVHRSIFDEF 318 A VK+VS ELGG +VF DAD+DAA++G L S + N+GQ C+C+ R++V + + F Sbjct: 246 ATSVKKVSMELGGNAPFIVFDDADIDAAVQGALISKYRNAGQTCVCTNRIFVQKGVAAAF 305 Query: 319 VSGLKVEAERLVVGYPDQDGVNMGPLISHGHRDKVLSYYRLAVDEGATVVTGGGVPKFND 378 L +G DGV +GP+IS VL V GA +VTGG + + Sbjct: 306 TEKFTAAVANLKLGDGLGDGVTVGPMISKDAVQNVLKLVDDTVASGAKLVTGGQPSELGE 365 Query: 379 ERDQGAYVQPTIWTGLSDKARCVTEEIFGPVCHISPFDDEDEVINRVNDSNYGLACAIWT 438 +++ P I T ++++ EIFGPV I FD E E + ND+ YGLA + Sbjct: 366 -----SFLAPVIVTDVTNEMPLARNEIFGPVTPIISFDSEAEALAMANDTEYGLAAYFYA 420 Query: 439 TNLSRAHRVSRQIHVGLVWVNTWYLRDLRTPFGGVKLSGLGREGGRFSMDFYSDIANICI 498 ++ R RV+ + G+V VN + + PFGGVK SG GREG ++ +D Y +I +C+ Sbjct: 421 RDIGRIFRVAEGLEYGMVGVNEGIISNAAAPFGGVKQSGNGREGSKYGLDDYLEIKYLCL 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: 520 Number of extensions: 25 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: 500 Length of database: 485 Length adjustment: 34 Effective length of query: 466 Effective length of database: 451 Effective search space: 210166 Effective search space used: 210166 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