Align α-ketoglutaric semialdehyde dehydrogenase subunit (EC 1.2.1.26) (characterized)
to candidate 5209916 Shew_2364 aldehyde dehydrogenase (RefSeq)
Query= metacyc::G1G01-1343-MONOMER (525 letters) >FitnessBrowser__PV4:5209916 Length = 521 Score = 470 bits (1210), Expect = e-137 Identities = 253/515 (49%), Positives = 331/515 (64%), Gaps = 5/515 (0%) Query: 6 NLLIGQRPVTGS----RDAIRAIDPTTGQTLEPAYLGGTGEHVAQACALAWAAFDAYRET 61 N L GQ + G DA ++ +P ++ + + E +AQA A AF++YR Sbjct: 7 NRLTGQHYINGEWQGEADAFQSFNPVANTQIDWHFASASDEQLAQATKAAEQAFNSYRNK 66 Query: 62 SLEQRAEFLEAIATQIEALGDALIDRAVIETGLPKARIQGERGRTCTQLRTFARTVRAGE 121 S +RA FL +IA IEA + +I+ A +ETGLP AR+QGE GRTC QLR FA+ + Sbjct: 67 SDSERAAFLSSIAEHIEADKETIIEAAHLETGLPLARLQGETGRTCGQLRLFAQNL-VNP 125 Query: 122 WLDVRIDSALPERQPLPRADLRQRQVALGPVAVFGASNFPLAFSVAGGDTASALAAGCPV 181 + D A PERQPLP+ D R +VALGPVAVFGASNFPLAFS AGGDTASALAAGCPV Sbjct: 126 IEQLIADMAQPERQPLPKPDTRLGKVALGPVAVFGASNFPLAFSTAGGDTASALAAGCPV 185 Query: 182 VVKAHSAHPGTSELVGQAVAQAVKQCGLPEGVFSLLYGSGREVGIALVSDPRIKAVGFTG 241 +VK H AHP TSELV QA+ +A+K C +P GVFSLL G ++ LV P IKAVGFTG Sbjct: 186 IVKGHPAHPATSELVTQAIEKAIKACDMPAGVFSLLQGHTPDLSTGLVEAPEIKAVGFTG 245 Query: 242 SRSGGMALCQAAQARPEPIPVYAEMSSINPVFLFDAALQARAEALAQGFVASLTQGAGQF 301 S G L ARPEPIP Y E+ S NP FL L +AE LA+ V S+ G GQF Sbjct: 246 SLKVGRILADRCAARPEPIPFYGELGSTNPQFLLPGILAEQAETLAETQVQSMMMGHGQF 305 Query: 302 CTNPGLVIARQGPALQRFITAAAGYVQQGAAQTMLTPGIFSAYQAGIAALADNPHAQAIT 361 CT+PGL++A +G AL R+ + + + AA MLTPGI + YQ AL +P ++ Sbjct: 306 CTSPGLIVAVKGEALTRYCDRLSQTLAEQAASAMLTPGIAATYQQQTEALLAHPQLTLLS 365 Query: 362 SGQAGQGPNQCQAQLFVTQAEAFLADPALQAEVFGAASLVVACTDDEQVRQVAEHLEGQL 421 G+A + + + A +LAD ALQ EVFG ++VV C D Q++ VAE +EGQL Sbjct: 366 QGKAAEASHHTRPAAVKVDAAGYLADSALQQEVFGPFAIVVECQDAAQMQAVAEQIEGQL 425 Query: 422 TATLQLDEADIDSARALLPTLERKAGRILVNGWPTGVEVCDAMVHGGPFPATSDARTTSV 481 TATL +E+D A +L+ + ++ GR++ N PTGVEVC +M HGGP+PA++D+R+TSV Sbjct: 426 TATLHGNESDWAHAHSLVDAIGQRVGRLIFNQMPTGVEVCHSMNHGGPYPASTDSRSTSV 485 Query: 482 GTAAILRFLRPVCYQDVPDALLPQALKHGNPLQLR 516 G+ AI R+ RP+CYQ++P ALLP+AL+ G L R Sbjct: 486 GSMAIHRWTRPICYQNMPTALLPEALRDGQSLLKR 520 Lambda K H 0.319 0.134 0.391 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: 741 Number of extensions: 20 Number of successful extensions: 2 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: 525 Length of database: 521 Length adjustment: 35 Effective length of query: 490 Effective length of database: 486 Effective search space: 238140 Effective search space used: 238140 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: 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