Align NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized)
to candidate WP_017220578.1 A923_RS0105090 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-15736 (480 letters) >NCBI__GCF_000276805.1:WP_017220578.1 Length = 487 Score = 291 bits (744), Expect = 4e-83 Identities = 168/467 (35%), Positives = 247/467 (52%), Gaps = 7/467 (1%) Query: 14 FIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALPAWRALTAKERA 73 +I G W A +N + LG + A+ +AI AA A P W +++ Sbjct: 15 YIGGEW-QAGVSTVANINPSDISQNLGNFAQASTAQVHQAISAAKHAQPTWEKTPLEQKQ 73 Query: 74 TKLRRWYELLIENQDDLGRLMTLEQGKPLAEAKGEIAYAASFIEWFAEEAKRIYGDVIPG 133 L+ + LI D+LGRL++ E+GKP E +GEI A F ++FA E R GD Sbjct: 74 AVLQGIGDELIARCDELGRLLSSEEGKPFLEGRGEIYRAGQFFQYFAAEVLRQIGDSAAS 133 Query: 134 HQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVIKPASQTPFSALALV 193 +P + V ++ +GV A I+PWNFP A K PALA G +++ KPA+ TP SA+AL Sbjct: 134 VRPGVTVEVTREAVGVVAIISPWNFPTATAAWKIAPALAFGNSVIWKPANLTPASAVALT 193 Query: 194 ELAHRAGIPKGVLSVVTGSAGDIGGELTSNPIVRKLSFTGSTEIGRQLMAECAKDIKKVS 253 E+ HR G+P G ++V GS ++G L ++ V +SFTGS + GR++ A A + + Sbjct: 194 EIIHRQGLPAGTFNLVLGSGSEVGNVLINSTEVNGVSFTGSVDTGRKIAAATAPNFVRCQ 253 Query: 254 LELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDSVYDAFAEKLKAAV 313 LE+G IV DDAD++ AVE I + GQ C ++RL + D ++DA+ E L + Sbjct: 254 LEMGSKNALIVADDADINIAVEATIAGSFSGAGQKCTASSRLVVMDGIHDAYVEALIKRM 313 Query: 314 AKLKIGNGLEEGTTTGPLIDEKAVAKVQEHIADALKKGATLLAGGKSM----EGNFFEPT 369 ++LK+G+ LE+G GP++D K + I A + G L GG+ + EG + PT Sbjct: 314 SQLKVGHALEDGVFMGPVVDGKQLDANLAWIDTARQSGGELAFGGERLSMEHEGFYMSPT 373 Query: 370 ILVNVPKDAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDLGRVFRVAE 429 + +N D +V +EE F P+A + R D E IA +NDT FGL S + L + Sbjct: 374 LFINTKNDWSVNQEEVFAPMASVIRVADLEEAIATTNDTRFGLTSGIITQSLRTSTLFKQ 433 Query: 430 ALEYGMVGVNTGLISNEV-APFGGIKASGLG-REGSKYGIEDYLEIK 474 + G V VN + PFGG K S G RE +Y E Y +K Sbjct: 434 QAQTGCVMVNLPTAGTDYHVPFGGRKESSFGPREQGQYAKEFYTVVK 480 Lambda K H 0.317 0.135 0.390 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: 506 Number of extensions: 18 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: 480 Length of database: 487 Length adjustment: 34 Effective length of query: 446 Effective length of database: 453 Effective search space: 202038 Effective search space used: 202038 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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 24 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