Align succinate-semialdehyde dehydrogenase (NAD+) (EC 1.2.1.24) (characterized)
to candidate WP_011385953.1 AMB_RS18195 DUF1487 domain-containing protein
Query= BRENDA::B0JFD4 (507 letters) >NCBI__GCF_000009985.1:WP_011385953.1 Length = 496 Score = 288 bits (736), Expect = 4e-82 Identities = 169/490 (34%), Positives = 280/490 (57%), Gaps = 11/490 (2%) Query: 22 MSSLLCSKALIDGKWVSALSGDTFEVKNPANGKVIGSVPNMNEKDAQMAITAARNAFYSE 81 ++ L K LI GK V A G+ FEV NPA G++IG+ ++D +A+ +A+ A + Sbjct: 12 LAKALSGKHLIGGKLVPAGCGEVFEVDNPATGEIIGTAAFGTKEDVDIAVISAKAA--QK 69 Query: 82 EWTSLTAKQRSQLLKNWYHLIEKHTQEIAEIMTAESGKPI-IESKAEVFYGNAFMEWFAE 140 +W +A+ R +L+ ++ H +E+ ++ E+GK + ES+ E +F Sbjct: 70 DWAKQSARARGKLVAECGRVLSAHVEELGRLVALETGKALRTESRVEAGVLADMFTFFGG 129 Query: 141 EARRIYGEIVPTPVPNRELIVMKQPLGVAALITPWNFPLAMITRKAGAALAAGCTVVIKP 200 + GE +P P+ + +++P+GV I PWN PL ++ KA AAL AG +VV+K Sbjct: 130 LGSELKGETIPFN-PDMLTVTVREPVGVVGCIIPWNVPLLLMAMKAAAALVAGNSVVVKS 188 Query: 201 AEDTPFTALAVAKLAEEAGIPKGVVNVVTSNKAPPIGELFCKSPDVQGISFTGSTEVGKI 260 AE+ P T L VA++ +P G+ N++ S P G + PDV+ ++FTGS E G+I Sbjct: 189 AEEAPLTVLRVAEIMNTV-LPPGLFNML-SGFGPECGAPLVEHPDVKKVTFTGSVETGRI 246 Query: 261 LFRQSADGIKRVSLELGGNAPFIVFDSANLEKAVDGAMAS-KFRNCGQTCVSSNRFFVQE 319 +++ +A+ + V+LELGG +P IV A++++AV GA+A +F GQ+C +S+R FV E Sbjct: 247 VYKAAAEKLIPVTLELGGKSPMIVCADADMDQAVAGALAGMRFTRQGQSCTASSRLFVHE 306 Query: 320 GIYDKFVAALKERVEALKIGPGDKDTTQVGPLVNAMQFNKVSGFVE-DARSKNA-EILCG 377 I+D+FVA +K +V+A+ +G + T +G +V+ Q +V +++ +K A + +C Sbjct: 307 SIHDEFVAKVKAKVDAMVMGDPLDEKTDIGTIVSDGQLERVRSYIKIGEETKGATKHVCS 366 Query: 378 GKPL--KELGDLFYAPTVVTNIPPNAKIYTEEVFGPVVSIIKFSTEEEALAKANESRRGL 435 P K F P + T + + ++ EE+FGPV ++IK+S E+ LA+AN+S GL Sbjct: 367 ALPTDPKLAKGRFVQPVIFTGMKNSDRLCQEEIFGPVCAVIKWSDYEDVLAQANDSEYGL 426 Query: 436 AGYFYSDNIQQIFRVAKRLEVGMVGVNEGLISAAEAPFGGIKESGIGREGSHHGIDEYTE 495 A ++ + + KRLE G V VN+ L+ +GG+K SGIG+E S + E+ Sbjct: 427 AASIWTRDFKLAMDATKRLEAGFVQVNQNLVVQPGLSYGGVKTSGIGKEASLESMLEHFT 486 Query: 496 VKYICIGNLK 505 K I N+K Sbjct: 487 HKKTIIFNMK 496 Lambda K H 0.317 0.134 0.388 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: 550 Number of extensions: 36 Number of successful extensions: 6 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: 507 Length of database: 496 Length adjustment: 34 Effective length of query: 473 Effective length of database: 462 Effective search space: 218526 Effective search space used: 218526 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 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