Align succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized)
to candidate PP_4422 PP_4422 succinate-semialdehyde dehydrogenase (NADP+)
Query= BRENDA::P25526 (482 letters) >lcl|FitnessBrowser__Putida:PP_4422 PP_4422 succinate-semialdehyde dehydrogenase (NADP+) Length = 490 Score = 494 bits (1273), Expect = e-144 Identities = 245/480 (51%), Positives = 324/480 (67%), Gaps = 2/480 (0%) Query: 2 KLNDSNLFRQQALINGEWLDANNGEAIDVTNPANGDKLGSVPKMGADETRAAIDAANRAL 61 KL ++L +A I+G W+ ++DVT+PAN + V A++AA+RA Sbjct: 11 KLRRNDLLETRAYIDGRWVTGEG--SLDVTDPANDQVIAQVAHCDESWVDLAVEAASRAF 68 Query: 62 PAWRALTAKERATILRNWFNLMMEHQDDLARLMTLEQGKPLAEAKGEISYAASFIEWFAE 121 WR +R +LR W LM E+Q+DLA +MT EQGKPL+E++GEI+Y A+F+EWFA Sbjct: 69 DGWRNTLPTQRGAVLRKWAALMRENQEDLAVIMTCEQGKPLSESRGEINYGANFVEWFAA 128 Query: 122 EGKRIYGDTIPGHQADKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKP 181 EG+R YG+TIP H + +L+ QPIGVT AITPWNFP+AMITRKA ALAAGC M++KP Sbjct: 129 EGERCYGETIPSHLPNSQLVTKLQPIGVTVAITPWNFPSAMITRKAAAALAAGCPMIVKP 188 Query: 182 ASQTPFSALALAELAIRAGVPAGVFNVVTGSAGAVGNELTSNPLVRKLSFTGSTEIGRQL 241 A +TP SALALA LA AG+P GVF V+TG A + L + VR SFTGSTE+GR L Sbjct: 189 APETPLSALALARLAEEAGIPGGVFQVLTGDAPKMSARLLAASAVRAFSFTGSTEVGRIL 248 Query: 242 MEQCAKDIKKVSLELGGNAPFIVFDDADLDKAVEGALASKFRNAGQTCVCANRLYVQDGV 301 + Q A +KKVSLELGG+APFIVFDDA + +AVEG + +KF +GQ C+ ANR+YV + Sbjct: 249 LRQSADTVKKVSLELGGHAPFIVFDDASIAEAVEGCIGAKFATSGQDCLGANRIYVHRNI 308 Query: 302 YDRFAEKLQQAVSKLHIGDGLDNGVTIGPLIDEKAVAKVEEHIADALEKGARVVCGGKAH 361 Y +F E+ +A KL +G GL+ GV IGP+ K E I++AL GA++ CGG + Sbjct: 309 YGQFVEEFTKATEKLRVGHGLEEGVDIGPMTRVTVANKCREQISNALSLGAKLTCGGIDN 368 Query: 362 ERGGNFFQPTILVDVPANAKVSKEETFGPLAPLFRFKDEADVIAQANDTEFGLAAYFYAR 421 G +F PT+L DV ++ EETFGP+A + F E +V+ +AN+TEFGLAAY Y Sbjct: 369 HLGSSFVLPTVLADVTDKMDIAFEETFGPVAAILPFDSEDEVVTRANNTEFGLAAYVYTN 428 Query: 422 DLSRVFRVGEALEYGIVGINTGIISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYMCIG 481 DL R RV + LEYG+V +NT + PFGG K SGLGREGSK+G+ +Y+E+KY+CIG Sbjct: 429 DLRRACRVSDRLEYGMVALNTPKFTGAPIPFGGWKQSGLGREGSKHGLAEYMELKYVCIG 488 Lambda K H 0.318 0.135 0.395 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: 622 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: 482 Length of database: 490 Length adjustment: 34 Effective length of query: 448 Effective length of database: 456 Effective search space: 204288 Effective search space used: 204288 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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