Align succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized)
to candidate 5210745 Shew_3173 succinic semialdehyde dehydrogenase (RefSeq)
Query= BRENDA::P25526 (482 letters) >FitnessBrowser__PV4:5210745 Length = 485 Score = 584 bits (1506), Expect = e-171 Identities = 284/480 (59%), Positives = 357/480 (74%), Gaps = 3/480 (0%) Query: 3 LNDSNLFRQQALINGEWLDANNGEAIDVTNPANGDKLGSVPKMGADETRAAIDAANRALP 62 + D+ L + + I+G W + DV NPA+ + + V D+T+ AI AA RALP Sbjct: 4 IKDTQLIKLSSYIDGRWTVGE--QRFDVVNPASQEVIAQVVDASLDDTQEAILAAKRALP 61 Query: 63 AWRALTAKERATILRNWFNLMMEHQDDLARLMTLEQGKPLAEAKGEISYAASFIEWFAEE 122 W +A ERA ++R WFNLMMEHQ+DL RL+TLEQGKPLAEAKGEI+Y A+FI+WFAEE Sbjct: 62 EWSKRSANERAALMRKWFNLMMEHQEDLGRLLTLEQGKPLAEAKGEIAYGAAFIDWFAEE 121 Query: 123 GKRIYGDTIPGHQADKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPA 182 GKR+YGDTIP DKR++VIKQP+GV A+ITPWNFP AMI RKA ALAAGCT V +P+ Sbjct: 122 GKRVYGDTIPAPANDKRILVIKQPVGVVASITPWNFPNAMIARKAAAALAAGCTFVARPS 181 Query: 183 SQTPFSALALAELAIRAGVPAGVFNVVTGS-AGAVGNELTSNPLVRKLSFTGSTEIGRQL 241 TP SALA+AELA RAG+PAGVFN+V G A +G LT +P V K +FTGST +G+ L Sbjct: 182 PLTPLSALAMAELAERAGIPAGVFNIVVGEDAVGMGKVLTQHPDVAKFTFTGSTAVGKIL 241 Query: 242 MEQCAKDIKKVSLELGGNAPFIVFDDADLDKAVEGALASKFRNAGQTCVCANRLYVQDGV 301 + QCA +KKVS+ELGGNAPFIVFDDAD+D AV+GAL SK+RNAGQTCVC NR++VQ GV Sbjct: 242 LAQCATSVKKVSMELGGNAPFIVFDDADIDAAVQGALISKYRNAGQTCVCTNRIFVQKGV 301 Query: 302 YDRFAEKLQQAVSKLHIGDGLDNGVTIGPLIDEKAVAKVEEHIADALEKGARVVCGGKAH 361 F EK AV+ L +GDGL +GVT+GP+I + AV V + + D + GA++V GG+ Sbjct: 302 AAAFTEKFTAAVANLKLGDGLGDGVTVGPMISKDAVQNVLKLVDDTVASGAKLVTGGQPS 361 Query: 362 ERGGNFFQPTILVDVPANAKVSKEETFGPLAPLFRFKDEADVIAQANDTEFGLAAYFYAR 421 E G +F P I+ DV +++ E FGP+ P+ F EA+ +A ANDTE+GLAAYFYAR Sbjct: 362 ELGESFLAPVIVTDVTNEMPLARNEIFGPVTPIISFDSEAEALAMANDTEYGLAAYFYAR 421 Query: 422 DLSRVFRVGEALEYGIVGINTGIISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYMCIG 481 D+ R+FRV E LEYG+VG+N GIISN APFGG+K SG GREGSKYG++DYLEIKY+C+G Sbjct: 422 DIGRIFRVAEGLEYGMVGVNEGIISNAAAPFGGVKQSGNGREGSKYGLDDYLEIKYLCLG 481 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: 703 Number of extensions: 21 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: 485 Length adjustment: 34 Effective length of query: 448 Effective length of database: 451 Effective search space: 202048 Effective search space used: 202048 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