Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate AZOBR_RS19635 AZOBR_RS19635 succinate-semialdehyde dehydrogenase
Query= SwissProt::Q9I6M5 (483 letters) >FitnessBrowser__azobra:AZOBR_RS19635 Length = 485 Score = 681 bits (1756), Expect = 0.0 Identities = 334/482 (69%), Positives = 399/482 (82%), Gaps = 1/482 (0%) Query: 1 MQLKDAKLFRQQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKA 60 + L D L R QAYV+G W DA +G+T V NPATGE + V +GA ETR+AI AAD A Sbjct: 1 LSLNDQSLLRTQAYVNGVWRDAFSGKTFAVTNPATGEELAQVADVGAEETRQAINAADAA 60 Query: 61 LPAWRALTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFG 120 LPAWRA TAKERA LRRWF+L++ Q+DLA LMT+EQGKPLAEA+GE+AY ASF+EWF Sbjct: 61 LPAWRAKTAKERAAILRRWFELIMAAQEDLAVLMTLEQGKPLAEARGEVAYGASFIEWFA 120 Query: 121 EEAKRIYGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLK 180 EE KR+YGD IP +KRI+V+K+PIGV AAITPWNFP+AMITRK GPALAAGCT+V+K Sbjct: 121 EEGKRVYGDVIPSFAGNKRIVVLKEPIGVVAAITPWNFPNAMITRKVGPALAAGCTIVVK 180 Query: 181 PASQTPYSALALAELAERAGIPKGVFSVVTGSAG-EVGGELTSNPIVRKLTFTGSTEIGR 239 PA TP SALALAELAERAG+P GVF++VTGS +GGELT++PIVRKL+FTGSTE+G+ Sbjct: 181 PAEDTPLSALALAELAERAGVPAGVFNIVTGSDPVAIGGELTASPIVRKLSFTGSTEVGK 240 Query: 240 QLMAECAQDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQD 299 LM + A +KKVSLELGGNAPFIVFDDADLD AV+GAL SKYRN+GQTCVCANRL VQ Sbjct: 241 ILMRQSADTVKKVSLELGGNAPFIVFDDADLDEAVKGALASKYRNSGQTCVCANRLLVQA 300 Query: 300 GVYDAFVDKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGK 359 GVYDAF KL AV ++ +GNG+EAGVT GP+I+ +AV KVEE + DA++KGAKV GGK Sbjct: 301 GVYDAFAAKLAEAVKQIRVGNGMEAGVTQGPMINGQAVEKVEELMGDALAKGAKVALGGK 360 Query: 360 PHALGGTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFY 419 H LGGTFFEPTIL V V+++E FGP+AP+F+F+ EA+ I M+NDTEFGLA+YFY Sbjct: 361 RHGLGGTFFEPTILTGVTTEMRVAREEIFGPVAPLFKFETEADAIRMANDTEFGLAAYFY 420 Query: 420 ARDLARVFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLC 479 +RD+ RV+RVAEQLEYGMVGIN G++S EVAPFGGIK SG+GREGSKYG+ED+LEIKYLC Sbjct: 421 SRDIGRVWRVAEQLEYGMVGINEGILSTEVAPFGGIKQSGIGREGSKYGVEDFLEIKYLC 480 Query: 480 LG 481 +G Sbjct: 481 VG 482 Lambda K H 0.317 0.135 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: 702 Number of extensions: 15 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: 483 Length of database: 485 Length adjustment: 34 Effective length of query: 449 Effective length of database: 451 Effective search space: 202499 Effective search space used: 202499 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