Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate SMa0805 SMa0805 GabD4 succinate-semialdehyde dehdyrogenase
Query= SwissProt::Q9I6M5 (483 letters) >FitnessBrowser__Smeli:SMa0805 Length = 490 Score = 623 bits (1606), Expect = 0.0 Identities = 308/482 (63%), Positives = 382/482 (79%), Gaps = 4/482 (0%) Query: 1 MQLKDAKLFRQQAYVDGAWVD-ADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADK 59 ++LKD L + + W+D +D+G+T V+NPATGE+I +P M +ET RAI+AA Sbjct: 9 VKLKDPSLAVDKGLIGAEWLDRSDSGKTFDVSNPATGEVIAILPDMSRSETARAIDAAHA 68 Query: 60 ALPAWRALTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWF 119 A AW T KERA LR +DL++ N DDLA ++T+E GKPL EAKGEI Y AS++EWF Sbjct: 69 AQRAWAEKTGKERAAVLRNLYDLVVANADDLATILTMEMGKPLTEAKGEILYGASYVEWF 128 Query: 120 GEEAKRIYGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVL 179 GEEAKR+YGDTIPGHQPDKRIIV+KQPIGV AAITPWNFP+AM+ RK PA AAGC +V Sbjct: 129 GEEAKRVYGDTIPGHQPDKRIIVLKQPIGVVAAITPWNFPNAMLARKLAPAAAAGCAVVS 188 Query: 180 KPASQTPYSALALAELAERAGIPKGVFSVVTGS-AGEVGGELTSNPIVRKLTFTGSTEIG 238 KPA++TP SALALA LAERAG+P GVF+V+ + + EVG E+ +N VRKLTFTGST +G Sbjct: 189 KPAAETPLSALALALLAERAGLPAGVFNVILSTDSAEVGKEMCANDKVRKLTFTGSTNVG 248 Query: 239 RQLMAECAQDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQ 298 + LM + A I K+ LELGGNAPFIVFDDADLDAAVEGA+++KYRNNGQTCVCANR++VQ Sbjct: 249 KILMRQGADQIMKLGLELGGNAPFIVFDDADLDAAVEGAMVAKYRNNGQTCVCANRIFVQ 308 Query: 299 DGVYDAFVDKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGG 358 G+YDAF +L A V+++ IG+G E V GPLI KA+AKVEEHI DAV+KGA +V GG Sbjct: 309 AGIYDAFAARLTAKVSEMTIGDGFEPDVDAGPLISEKALAKVEEHIRDAVTKGADLVLGG 368 Query: 359 KPHALGGTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYF 418 +A GG FFEPT+L + ++ +ETFGP+AP+F+F+ E EV++M+N TEFGLASYF Sbjct: 369 --NARGGLFFEPTVLTGATMDMKIAGEETFGPVAPLFKFETENEVVSMANKTEFGLASYF 426 Query: 419 YARDLARVFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYL 478 Y++D+++VFRVAE LEYGMVGINTGLIS EVAPFGG+K SG GREGSKYGI+DY+E KYL Sbjct: 427 YSKDVSKVFRVAEALEYGMVGINTGLISTEVAPFGGVKQSGQGREGSKYGIDDYVETKYL 486 Query: 479 CL 480 CL Sbjct: 487 CL 488 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: 711 Number of extensions: 17 Number of successful extensions: 3 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: 490 Length adjustment: 34 Effective length of query: 449 Effective length of database: 456 Effective search space: 204744 Effective search space used: 204744 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