Align NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized)
to candidate SMa0805 SMa0805 GabD4 succinate-semialdehyde dehdyrogenase
Query= metacyc::MONOMER-15736 (480 letters) >FitnessBrowser__Smeli:SMa0805 Length = 490 Score = 612 bits (1578), Expect = e-180 Identities = 297/482 (61%), Positives = 372/482 (77%), Gaps = 2/482 (0%) Query: 1 MQLKDAQLFRQQAFIDGAWVD-ADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADK 59 ++LKD L + I W+D +D+G+T V+NPATGE++ +P M +ET RAI+AA Sbjct: 9 VKLKDPSLAVDKGLIGAEWLDRSDSGKTFDVSNPATGEVIAILPDMSRSETARAIDAAHA 68 Query: 60 ALPAWRALTAKERATKLRRWYELLIENQDDLGRLMTLEQGKPLAEAKGEIAYAASFIEWF 119 A AW T KERA LR Y+L++ N DDL ++T+E GKPL EAKGEI Y AS++EWF Sbjct: 69 AQRAWAEKTGKERAAVLRNLYDLVVANADDLATILTMEMGKPLTEAKGEILYGASYVEWF 128 Query: 120 AEEAKRIYGDVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVI 179 EEAKR+YGD IPGHQPDKR+IV+KQPIGV AAITPWNFP AM+ RK PA AAGC +V Sbjct: 129 GEEAKRVYGDTIPGHQPDKRIIVLKQPIGVVAAITPWNFPNAMLARKLAPAAAAGCAVVS 188 Query: 180 KPASQTPFSALALVELAHRAGIPKGVLSVVTGS-AGDIGGELTSNPIVRKLSFTGSTEIG 238 KPA++TP SALAL LA RAG+P GV +V+ + + ++G E+ +N VRKL+FTGST +G Sbjct: 189 KPAAETPLSALALALLAERAGLPAGVFNVILSTDSAEVGKEMCANDKVRKLTFTGSTNVG 248 Query: 239 RQLMAECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQ 298 + LM + A I K+ LELGGNAPFIVFDDADLD AVEGA+++KYRNNGQTCVCANR+++Q Sbjct: 249 KILMRQGADQIMKLGLELGGNAPFIVFDDADLDAAVEGAMVAKYRNNGQTCVCANRIFVQ 308 Query: 299 DSVYDAFAEKLKAAVAKLKIGNGLEEGTTTGPLIDEKAVAKVQEHIADALKKGATLLAGG 358 +YDAFA +L A V+++ IG+G E GPLI EKA+AKV+EHI DA+ KGA L+ GG Sbjct: 309 AGIYDAFAARLTAKVSEMTIGDGFEPDVDAGPLISEKALAKVEEHIRDAVTKGADLVLGG 368 Query: 359 KSMEGNFFEPTILVNVPKDAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYA 418 + G FFEPT+L D +A EETFGP+APLF+F+ E EV++M+N TEFGLASYFY+ Sbjct: 369 NARGGLFFEPTVLTGATMDMKIAGEETFGPVAPLFKFETENEVVSMANKTEFGLASYFYS 428 Query: 419 RDLGRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCL 478 +D+ +VFRVAEALEYGMVG+NTGLIS EVAPFGG+K SG GREGSKYGI+DY+E KYLCL Sbjct: 429 KDVSKVFRVAEALEYGMVGINTGLISTEVAPFGGVKQSGQGREGSKYGIDDYVETKYLCL 488 Query: 479 GI 480 I Sbjct: 489 SI 490 Lambda K H 0.317 0.135 0.390 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: 686 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: 480 Length of database: 490 Length adjustment: 34 Effective length of query: 446 Effective length of database: 456 Effective search space: 203376 Effective search space used: 203376 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