Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate Ac3H11_4184 Aldehyde dehydrogenase B (EC 1.2.1.22)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_495 (480 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4184 Length = 498 Score = 578 bits (1490), Expect = e-169 Identities = 285/484 (58%), Positives = 356/484 (73%), Gaps = 9/484 (1%) Query: 3 LKDTQLFRQQAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALP 62 L D L + I+G WV + VN+PATG L V +G A+ AI AA+ A Sbjct: 11 LNDPTLLKTDGLINGQWVVGSS--RFDVNDPATGLKLADVANLGPADAEAAIAAANAAWG 68 Query: 63 AWRALTAKERATKLRRWYELIIENQDDLARLMTLEQGKPLAEAKGEIVYAASFIEWFAEE 122 W+ TAKER+ LR+W++L++ NQDDL R+MT EQGKPLAEAKGE+ Y ASF+EWFAEE Sbjct: 69 PWKTKTAKERSIILRKWFDLLMANQDDLGRIMTAEQGKPLAEAKGEVAYGASFVEWFAEE 128 Query: 123 AKRIYGDVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPA 182 AKRI G+ +P ++RL+V+KQPIGV AAITPWNFP AMITRK PALAAGC +V+KPA Sbjct: 129 AKRINGETLPQFDNNRRLMVLKQPIGVCAAITPWNFPLAMITRKVAPALAAGCPVVIKPA 188 Query: 183 SQTPFSAFALAELAQRAGIPAGVFSVVSGSAGD---IGSELTSNPIVRKLSFTGSTEIGR 239 TP +A A AELA RAGIPAGVF+++ + + IG L ++ +VR +SFTGSTE+GR Sbjct: 189 ELTPLTALAAAELAIRAGIPAGVFNILPADSDNSIAIGKVLCASDVVRHISFTGSTEVGR 248 Query: 240 QLMSECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQD 299 LM++ A +KK+SLELGGNAPFIVFDDAD+D AVEGA SKYRN GQTCVC NR Y+Q+ Sbjct: 249 ILMAQSAPTVKKMSLELGGNAPFIVFDDADIDSAVEGAFASKYRNAGQTCVCTNRFYVQE 308 Query: 300 GVYDAFAEKLKVAVAKLKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVLAGGK 359 GVYD F K V K+GNG EAG GPLI+E A+ KVQ H+ DAL+KG V+AGG+ Sbjct: 309 GVYDEFVAKFAAKVKTAKVGNGFEAGVNQGPLIEEAALTKVQRHVDDALAKGGQVVAGGQ 368 Query: 360 PM----EGNFFEPTILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASY 415 + G FFEPT++ N + A+EETFGP AP+F+FK E + I +N+TEFGLASY Sbjct: 369 RLTALGSGQFFEPTVVANATADMLCAREETFGPFAPVFKFKTEQEAIDAANNTEFGLASY 428 Query: 416 FYARDLGRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKY 475 FY+RD+GR+FRV EALEYGMVG N G+++ E PFGG+K SGLGREGS +G++DY+EIKY Sbjct: 429 FYSRDVGRIFRVTEALEYGMVGANVGILATEHVPFGGVKQSGLGREGSHHGMDDYVEIKY 488 Query: 476 LCLG 479 LCLG Sbjct: 489 LCLG 492 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: 708 Number of extensions: 18 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: 480 Length of database: 498 Length adjustment: 34 Effective length of query: 446 Effective length of database: 464 Effective search space: 206944 Effective search space used: 206944 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