Align succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] (characterized)
to candidate Ac3H11_4184 Aldehyde dehydrogenase B (EC 1.2.1.22)
Query= reanno::MR1:200453 (482 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4184 Length = 498 Score = 591 bits (1523), Expect = e-173 Identities = 299/484 (61%), Positives = 365/484 (75%), Gaps = 7/484 (1%) Query: 2 LLNDPSLLRQQCYINGQWCDANSKETVAITNPATGAVIACVPVMGQAETQAAIAAAEAAL 61 LLNDP+LL+ INGQW +S+ V +PATG +A V +G A+ +AAIAAA AA Sbjct: 10 LLNDPTLLKTDGLINGQWVVGSSRFDV--NDPATGLKLADVANLGPADAEAAIAAANAAW 67 Query: 62 PAWRALTAKERGAKLRRWFELLNENSDDLALLMTSEQGKPLTEAKGEVTYAASFIEWFAE 121 W+ TAKER LR+WF+LL N DDL +MT+EQGKPL EAKGEV Y ASF+EWFAE Sbjct: 68 GPWKTKTAKERSIILRKWFDLLMANQDDLGRIMTAEQGKPLAEAKGEVAYGASFVEWFAE 127 Query: 122 EAKRIYGDTIPGHQGDKRIMVIKQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMVVKP 181 EAKRI G+T+P ++R+MV+KQP+GV AAITPWNFP AMITRK APALAAGC +V+KP Sbjct: 128 EAKRINGETLPQFDNNRRLMVLKQPIGVCAAITPWNFPLAMITRKVAPALAAGCPVVIKP 187 Query: 182 APQTPFTALALAVLAERAGIPAGVFSVITGD---AIAIGNEMCTNPIVRKLSFTGSTNVG 238 A TP TALA A LA RAGIPAGVF+++ D +IAIG +C + +VR +SFTGST VG Sbjct: 188 AELTPLTALAAAELAIRAGIPAGVFNILPADSDNSIAIGKVLCASDVVRHISFTGSTEVG 247 Query: 239 IKLMAQCAPTLKKLSLELGGNAPFIVFDDANIDAAVEGAMIAKYRNAGQTCVCANRIYVQ 298 LMAQ APT+KK+SLELGGNAPFIVFDDA+ID+AVEGA +KYRNAGQTCVC NR YVQ Sbjct: 248 RILMAQSAPTVKKMSLELGGNAPFIVFDDADIDSAVEGAFASKYRNAGQTCVCTNRFYVQ 307 Query: 299 AGVYDEFAEKLSMAVAKLKVGEGIIAGVTTGPLINAAAVEKVQSHLEDAIKKGATVLAGG 358 GVYDEF K + V KVG G AGV GPLI AA+ KVQ H++DA+ KG V+AGG Sbjct: 308 EGVYDEFVAKFAAKVKTAKVGNGFEAGVNQGPLIEEAALTKVQRHVDDALAKGGQVVAGG 367 Query: 359 -KVHELG-GNFFEPTVLTNADKSMRVAREETFGPLAPLFKFNDVDDVIKQANDTEFGLAA 416 ++ LG G FFEPTV+ NA M AREETFGP AP+FKF + I AN+TEFGLA+ Sbjct: 368 QRLTALGSGQFFEPTVVANATADMLCAREETFGPFAPVFKFKTEQEAIDAANNTEFGLAS 427 Query: 417 YFYGRDISLVWKVAESLEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKYGIEEYLEIK 476 YFY RD+ +++V E+LEYGMVG N G+++TE PFGG+K SGLGREGS +G+++Y+EIK Sbjct: 428 YFYSRDVGRIFRVTEALEYGMVGANVGILATEHVPFGGVKQSGLGREGSHHGMDDYVEIK 487 Query: 477 YICM 480 Y+C+ Sbjct: 488 YLCL 491 Lambda K H 0.318 0.133 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: 718 Number of extensions: 20 Number of successful extensions: 4 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: 498 Length adjustment: 34 Effective length of query: 448 Effective length of database: 464 Effective search space: 207872 Effective search space used: 207872 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