Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate Synpcc7942_0489 Synpcc7942_0489 aldehyde dehydrogenase
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__SynE:Synpcc7942_0489 Length = 459 Score = 146 bits (369), Expect = 1e-39 Identities = 132/433 (30%), Positives = 206/433 (47%), Gaps = 26/433 (6%) Query: 67 RATFNSGVWSQLAPAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQ 126 +ATF+ G LA R A+L A L+ N EL D+ KP ++ + +I Sbjct: 17 QATFDRGDTRTLA--FRLARLQDLAKLVADNEAELLQALASDLRKPALEAYASEIYFVRD 74 Query: 127 AIHWTAEAIDKVY--DEVAPTPHDQLGLVTR--EPVGVVGAIVPWNFPLLMACWKLGPAL 182 I T + + + ++ + + Q G R EP+GVV I PWN+P + L A+ Sbjct: 75 QIKLTCKHLRRWMQPEKQSISLMQQPGQAYRQAEPLGVVLIIGPWNYPFQLLITPLIGAI 134 Query: 183 ATGNSVVLKPSEKSPLTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVF 242 A GN VLKPSE +P T+ I +L + P + VL G +V +AL + D + F Sbjct: 135 AAGNCAVLKPSELAPATSSLIQRLISDRFDP-DYIRVLEG-DASVSQAL-ITQPFDHIFF 191 Query: 243 TGSTKIAKQLMVYAGESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVC 302 TG T I +++M A E N+ + LE GGKSP IV D DL AA A FN G+ C Sbjct: 192 TGGTAIGRKVMAAAAE-NLTPVTLELGGKSPCIVDTDI-DLDVAARRIAWGKFFNAGQTC 249 Query: 303 TAGSRLLVERSIKDKFLPMVVEALKGWKPGNPLDPQTTVGALVDT--QQMNTVLSYIEAG 360 A LLV+R++ + F+ +++ ++ + +P + D Q++N++L ++ Sbjct: 250 IAPDYLLVQRTVAEPFIEALIDNIQQFYGEDPQQSADYARIVSDRHWQRLNSLL--VDGT 307 Query: 361 HKDGAKLLAGGKRTLEETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVA 420 + G ++ + Y+ PT+ V I QEEIFGP+L ++ +D +EA+A Sbjct: 308 IRHGGQV---------DRSDRYIAPTLITDVNWRDPILQEEIFGPLLPILIYDQLDEAIA 358 Query: 421 IANDTPYGLAAGIWTSDISKAHKTARAVRAGSVWVNQ--YDGGDMTAPFGGFKQSGNGRD 478 P LA +++ D + AGSV +N G A FGG SG G Sbjct: 359 QIRAQPKPLALYLFSRDRQVQERVLAETSAGSVCLNDTILQVGVPDAAFGGVGPSGMGGY 418 Query: 479 KSLHALEKYTELK 491 + E ++ K Sbjct: 419 HGKASFETFSHYK 431 Lambda K H 0.316 0.132 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: 494 Number of extensions: 23 Number of successful extensions: 5 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: 497 Length of database: 459 Length adjustment: 34 Effective length of query: 463 Effective length of database: 425 Effective search space: 196775 Effective search space used: 196775 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 (21.6 bits) S2: 51 (24.3 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