Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate HSERO_RS11260 HSERO_RS11260 aldehyde dehydrogenase
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__HerbieS:HSERO_RS11260 Length = 477 Score = 317 bits (812), Expect = 6e-91 Identities = 192/475 (40%), Positives = 265/475 (55%), Gaps = 11/475 (2%) Query: 23 FINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAK 82 FI + A E+ +DP P IARG + DID+A+ AAR +E G W S A+ Sbjct: 5 FIANRWVAPTSGESIPVLDPSDGQPFDAIARGNATDIDQAVRAARLAYE-GAWGRLSAAE 63 Query: 83 RKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEV 142 R +L KLA ++ H EELA LE D GKP++ + R D R +YA A DK++G+ Sbjct: 64 RSRLLMKLAYKLQDHQEELAQLEGRDCGKPMKQA-RADAAAIVRYFEFYAGAADKLHGDT 122 Query: 143 ATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIR 202 + + +REP GV IVPWN+P+ + +G ALAAGN+ ++KP+E + LS +R Sbjct: 123 IPYQAGYTVLTLREPHGVTGHIVPWNYPMQIFGRCVGGALAAGNTCVVKPAEDACLSILR 182 Query: 203 LAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMK 262 +A LA E G P+G LN+VTG+GHEAG L +H D++ I+FTGS GK +++ A + + Sbjct: 183 VAELAAEVGFPEGALNIVTGYGHEAGDLLVKHPDVNHISFTGSPNVGKLVVRAAAEHHTP 242 Query: 263 RVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLALL 322 V LE GGKS IVF D D++ I N GQ C AG+RLL++ ++ L L Sbjct: 243 -VTLELGGKSPQIVFEDA-DMEAMLPVVVNAIVQNAGQTCSAGSRLLVQRGAYEQVLERL 300 Query: 323 KQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKG-QLLLDGRNAGLAAAIG- 380 Q G G LI + V F+ + + G L G+ A G Sbjct: 301 SGLFSQLQVGSS-QMDLDCGPLIRKTQQERVAGFLSDAQRDGIALAAQGKIAAGVPTGGF 359 Query: 381 ---PTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDLSRA 437 P + DV P L++EE+FGPVL F E A+ LAN + YGL A+VWTRD R Sbjct: 360 YQAPALLRDVPPRHRLAQEEVFGPVLAAMPFEDEAHAIALANGTDYGLVASVWTRDGGRQ 419 Query: 438 HRMSRRLKAGSVFVNNYN-DGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWI 491 R++R +++G VF+NNY G + +PFGG K SG+GR+K AL FT LKTI I Sbjct: 420 MRLARAIRSGQVFINNYGAGGGVELPFGGVKASGHGREKGFEALYGFTVLKTIAI 474 Lambda K H 0.317 0.133 0.389 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: 563 Number of extensions: 30 Number of successful extensions: 7 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: 495 Length of database: 477 Length adjustment: 34 Effective length of query: 461 Effective length of database: 443 Effective search space: 204223 Effective search space used: 204223 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