Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate GFF964 HP15_943 aldehyde dehydrogenase family protein
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__Marino:GFF964 Length = 505 Score = 563 bits (1452), Expect = e-165 Identities = 279/493 (56%), Positives = 360/493 (73%), Gaps = 6/493 (1%) Query: 7 AYWQDKALSLAIENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAA 66 A WQ A +L +E R ++NG Y AA E F +V P+ LA IA D D+A+ AA Sbjct: 14 AEWQALATNLTLEGRAYLNGTYQWAANGEAFTSVSPIDGRELASIASCDQSDADQAVMAA 73 Query: 67 RGVFERGDWSLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAAR 126 R FE G WS +PAKRKAVL + A+L+EAH +ELALLETLD GKPI H+ D+P AR Sbjct: 74 RAAFEAGIWSQLAPAKRKAVLLRFAELIEAHGDELALLETLDMGKPINHASNVDVPATAR 133 Query: 127 AIRWYAEAIDKVYGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGN 186 AIRW AEAIDKVYGE+A T +++ MI REP+GV+AAIVPWNFP+++ WK+ PALA GN Sbjct: 134 AIRWTAEAIDKVYGELAPTPHNQIGMISREPMGVVAAIVPWNFPMIMAAWKIAPALATGN 193 Query: 187 SVILKPSEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGST 246 SVILKPSEKSPLSAIRLA LA EAG+P GV NV+ G+GH G+AL+ H D+D + FTGST Sbjct: 194 SVILKPSEKSPLSAIRLAALAGEAGVPAGVFNVLPGYGHTVGKALALHMDVDCLVFTGST 253 Query: 247 RTGKQLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGT 306 KQL+ AG SNMKRVWLEAGGKS NIVFAD PDL++AA+ A+ I +NQG+VC AG+ Sbjct: 254 NVAKQLMIYAGQSNMKRVWLEAGGKSPNIVFADAPDLKKAAAEAASAIAFNQGEVCTAGS 313 Query: 307 RLLLEESIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQL 366 RLL+E SI EF+ L+ + + W+PGHPLDPATT G ++D A D + +I G+S+G Sbjct: 314 RLLVENSIRAEFVRLICEALKTWRPGHPLDPATTCGAIVDQAQLDRIIDYIGIGQSEGAR 373 Query: 367 LLDG-----RNAGLAAAIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDS 421 L++G N G + PT+F V+ ++ EEIFGPVL V F + ++A+ +ANDS Sbjct: 374 LVEGGQRILENTG-GLFVQPTVFDGVNNQMRIASEEIFGPVLSVIGFDTADEAVAIANDS 432 Query: 422 QYGLGAAVWTRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALE 481 YGL AAVWT +++ AH++++ L+AGSV++N+Y+ GDMT PFGG+KQSGNGRDKS+HA + Sbjct: 433 IYGLAAAVWTSNINTAHKVAKALRAGSVWINHYDGGDMTAPFGGFKQSGNGRDKSVHAFD 492 Query: 482 KFTELKTIWISLE 494 K+TELK W+ LE Sbjct: 493 KYTELKATWLVLE 505 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: 675 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: 495 Length of database: 505 Length adjustment: 34 Effective length of query: 461 Effective length of database: 471 Effective search space: 217131 Effective search space used: 217131 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 Apr 09 2024. 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