Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate PfGW456L13_2360 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= BRENDA::Q4DRT8 (561 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2360 Length = 496 Score = 141 bits (355), Expect = 7e-38 Identities = 136/452 (30%), Positives = 203/452 (44%), Gaps = 33/452 (7%) Query: 83 ATPELAQKAIDTALQASRE--WSQTSFRDRAAIFLHAAHLISTKYRHELRAATMLGQSKS 140 ATPE +A+ A QA + W++T R+R + A L+ + L L KS Sbjct: 52 ATPEDVDRAVLAARQAFDDSAWTRTRPRERQNLLWKLADLMQ-RDAELLAQLECLNNGKS 110 Query: 141 PFQAEIDVIAESCDFLRFSVHYAENLYRDQ-----PLSPSSGAVWNSLDYRPLEGFVSTI 195 A++ + + DFLR+ +A + PL P+ ++S R G V I Sbjct: 111 AAVAQVMDVQLAIDFLRYMAGWATKIEGSTVDVSAPLMPNDQ--FHSFIRREAVGVVGAI 168 Query: 196 APFNFAAIAANLVACPALM-GNVVLWKPSPHAVLSNYLLYKVFEEAGLPAGVVNFLPCEP 254 +NF + A PAL G V+ KP+ L+ L ++ EAG P GV N + Sbjct: 169 VAWNFPLLLACWKLGPALATGCTVVLKPADETPLTALKLAELVLEAGYPEGVFNVVT-GT 227 Query: 255 DVMTNFVNSHRDLAG-VAFTGSTKVFMSINKQIYARLEEYRNIPRISGETGGKDFHLVHP 313 + +H L + FTGST V I K ++ R++ E GGK +V Sbjct: 228 GITAGSALTHNPLVDKLTFTGSTAVGKQIGKIAMD------SMTRVTLELGGKSPTIVMA 281 Query: 314 SADLKLAAALTVRGAFEFQGQKCSATSRLYAPKSRWEELKNYMLGVHEQLKMGQPDDFKS 373 ADLK AAA F QGQ C A SRLY + ++ + + + +K+G D Sbjct: 282 DADLKTAAAGAASAIFFNQGQVCCAGSRLYVQRKHFDNVVADISDIANAMKLGNGLDPSV 341 Query: 374 FMCAVIDETAFERNKKYIDIAKSSPSTYSVIAGGGYDKTEGWFVQPTIVESKDSQAQLMH 433 M +I ER YI+ + S +T IA GG G+FV+PT++ D + L+ Sbjct: 342 DMGPLISARQQERVYGYIEKGRESGAT---IACGGEQFGPGFFVKPTVIVDVDQKHSLVQ 398 Query: 434 EEIFGPILTVHVYDDSKPGFWSDVCDVVNRSTKYALTGSIFAQDRQAIRDATTKHLRYAA 493 EEIFGP+L +DD +D + N S Y L SI++ D A+ R + Sbjct: 399 EEIFGPVLVAIPFDDE-----ADALRMANDS-PYGLGASIWSNDLAAVHRMIP---RIKS 449 Query: 494 GNYYINDKCTGAVVGQQPFGGARASGSNDKPG 525 G+ ++N C A+ PFGG + SG + G Sbjct: 450 GSVWVN--CHSALDPALPFGGYKMSGVGREMG 479 Lambda K H 0.320 0.133 0.402 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: 569 Number of extensions: 26 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: 561 Length of database: 496 Length adjustment: 35 Effective length of query: 526 Effective length of database: 461 Effective search space: 242486 Effective search space used: 242486 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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