Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate GFF964 HP15_943 aldehyde dehydrogenase family protein
Query= BRENDA::Q4DRT8 (561 letters) >FitnessBrowser__Marino:GFF964 Length = 505 Score = 140 bits (354), Expect = 9e-38 Identities = 134/442 (30%), Positives = 202/442 (45%), Gaps = 32/442 (7%) Query: 89 QKAIDTALQASRE------WSQTSFRDRAAIFLHAAHLISTKYRHELRAATMLGQSKSPF 142 Q D A+ A+R WSQ + R A+ L A LI + EL L K Sbjct: 63 QSDADQAVMAARAAFEAGIWSQLAPAKRKAVLLRFAELIEA-HGDELALLETLDMGKPIN 121 Query: 143 QAEIDVIAESCDFLRFSVHYAENLYRDQPLSPSSGAVWNSLDYRPLEGFVSTIAPFNFAA 202 A + + +R++ + +Y + L+P+ + P+ G V+ I P+NF Sbjct: 122 HASNVDVPATARAIRWTAEAIDKVYGE--LAPTPHNQIGMISREPM-GVVAAIVPWNFPM 178 Query: 203 IAANLVACPALM-GNVVLWKPSPHAVLSNYLLYKVFEEAGLPAGVVNFLPCEPDVMTNFV 261 I A PAL GN V+ KPS + LS L + EAG+PAGV N LP + + Sbjct: 179 IMAAWKIAPALATGNSVILKPSEKSPLSAIRLAALAGEAGVPAGVFNVLPGYGHTVGKAL 238 Query: 262 NSHRDLAGVAFTGSTKVFMSINKQIYARLEEYRNIPRISGETGGKDFHLVHPSA-DLKLA 320 H D+ + FTGST V + IYA N+ R+ E GGK ++V A DLK A Sbjct: 239 ALHMDVDCLVFTGSTNVAKQL--MIYA---GQSNMKRVWLEAGGKSPNIVFADAPDLKKA 293 Query: 321 AALTVRGAFEFQGQKCSATSRLYAPKSRWEELKNYMLGVHEQLKMGQPDDFKSFMCAVID 380 AA QG+ C+A SRL S E + + + G P D + A++D Sbjct: 294 AAEAASAIAFNQGEVCTAGSRLLVENSIRAEFVRLICEALKTWRPGHPLDPATTCGAIVD 353 Query: 381 ETAFERNKKYIDIAKSSPSTYSVIAGGG--YDKTEGWFVQPTIVESKDSQAQLMHEEIFG 438 + +R YI I +S + ++ GG + T G FVQPT+ + ++Q ++ EEIFG Sbjct: 354 QAQLDRIIDYIGIGQSEGA--RLVEGGQRILENTGGLFVQPTVFDGVNNQMRIASEEIFG 411 Query: 439 PILTVHVYDDSKPGFWSDVCDVVNRSTKYALTGSIFAQDRQAIRDATTKHLRYAAGNYYI 498 P+L+V +D +D + + Y L +++ + K LR AG+ +I Sbjct: 412 PVLSVIGFDT------ADEAVAIANDSIYGLAAAVWTSNINTAH-KVAKALR--AGSVWI 462 Query: 499 NDKCTGAVVGQQPFGGARASGS 520 N G + PFGG + SG+ Sbjct: 463 NHYDGGDMTA--PFGGFKQSGN 482 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: 627 Number of extensions: 38 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: 505 Length adjustment: 35 Effective length of query: 526 Effective length of database: 470 Effective search space: 247220 Effective search space used: 247220 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 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