Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate PP_4667 PP_4667 methylmalonate-semialdehyde dehydrogenase
Query= BRENDA::P07275 (575 letters) >FitnessBrowser__Putida:PP_4667 Length = 508 Score = 137 bits (345), Expect = 1e-36 Identities = 132/420 (31%), Positives = 202/420 (48%), Gaps = 42/420 (10%) Query: 60 EVPLVINGERIYDNNERALFPQTNPANHQQVLANVTQATEKDVMNAVKAAKDAKKDWYNL 119 +V L+I+G+ + ++ NPA Q+VLA V AT ++V AV AA+ A + W N Sbjct: 14 QVKLLIDGQWV-ESKTTEWRDIVNPAT-QEVLARVPFATVEEVDAAVAAAQRAFQTWRNT 71 Query: 120 PFYDRSAIFLKAADLIS--TKYRYDMLAATMLGQGKNVYQAEIDCITELSDFFRYYVKYA 177 P R I LK LI TK +L+A QGK + AE D L V++A Sbjct: 72 PIGARMRIMLKLQALIREHTKRIAQVLSAE---QGKTLADAEGDIFRGLE-----VVEHA 123 Query: 178 SDLYAQQPVESADGTWNKAEYRPLE---GFVYAVSPFNFTAIAANLIGAPALM-GNTVVW 233 + + Q E A+ + L G ++PFNF A+ + A++ GNT V Sbjct: 124 ASIGTLQMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIVCGNTFVL 183 Query: 234 KPSQTAALSNYLLMTVLEEAGLPKGVINFIPGDPVQVTDQVLADKDFGALHFTGSTNVFK 293 KPS+ LS LL+ + EAG+P GV+N + G QV D + +D A+ F GST V Sbjct: 184 KPSEQDPLSTMLLVELALEAGVPAGVLNVVHGGK-QVVDAICTHQDIKAISFVGSTEVGT 242 Query: 294 SLYGKIQSGVVEGKYRDYPRIIGETGGKNFHLVHPSANISHAVLSTIRGTFEFQGQKCSA 353 +Y G GK R+ G KN +V P AN + + + + F GQ+C A Sbjct: 243 HVY---NLGSQHGK-----RVQSMMGAKNHAVVLPDANRTQTINALVGAAFGAAGQRCMA 294 Query: 354 ASRLYLPESKSEEFLSDMFGILQSQNVVPMNTSASPISGGNLRGFMGPVIHEQSFDKLVK 413 S L K+ E+L D I ++ + + +N P + +GPV+ +++ ++++ Sbjct: 295 TSVAVL-VGKAREWLPD---IKEAASKLKVNAGCEPGTD------VGPVVSKRAKERVLG 344 Query: 414 VIEDA-KKDPELEILYGGQYDK----SQGWFVGPTVIKAKRPDHPYMSTEFFGPILTVYE 468 +IE K+ +LE+ G+ K QG FVGPT+ + D + E FGP+L E Sbjct: 345 LIESGIKEGAKLEL--DGRDVKVPGYEQGNFVGPTLFSGVKTDMQVYTQEIFGPVLVTLE 402 Lambda K H 0.318 0.135 0.401 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: 600 Number of extensions: 30 Number of successful extensions: 4 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: 575 Length of database: 508 Length adjustment: 35 Effective length of query: 540 Effective length of database: 473 Effective search space: 255420 Effective search space used: 255420 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