Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate WP_015798219.1 AFER_RS04025 glutamate-5-semialdehyde dehydrogenase
Query= metacyc::AT2G39800-MONOMER (717 letters) >NCBI__GCF_000023265.1:WP_015798219.1 Length = 425 Score = 250 bits (638), Expect = 1e-70 Identities = 155/410 (37%), Positives = 229/410 (55%), Gaps = 15/410 (3%) Query: 298 MAVAARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGLEESMVA 357 +AVAAR + +L A E R+ LL A L A+ I NE DVA A + L + Sbjct: 21 VAVAARAAQPQLAAAPGEQRRAALLAAARELRASRAAILEANERDVADAVD--LTSAQRD 78 Query: 358 RLVMTPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIVFESRPD 417 RL + +I +A V +A D +GRV+ + +GL + + PLGV+ +++E+RP+ Sbjct: 79 RLRLDDARIEQMAQGVEAVAAQPDVVGRVVDGWTLPNGLRVRRVRVPLGVVGVIYENRPN 138 Query: 418 ALVQIASLAIRSGNGLLLKGGKEARRSNAILHKVITDAIPET-VGGKLIGLV--TSREEI 474 A+LA+ SGN ++L+G +A SN ++ I + + L+GLV TSRE Sbjct: 139 VTADAAALALASGNAIVLRGSSQALASNRVIRGAIARGVASVGLPEALVGLVEDTSREGA 198 Query: 475 PDLLKLDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMAKRIVSD 534 ++L+ +ID+++PRG L+ +++ ++PV+ DG CHVYVD+A D A IV + Sbjct: 199 RAFMRLEGIIDVLVPRGGPGLLRAVRDEARVPVIIDGDGNCHVYVDRAADLAKAAAIVEN 258 Query: 535 AKLDYPAACNAMETLLVHKDLEQNAVLNELI--FALQSNGVTLYGGPRASKILN--IPE- 589 AKL P CNA ETLLVH AV +E + A + L G R ++ +P Sbjct: 259 AKLQRPGVCNAAETLLVHA-----AVADEFLPQLAERLGSCELRGDERTRALVPRALPAT 313 Query: 590 ARSFNHEYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFLRQVDSAAVF 649 A + EY A V VV+ + AI HI R+ S H++ IVTED A F +VD+AAV Sbjct: 314 AADWETEYLAPILAVRVVDTLEDAIAHIRRYSSGHSEAIVTEDLAAATRFTGEVDAAAVL 373 Query: 650 HNASTRFSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGKGQV 699 NASTRF DG + G GAE+G+ST ++H RGP+G E L + + ++ G G V Sbjct: 374 VNASTRFVDGGQLGFGAEIGISTQKLHWRGPMGTEALTSVKLVIWGDGHV 423 Lambda K H 0.318 0.135 0.378 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: 594 Number of extensions: 33 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: 717 Length of database: 425 Length adjustment: 36 Effective length of query: 681 Effective length of database: 389 Effective search space: 264909 Effective search space used: 264909 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: 53 (25.0 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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