Align N-succinylornithine aminotransferase (EC 2.6.1.81) (characterized)
to candidate SMc00675 SMc00675 hypothetical protein
Query= reanno::Btheta:353284 (373 letters) >FitnessBrowser__Smeli:SMc00675 Length = 975 Score = 154 bits (389), Expect = 1e-41 Identities = 122/402 (30%), Positives = 197/402 (49%), Gaps = 46/402 (11%) Query: 14 IVKGQGCKVWDENGTEYLDLYGGHAVISIGHAHPHYVEMISNQVATLGFYSNSVINKLQQ 73 I +G ++D G YLD+ V +GH HP + Q + L S + + Sbjct: 574 IERGWKEHLFDVEGRAYLDMVNN--VTLVGHGHPRLSAAVGRQWSLLNTNSRFHYAAVTE 631 Query: 74 QVAERLGKISGYEDYSLFLINSGAEANENALKLASFYNGRTKVISFSKAFHGRT----SL 129 +ERL ++ ++FL+NSG+EAN+ A++LA ++G +IS +A+HG T ++ Sbjct: 632 -FSERLAALAPEGLDTVFLVNSGSEANDLAIRLAWAHSGARNMISLLEAYHGWTVASDAV 690 Query: 130 AVEATNNPTIIAPINNNGHVTYLP-------------LNDIEAMKQELAK-----GDVCA 171 + +NP + + H P + ++A+ ++LA G + Sbjct: 691 STSIADNPQALTTRPDWVHPVVSPNTYRGPFRGEDSTVGYVDAVSRKLADLDEKGGKLAG 750 Query: 172 VIIEGIQG-VGGIKIPTTEFMQELRKVCTETGTILILDEIQSGYGRSG-KFFAHQYNHIQ 229 I E + G GGI +P + +++ + + E + I DE+Q GYGR G F+ + + Sbjct: 751 FISEPVYGNAGGIPLP-SGYLEAVYAMVRERSGVCIADEVQVGYGRLGHHFWGFEQQGVV 809 Query: 230 PDIITVAKGIGNGFPMAGVLISPMFKPVYGQLGTTF---GGNHLACSAALAVMDVIEQDN 286 PDIITVAKG+GNG P+ V+ + G F GG+ ++ L V+D++ D Sbjct: 810 PDIITVAKGMGNGHPLGAVITRREIADALEKEGYFFSSAGGSPVSSVVGLTVLDILHDDA 869 Query: 287 LVENAKAVGDYLLEELK----KFPQIKEVRGRGLMIGLEFE------EPIKELRSRL--- 333 L ENA+AVG +L L+ +FP + V G GL +G+EF EP E + + Sbjct: 870 LQENARAVGTHLKSRLEALGDRFPLVGAVHGMGLYLGVEFVRDRETLEPATEETAAICDR 929 Query: 334 IYDEHVFTGASG--TNVLRLLPPLCLSMEEADEFLARFKRVL 373 + D + +G NVL++ PPLCL+ E AD F RVL Sbjct: 930 LLDLGIVMQPTGDHLNVLKIKPPLCLARESADFFADMLGRVL 971 Lambda K H 0.320 0.139 0.403 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: 758 Number of extensions: 38 Number of successful extensions: 7 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: 373 Length of database: 975 Length adjustment: 37 Effective length of query: 336 Effective length of database: 938 Effective search space: 315168 Effective search space used: 315168 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: 53 (25.0 bits)
This GapMind analysis is from Apr 09 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