Align Alpha-aminoadipic semialdehyde dehydrogenase; Alpha-AASA dehydrogenase; Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Betaine aldehyde dehydrogenase; Delta1-piperideine-6-carboxylate dehydrogenase; P6c dehydrogenase; EC 1.2.1.31; EC 1.2.1.3; EC 1.2.1.8 (characterized)
to candidate 6938573 Sama_2676 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase (RefSeq)
Query= SwissProt::Q64057 (539 letters) >FitnessBrowser__SB2B:6938573 Length = 1058 Score = 158 bits (399), Expect = 1e-42 Identities = 137/461 (29%), Positives = 216/461 (46%), Gaps = 26/461 (5%) Query: 63 GEVITTYCPANNE-PIARVRQASMKDYEETIGKAKKAWNIWADIPAPKRGEIVRKIGDAL 121 GEV P N + +V A+ E+ I A KA+ W P R ++K+ D L Sbjct: 576 GEVRDVVSPYNTTLKVGQVAFANEATIEQAIAGADKAFASWCRTPVETRANALQKLADLL 635 Query: 122 REKIQLLGRLVSLEMGKILVEGIGEVQEYVDVCDY-AAGLSRMIGGPTLPSERPGHALME 180 E + L L + E GK + +GI EV+E VD C Y A +M+ P L G Sbjct: 636 EENREELIALCTREAGKSIQDGIDEVREAVDFCRYYAVQAKKMMSKPELLPGPTGELNEL 695 Query: 181 QWNPLGLVGIITAFNFPVAVFGWNNAIALITGNVCLWKGAPTTSLVSIAVTKII--AKVL 238 G+ I+ +NFP+A+F A AL TGN + K A T L+ ++ A + Sbjct: 696 FLQGRGVFVCISPWNFPLAIFLGQVAAALATGNTVIAKPAEQTCLIGFRAVQLAHEAGIP 755 Query: 239 EDNL--LPGAICSLTCGGADMGTAMARDERVNLLSFTGSTQVGKQVALMVQERFGKSL-- 294 +D L LPG GA +G + DER+ + FTGST K + + R G + Sbjct: 756 KDVLQFLPGT-------GAVVGAKLTSDERIGGVCFTGSTTTAKVINRALAGRDGAIIPL 808 Query: 295 -LELGGNNAIIAFEDADLSLVLPSALFAAVGTAGQRCTTVRRLFLHESIHDEVVDRLKNA 353 E GG NA++ + V+ + +A +AGQRC+ +R L+L E I + V+D LK A Sbjct: 809 IAETGGQNAMVVDSTSQPEQVVNDVVSSAFTSAGQRCSALRVLYLQEDIAERVLDVLKGA 868 Query: 354 YSQIRVGNPWDPNILYGPLHTKQAVSMFVQAVEEAKKEGGTVVYGGKVMD--HPGNYVEP 411 ++ +GNP GP+ A + A + K+ G +++ + + G++V P Sbjct: 869 MDELTLGNPGSVKTDVGPV-IDAAAKANLNAHIDHIKQVGRLIHQLSLPEGTENGHFVAP 927 Query: 412 TIVTGLVHDAPIVHKETFAPILYVFKFK--NEEEVFEWNNEVKQGLSSSIFTKDLGRIFR 469 T V + ++ KE F PIL+V ++K ++V + N GL+ I +++ G Sbjct: 928 TAVE--IDSIKVLTKENFGPILHVVRYKAAGLQKVIDDINSTGFGLTLGIHSRNEGHALE 985 Query: 470 WLGPKGSDCGIVNVNIPTSGAEIG-GAFGGEKHTGGGRESG 509 + G V +N GA +G FGG+ +G G ++G Sbjct: 986 VADK--VNVGNVYINRNQIGAVVGVQPFGGQGLSGTGPKAG 1024 Lambda K H 0.319 0.137 0.417 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: 1173 Number of extensions: 70 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 539 Length of database: 1058 Length adjustment: 40 Effective length of query: 499 Effective length of database: 1018 Effective search space: 507982 Effective search space used: 507982 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 (21.7 bits) S2: 55 (25.8 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