Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate Pf6N2E2_1309 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase (EC 1.2.1.60)
Query= reanno::pseudo6_N2E2:Pf6N2E2_4383 (497 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1309 Length = 486 Score = 334 bits (857), Expect = 4e-96 Identities = 188/474 (39%), Positives = 272/474 (57%), Gaps = 19/474 (4%) Query: 33 SGETFDCLSPVDGRLLGKIASCDVADAQRAVENARATFSSGVWSRLAPSKRKATMIRFAG 92 S + F +P G +G++AS + +AV A+ F W+ P+K +A ++R G Sbjct: 13 SKDVFVNYNPATGEAIGEVASGGAEEVAQAVAAAKEAFPK--WAN-TPAKERARLMRKLG 69 Query: 93 -LLKQHAEELALLETLDMGKPISDSLNIDVPGAAQALSWSGEAIDKLYDEVAATPHDQLG 151 L++Q+ +LA LETLD G PI + N+ +P A+ + E ++ L Sbjct: 70 ELIEQNVPQLAELETLDTGLPIHQTKNVLIPRASHNFDFFAEVCTRMDGHTYPVDDQMLN 129 Query: 152 LVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVVLKPSEKSPLTALRIAALAIEAG 211 +PVGV + PWN P M A WK P L+ GN+ VLK SE SPLTA + LA+EAG Sbjct: 130 YTLYQPVGVCALVSPWNVPFMTATWKTAPCLALGNTAVLKMSELSPLTANELGRLAVEAG 189 Query: 212 IPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMIYSGESNMKRIWLEAGGK 271 IP GVLNV+ GYG T G AL H DV + FTG T K++M +G +K+ +E GGK Sbjct: 190 IPNGVLNVIQGYGATAGDALVRHPDVRAISFTGGTATGKKIMQTAG---LKKYSMELGGK 246 Query: 272 SPNIVFADAPDLQAAAESAASAIAFNQGEVCTAGSRLLVERSIKDTFLPLVIEALKGWKP 331 SP ++F DA DL+ A ++A I GE CTAGSR+ ++ S+ F+ K Sbjct: 247 SPVLIFEDA-DLERALDAALFTIFSLNGERCTAGSRIFIQESVYPQFVAEFAARAKRLIV 305 Query: 332 GNPLDPATNVGALVDTQQMNTVLSYIEAGHSDGAKLVAGGKRILEE--------TGGTYV 383 G+P DP T VG+++ + V YI+ G +GA L+AGG LE + G ++ Sbjct: 306 GDPQDPKTQVGSMITQAHYDKVTGYIKIGLEEGATLLAGG---LERPANLPAHLSRGQFI 362 Query: 384 EPTIFDGVSNAMKIAQEEIFGPVLSVIAFDTAEQAIEIANDTPYGLAAAVWTKDISKAHL 443 +PT+F V+N M+IAQEEIFGPV+ +I F +A+ +ANDT YGLA+ +WT+DI KAH Sbjct: 363 QPTVFADVNNKMRIAQEEIFGPVVCLIPFKDEAEALHLANDTEYGLASYIWTQDIGKAHR 422 Query: 444 TAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHAFDKYTELKSTWIKL 497 A + AG V++N + D+ PFGG K SG GR+ ++F+ + E+K+ I + Sbjct: 423 LAHGIEAGMVFINSQNVRDLRQPFGGVKGSGTGREGGQYSFEVFAEIKNVCISM 476 Lambda K H 0.316 0.132 0.389 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: 589 Number of extensions: 24 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: 497 Length of database: 486 Length adjustment: 34 Effective length of query: 463 Effective length of database: 452 Effective search space: 209276 Effective search space used: 209276 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 (21.6 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