Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate HSERO_RS05115 HSERO_RS05115 aldehyde dehydrogenase
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__HerbieS:HSERO_RS05115 Length = 793 Score = 313 bits (802), Expect = 1e-89 Identities = 188/456 (41%), Positives = 263/456 (57%), Gaps = 23/456 (5%) Query: 23 FINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAK 82 FI G +T + + +DP + LA +++G + D+D A+ AA+ W Sbjct: 36 FIAGRFTQPKAD--LDDIDPASGKLLAHLSQGSAADVDAAVQAAQAALP--GWQALGGHG 91 Query: 83 RKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEV 142 R L LA ++ HA LA+LETLD GKP+R S D+P AR YA Sbjct: 92 RARHLYALARTVQRHARLLAVLETLDNGKPLRESRDVDVPLVARHFYHYA---------- 141 Query: 143 ATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIR 202 E PVGV+ IVPWNFPLL+ WK+ PALA GN+V+LKP+E + L+A+ Sbjct: 142 GWAQLQESEFPDHVPVGVVGQIVPWNFPLLMLAWKIAPALALGNTVVLKPAENTSLTALL 201 Query: 203 LAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMK 262 A LA++AGLP GVLN+VTG G G A+ H I IAFTGST G+ L+++ + K Sbjct: 202 FAELAQQAGLPAGVLNIVTGDG-ATGAAVVAHPGIQKIAFTGSTEVGR-LIREQTAGSGK 259 Query: 263 RVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLALL 322 + LE GGKS IVF D D+ A I++NQGQVC AG+RLL++E I D F+A L Sbjct: 260 SLTLELGGKSPFIVFEDA-DIDAAIEGVVDAIWFNQGQVCCAGSRLLVQEGIHDLFIARL 318 Query: 323 KQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKG----QLLLDGRNAGLAAA 378 K + Q + G PLD + MG LI + V S + +G +G Q++LD G Sbjct: 319 KTRMQKLKVGAPLDKCSDMGALISPVQLERVRSLVEQGVREGAQCHQVVLDTPPGG--CF 376 Query: 379 IGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDLSRAH 438 PT+ V P A+++ EEIFGPVLV F + ++A+QLAN+S+YGL A++W+ + A Sbjct: 377 YPPTLLTGVHPAATVASEEIFGPVLVAMSFRTPDEAVQLANNSRYGLAASIWSETIGLAL 436 Query: 439 RMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRD 474 ++ +LKAG V++N+ N D V FGG ++SG GR+ Sbjct: 437 GVAPQLKAGVVWINSTNQFDAAVGFGGVRESGYGRE 472 Score = 92.0 bits (227), Expect = 7e-23 Identities = 65/225 (28%), Positives = 110/225 (48%), Gaps = 11/225 (4%) Query: 48 LAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAKRKAVLNKLADLMEAHAEELALLETL 107 L + G DI A++AA + G W+ +SP +R L +A+ + A EE A Sbjct: 545 LEDVGLGNRKDIRNAVAAA---VKAGGWTSASPHRRAQGLYYIAENLSARTEEFARRIAS 601 Query: 108 DTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEVATTSSHELAMIVREPVGVIAAIVPW 167 TG + R ++ + + + Y DK G V +A+ + E +GV+ + P Sbjct: 602 TTGVTADEA-RAEVDASIKRLFTYGAWADKFEGAVHQPPMRGVALAMPEAIGVVGVVCPE 660 Query: 168 NFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEA 227 PLL + P +A GN V++ PSE++PL A L + + LP GV+N+VTG E Sbjct: 661 EKPLLALISLVAPLIAMGNRVVVVPSEQAPLVATDLYQVLDTSDLPAGVINIVTGKSAEL 720 Query: 228 GQALSRHNDIDAIAFTGS---TRTGKQLLKDAGDSNMKRVWLEAG 269 L+ H++++A+ G + T ++L N+KR +++ G Sbjct: 721 LPVLAEHDEVEALWVRGPAEFSATAERL----STGNLKRCFVDHG 761 Lambda K H 0.317 0.133 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: 929 Number of extensions: 45 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 495 Length of database: 793 Length adjustment: 38 Effective length of query: 457 Effective length of database: 755 Effective search space: 345035 Effective search space used: 345035 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: 54 (25.4 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